Final Exam Flashcards
What is the ratio of our microbiome open reading frames to ours?
150:1
microhabitats
different environments with different physical characteristics
Each microhabitat is NOT homologous. ie. There can be differences in the same microhabitat
Microbiota
describes all of the microbes in a microhabitat
microbiome
the entire collection of microbes living in all of the microhabitats
ie there is a human microbiome and a cat microbiome but there is no gut or skin microbiome (these are microbiota)
Which dominate in most microbiota, Gram - or Gram +?
Gram positive organisms dominate. When gram-negative organisms dominate - it is an indication of a diseased state
Bacteria get increasingly _______ and _______ the deeper we get into the GI system?
anaerobic and neutral in pH
GI microbiota
10 trillion microbial cells
Primarily fermentative Bacteroidetes (Gram-negative), Firmicutes (Gram+), Actinobacteria, Proteobacteria
First two dominate the GI tract
The colon resembles a continuous culture system (environment where they can grow close to exponentially)
We shed 10^11 cells a day (1/3 of fecal mass)
WHere is the diversity of microbes the highest in the GI tract?
Where it is closest to neutral in pH and most anaerobic
What type of bacteria are most microbiota dominated by? What is the exception?
Gram positive
The GI microbiota - about 50/50 dominated by Gram - and Gram + bacteria
What percentage of human nutrition is from short chain fatty acids ?
10% of human nutrition is from short chain fatty acids produced by Bacteroidetes and Firmicutes in the GI tract ex. citrate
microbial fermentation produces SCFA (butyrate, propionate, acetate)
Hygiene hypothesis
Exposure to microbe-associated molecular patterns (MAMPs) early in life is crucial to neonatal gut maturation and immune system development
MAMPs - series of carbs, amino acids, LPS that are specific to bacteria (identify the healthy ones here)
Insufficient exposure to MAMPs can result in reduced colonization resistance and susceptibility to immune-mediated disease (IBD, Type2 Diabetes, obesity, asthma)
- If we are initially not exposed to the right ‘patterns’ our IS has a tough time when exposed to these patterns later on
SCFA
Short chain fatty acids produced by microbial fermentation
ex. citrate, butyrate, propionate, acetate
Important signalling molecules that suppress inflammation, strengthen tight junctions between epithelial cells, promote B-oxidation of fatty acids, and repressed glycolysis
What happens in intestinal bowel disease?
Likely a result of: improper colonization/development of the gut in infancy
Massive changes to diet and lifestyle, changes to environment
Pathogenic species gain access to the gut epithelium altering normal functioning
- immune system responds with an inflammatory response
- immune system learns to view normal bacteria as pathogenic
- gut becomes more aerobic -facilitates the growth of pathogenic bacteria, causing greater inflammatory response - can lead to more serious problems.
How do the gut microbiota differ in obese animals from lean animals?
Obese - fewer Bacteroidetes (gram neg) , more Fermicutes, and WAY more methanogens. usually there is slightly more Bacteroidetes in the gut microbiota
more methanogens in the gut associated with
obesity
How do diet changes in terms of fat and fiber change the type of bacteria in the gut microbiota?
high fat/ low fibre diet –> promote colonization of obese-like microbiota (fewer Bacteroidetes, more Fermicutes, more methanogens)
low fat/high fiber diet –> promote the colonization of lean-like microbiota (More Bacteroidetes, less Firmicutes (50/50ish, less methanogens)
Fecal transplants in Mice GI microbiota experiments
Germ free mice have 40% less body fat than wildtype mice
Transplant poop from WT mice - the germ free mice gain 60% more body fat without changes to diet.
What happened when fecal transplants from obese human were transplanted to a GF mouse?
Mouse acquired comparable GI microbiota
Mouse gained mass, despite no changes in diet
What happened when fecal transplants from lean human were transplanted to a GF mouse?
Mouse acquired comparable GI microbiota. Mouse did not gain mass, and no changes in diet
What is the role of methanogens?
