BIMM 120 - Midterm 2 (Saier) - week 5

positive feedback loop example in P. aeruginosa

flagella/pili attachment increases cAMP —> increase Vfr activity (virulence factor gene expression) —> immobility —> biofilm formation —> attachment —> more virulence

negative and positive feedback loop

negative - inhibits further expression

positive - encourages more expression

chemotaxis

directed movement of a cell/microbe toward attractants and away from repellants (ie. toxins), the high point in a chemical gradient

possibly plays a role in secreted attractant/quorum sensing —> modulator —> biofilm formation

chemotaxis - attractants and repellants characteristics

attractants tend to be hydrophilic substances, often attract

repellants tend to be hydrophobic (think dissolve membranes) substances, often repel

what’s the bacterial chemotaxis system?

it’s a two-component system with MCP sensing and CheY as a response regulator

MCP - receptor that senses external chemical signals (attractants/repellants), methylation will decrease its sensitivity to attractants

CheY - response regulator, when inactive, flagella run CCW, when active (phosphorylated), flagella run CW

two-component system process

MCP (methyl-accepting chemotaxis proteins) senses —> activates CheA which autophosphorylates —> phosphorylate CheB and CheY —> flagellar motor —> CheZ resets CheY

two-component system - cheY activity

when phosphorylated, CheY-P binds to flagellar motor (FliM) —> changes rotation, causes tumbling (CW rotation) and scatters flagella

low CheY-P leads to smooth “runs” toward attractant, causes running (CCW rotation) and bundles flagella

two-component system - cheB vs cheR activity

both modify MCPs to adjust sensitivity

CheB = demethylase, is activated by phosphorylation

CheR = methylase, is always active

importance of two-component system

allows bacteria to move based on signal strength —> run toward attractants and tumble to reorient away from repellants

why is the two-component system with methylation needed?

because de/methylation is slower (activation = fast, adaptation = slow) so can detect differences in concentration over time

this expands measurable range of chemoattractant/repellant concentrations

importance of an adaptation (slow) pathway aka what happens without adaptation?

de/methylation allows detection of gradients

w/o adaptation, run/tumble will be based on absolute concentrations, not gradient —> ie. forced to constantly run/tumble from attractant

flagella movement + direction

CCW = run, bundle flagella

CW = tumble/reverse, scatter flagella (reverse depends on flagella placement), flagella = random/peritrichous to tumble and flagella = polar to reverse

chemotaxis and neighbor motility

below threshold - neighbor motility helps smooth chemotactic motion, good amount of neighbors = more chance they’ll push you to right direction and get to chemotaxis faster

above threshold - neighbor motility —> self-reinforcing and interferes with chemotaxis, too many neighbors will interfere with path

flagella movement strategies

search strategy - benefits of sampling more space to find nutrients outweigh metabolic costs (individual cells may starve but couple succeed = better than all stay and die)

growth strategy - risks of sampling more space to find even more nutrients outweigh benefits of staying on a species level (don’t waste energy greeding for more if already rich)

replication initiation process in bacteria

replication starts at OriC:

DnaA bind to OriC —> recruits DnaB and DnaC —> DnaC activates DnaB via phosphorylation to unwind DNA

replication initation components in bacteria

OriC - origin of chromosomal replication, replication occurs bidirectionally, special because is AT-rich so weaker base pairs on average so easier to open/replicate

DnaA - origin binding protein, prepares strands for separation by helicase

DnaB - inactive helicase

DnaC - DnaB kinase, phosphorylates it

challenges of DNA packing in bacteria and their solutions

1. negative charge —> repels each other, solution = use counterions (Mg2+) to neutralize 2 charges each and/or use histone-like proteins (very basic, neutralize pH)

2. stiffness, solution = use histone-like proteins to bend DNA 180˚

3. total size in general, solution = supercoiling - added by using gyrase (topoiso III, ATP-dependent), reduced by using topoiso I (ATP-independent)

quorum sensing signals

chemical communication used by bacteria, not just bacteria-bacteria though, mammalian host cells are affected too

can sense cell population density to regulate gene expression

common signals that can cross kingdom barriers

noradrenaline and AHLs

Noradrenaline

hydrophilic, small

released by human cells, correlated w stress, sensed by opportunistic bacteria to turn on virulence factors in response

acyl-homoserine lactones (AHLs)

lipid

produced by bacteria, eukaryotes & humans) can eavesdrop on this and degrade —> QS jamming

induces proinflammatory expression patterns in mammalian cells —> sensed by some pathogens to increase virulence in response

also provoke immune response in plants

mammalian cell-cell signaling origin

probably arose from horizontal gene transfer from bacteria

intracellular vs cell surface receptors

intracellular - for molecules that can cross membrane, lipids (ie. AHLs)

cell surface - for those that can’t (ie. NA)

nonpathogenic communication example in legumes

root nodule formation in legumes:

legumes secrete flavinoids (hormones) —> NodD (bacterial receptor) —> activate NodD factors —> plant hosts initiate nodulation (nodules house nitrogen-fixing bacteria)

adhesion and immune evasion

adhesion - sticky polysaccharide-rich slime

immune