Increased in obese animals (have fewer bacteroidetes, more fermicutes)
Methanogens remove hydrogen gas which FAVOURS the growth of Fermicutes (which are moreso present in obese animals compared to lean)
Fewer methanogens also mean less SCFAs are available to the host
Greater Hydrogen concentrations
Restrict fermicute growth
so more hydrogen in the gut in lean-individuals
the methanogens that are more present in obese animal micriobiota… they REMOVE hydogen from the gut, which promotes the present of Fermicutes
probiotics
ingestions of live beneficial bacteria - promote healthy gut bacteria
-ingestions of some Bacillus species can prevent the colonization of pathogenic S. aureus strains
prebiotics
ingestion of nutrients that promote the growth of the beneficial bacteria (probiotics)
synbiotics
A mic of pre- and pro-biotics
Translocate systems moderate the transport of proteins using
ATP, GTP, PMF (proton motive force)
Sec and Tat
Two universal translocases (ie they are in both gram neg and Gram pos bacteria)
Sec
A universal translocase system. Translocase systems moderate the transport of microbial proteins into the membrane or released outside the cell
Sec is a general secretory system that
1. facilitates the co-translation of transmembrane proteins into the cytoplasmic membrane (SRP and GTP mediated)
SRP = signal recognition particle –> will bind the signal sequence on these folded and unfolded molecules
- Transports unfolded extracellular proteins out of the cytosol into the periplasm (SecA and ATP mediated)
Tat
A universal translocase system. Translocase systems moderate the transport of microbial proteins into the membrane or released outside the cell
(twin-arginine transport)
- Transports folded extracellular proteins out of the cytosol: response regulator and proton motive force mediated
Gram-negative secretion systems
These bacteria may require proteins to be embedded in the outer membrane or released on the outside of the cell
- Two-step translocases (Type II and V)
- One Step translocations (Type I, III, IV and VI)
Type II Secretion Systems T2SS
Either Sec or Tat move proteins across the inner membrane
Proteins attach to a secretion pore and are pushed out of the cell by ATP-mediated pseudopolin extension (Type 4 SS)
Common for secretion of AB toxins such as ExoA and CT (cholera toxin)
The translocase machinery of
type II systems includes a secretion pore in the outer membrane that is anchored to the cytoplasmic membrane by proteins that span the periplasm. While the type II system does possess cytoplasmic membrane and periplasmic components, proteins to be
secreted do not translocate through these and are instead delivered to the secretion pore in the outer membrane by either the Sec or Tat system
typically SecA binds to
proteins that are to be exported into the periplasm (or outside)
typically SRP binds to
signal sequences on proteins that are to be inserted into the membrane
What are the two-step translocase systems?
Type II and V
Type V secretion system (T5SS)
A two step translocase
Sec moves autotransporter proteins across the inner membrane
The transporter (AMINO end) domain of the autotransporter forms a pore in the outer membrane for the passenger domain (CARBOXY) to exit the cell.
Autoproteolysis separates the two domains
Common for secretion of exonucleases (IgA protease), adhesins (perlactin), cytotoxins (vacuolating cytotoxin)
The proteins to be moved outside the cell via this system are initially transported in an unfolded state.
T1SS
One-step Translocase
Involve ABC-binding cassettes (use ATP)
ABC transporters that move proteins across both bilayers in one step
An inner membrane ABC transporter delivers proteins to a periplasmic membrane fusion protein via ATP hydrolysis, which pushes the proteins out an outer membrane pore
Common for secretion of bacteriocin, biofilm mediators, RTX toxins
T3SS
One step translocase - Injectisomes
Puncture adjacent cells!
Transports proteins directly from the cytosol of the bacterial cell into the cytosol of the recipient cell (prokaryote or eukaryote) - good for delivery of toxins as it goes directly to the other cell
Found in both pathogens and symbionts
Upon contact, the tip fuses with the host cell membrane and proteins are transported via PMF
Use to transport a variety of proteins
T4SS
A one-step translocase. Most common one, ATP-mediated
Transports proteins/DNA directly from the cytosol of the bacterial cell into the cytosol of a recipient cell (prokaryote or eukaryote)
Conjugation systems
- responsible for the majority of horizontal gene transfer in prokaryotes. Used to transfer F plasmids and Ti plasmids
Protein transport systems
transfers proteins into other cells or into the extracellular space (pertussis toxin)
T6SS
One step-translocase
Transports proteins directly from the cytosol from the bacterial cell into the cytosol of a recipient prokaryotic or eukaryotic cell via an ATP-mediated T4-phage like injection system
When close to a target, contractile sheath proteins under undergo a conformational change that extends a spike out of the donor cell and into the recipient, delivering the exoproteins
Primarily used in microbial warfare and may help maintain stable species composition in complex communities (microbiome)
Modification of the T4 infection mechanism… cells comes closer together – inverted punching mechanism that delivers toxins
Inducers vs corepressors
Inducers bind to TF’s (activators or repressors) and turn transcription on. Corepressors bind to to repressors and turn transcription off
What do two-component regulatory systems involve?
Component 1: Sensor kinase is a transmembrane histidine kinase that autophosphorylates @ histidine residue
Component 2: Response Regulator - RR is phosphorylated by the histidine kinase and then becomes active. The RR is a transcription factor (activator or inhibitor)
“Component 3” –> desphosphorylation mechanism to remove the phosphate from the response regulator.
What does it mean when quorum is reached?
The population reaching quorum means that a high enough concentration of a signal is reached and coordinated gene regulation is then activated.
Gram-negative bacteria that regulate gene expression by quorum sensing produce a
unique acyl homoserine lactone (thousands of types)
Gram negative autoinducers
Acyl homoserine lactones
Gram positive autoinducers
Gram positive bacteria (and archaea) that regulate gene expression by quorum sensing produce a unique oligopeptide autoinducer (AIP).
Hydrophilic - cant diffuse out of cell alone- need to be actively transported. So they are often in an inactive form
When cell densities are high, the autoinducer concentration increases outside the cells
AIPs bind sensor kinases - which then phosphorylate response regulators which results in the upregulation of quorum specific genes
Upregulation of quorum-sensing genes.
Sometimes down regulator - biofilm gets too large. Cells may leave by shutting down the biofilm promoting operons
Gram positive autoinducers
Gram positive bacteria (and archaea) that regulate gene expression by quorum sensing produce a unique oligopeptide autoinducer (AIP).
Hydrophilic - cant diffuse out of cell alone- need to be actively transported. So they are often in an inactive form
When cell densities are high, the autoinducer concentration increases outside the cells
AIPs bind sensor kinases - which then phosphorylate response regulators which results in the upregulation of quorum specific genes
Upregulation of quorum-sensing genes.
Sometimes down regulator - biofilm gets too large. Cells may leave by shutting down the biofilm promoting operons
How do autoinducers vary from one another?
Structural variations:
- Length of the acyl chain
- R group (hydroxyl, ketones, just hydrogens)
- Units of unsaturation
Aliivibrio fischeri
bioluminescent bacteria and colonize the light organ of bobtail squid (Euprymna scolopes)
At high concentrations, A. fischeri is bioluminescent (has reached quorum) and protects the squid by providing counter illumination at night when the squid is hunting
produces the autoinducer (acyl homoserine lactone) (AI-1) - first autoinducer discovered!
Euprymna scolopes
Bobtail squid that has a mutualistic relationship with Aliivibrio fischeri (bacteria)
Quorum sensing in Aliivibrio fischeri
Aliivibrio fischeri produces the AI-1, an acyl homoserine lactone
The AHL diffuses throughout the light organ
At high concentrations the AI-1 binds LuxR (transcriptional regulator) - get transcriptional activation of the lux operon
This produces the enzyme luciferase (produces light in the presence of luciferin and oxygen
Lux Operon
An inducible operon that produces LuxI (AHL synthase gene) at basal levels
- constitutive activation of this gene
LuxI
constitutively expressed on the lux operon
gene codes for the AHL synthase enzyme
LuxR
Gene product is the response regulator (TF that works as a transcriptional activator)
At high concentrations, the AHL (AI-1) binds LuxR and activated it –> LuxR then binds to activator binding sites on the LuxICDABEG operon to promote its transcription
LuxICDABEG operon
At high concentrations, the AHL activates LuxR, which binds to activator binding sites on the LuxICDABEG promoter - get upregulation of the entire operon
LuxCDE - multicomponent fatty acid reductase that synthesizes RCHO (part of the lucerifin - substrate molecule for forming light)
LuxAB - is the luciferase heterodimer
Lux G - an FMN reductase
The Staphylococcus aureus global control system
An inducible set of regulons (group of operons under the control of the same TF) controlled by quorum sensing
What does the AgrD gene product mke?
Autoinducing peptide (AIP)
AIPs are hydrophilic - used by Gram+ organisms
What does the AgrB gene product mke?
a cell membrane transporter than exports the AgrD (AIP) out of the cell - makes it into its active form
AgrC is a?
sensor kinase - When AgrC is bound by AIP - it autophosphorylates - passes its phosphate to the response regulator AgrA
AgrA
Is the response regulator that is phosphorylated by AgrC sensor kinase
When Phosphorylated, AgrA-P binds at activator binding sites within multiple regulons
Upregulates the production of a host of virulence factors in S. aureus
What molecule does Bacillus use that helps them, as a probiotic, outcompete S. aureus in stomach infections?
fengicin - this molecule is a structural analog of the AIP that binds to AgrC.
When Bacillus is present, it will produce fengicin which will bind to AgrC on S. aureus cells. This competitively inhibits AgrC –> so virulence factors for S. aureus are NOT expressed.
Helicobacter pylori
Found in 50% of the human population
Leading cause of gastric inflammation (gastritis) and ulcers
corkscrews into the mucous layer
uses urease to generate ammonia
produces toxins (VacA) to damage epithelial cells in order to gain nutrients
Infection
Growth of a pathogenic microbe in/on a host
Micriobiota - not an infection
- if these speciies go to new microbiota - potential infection
disease
injury of a host due to infection
pathogen
a microorganism that causes disease
pathogenicity
the ability of a pathogen to cause disease
pathogenesis
process by which a pathogen causes disease (steps in the infection process)
Opportunistic pathogen
causes disease only under certain circumstances
virulence
relative ability of a pathogen to cause disease
virulence factors
molecules produced by, or strategies used by, a pathogen to cause disease
If it helps to:
- achieve attachment and colonization
- evade host immune system
- invade and disseminate (spread) to other host cells
- acquire nutrients and grow
- release into external environment to find new hosts
It is a virulence factor
Basically any part of the infection process
LD50
lethal dose.
Is the dose required to kill half of model animal hosts
ID50
infective dose
is the dose required to infect half of model animal hosts
The lower the LD50 0r ID50…..the __________ its virulence
greater
and the more virulence factors it has
The lower the number of virulence factors a pathogen has….
The less pathogenic it is and the greater the LD50 and ID50
Mucous is composed of
mucin (glycoproteins and polysaccharides)
- mucin contains SlgA (secreted immunoglobulin) and defensins (produced by our cells, punch holes in pathogens)
On mucous membranes (portal of entry into the body)
Most normal microbiota cannot penetrate the mucous layer
pathogenic virulence factors include flagella and enzymes that degrade mucin
Are adhesins microbial or host produced?
Adhesins are produced by the microbe
Adhesins
Microbial Extracellular glycoproteins or lipoproteins that bind to host receptors
Fimbrial - initial attachment
Afimbrial - close (intimate) contact. Get even closer
The host receptors are structural or essential functional cell components that the pathogen has used to its advantage
- Fibrinogen, fibronectin, elastin, collagen, glycoproteins, glycolipids, lectins (carbohydrate binding proteins), cell receptor proteins
Pili/Fimbriae
Specific for attachment to host cells
Proteinaceous appendages that bind to specific host glycoproteins via adhesins at the tip
Some pathogens produce many types of fimbriae
cAPSULES
Extracellular polysaccharide or polypeptide coat that mediates attachment to host epithelial cells, while also protecting from the host phagocytosis (Abs and complements) and lysis (defensins)
Which Secretion systems are used to inject proteins/toxins directly into host cells?
T3SS, T6SS, and sometimes T4SS
How does pathogenic E. coli (O157:H7) inject?
It injects a protein (Tir) into host cells using a T3SS
- has adhesins and injects into our membranes
Tir becomes a receptor on the host cell membranes for an E coli surface adhesin (intimin) that adheres the cells tightly
Cause actin to be rearranged, and then pulls the E. coli cell inside the cell so that it can begin to reproduce
Biofilm formation
Dense, multi-species layers of bacterial communities attached to surfaces and enclosed within an exopolysaccharide matrix
- Resistant to: antibiotics and disinfectants, phagocytosis and other immune responses
invasion is the ability of a pathogen to
enter host cells/tissues, spread, and cause disease
bacteremia
Presence of bacteria in the blood
septicemia
Growth of bacteria in the blood
Thinks get scary when things start to grow and divide in the blood….
can lead to septic shock and multi-organ system failure
invasins
microbial things that activate host cell signalling pathways that results in the reorganization of cytoskeletal actin to form pseudopod-like structures that engulf the bacterium (takes advantage of how the cell takes in food molecules)
L. monocytogenes use _________
invasins called internalins to induce endocytosis and then release lysteriolysin O to dissolve the phagosome membrane
Salmonella uses______
A T3SS to deliver invasins and induce endocytosis and form a second T3SS to insert proteins in the phagosome membrane that prevents lysosome fusion
- instead tells message to deliver them to Golgi
Immunoglobulin Protease
destroy immunoglobulin proteins to evade opsonization (coating of antibodies)
enzymes that destroy antibody proteins
IgA protease
a major virulence factor of many intestinal pathogens
- mucin is full of sIgA
WAYS pathogens acquire nutrients
Degradative enzymes
Elicit minor immune response (our IS destroys cells that release nutrients)
Iron acquisition (via siderophores, receptors for host iron binding proteins (or exoenzymes that destroy them)), iron abstinence).
Where are chromosomal genes for virulence factors generally?
They are clustered on pathogenicity islands which facilitates their spread to other organisms by horizontal gene transfer
Where are many/most genes for VFs?
In plasmids! This facilitates spread by horizontal gene transfer events
Some genes for virulence factors are not bacterial in origin, but are found on prophage DNA within the pathogen’s chromosome.
Exoenzymes
Are secreted (generally by pathogens) into the surroundings. Enzymes active outside the bacterium but still acting for the bacterium
toxins
are protein molecules that affect host cell/tissue function. These are not enzymes but generally act by being TF’s or interferring with signalling pathways
exotoxins
are secreted into the surroundings. the pathogen benefits from the damage done
enterotoxins
are active in the GI tract
endotoxins
are part of the cell wall structure
- LipidA is the endotoxin in Gram-neg cells
- Teichoic acids are the endotoxins in Gram-pos cells
both of these stimulate our immune system - then our bodies freak out
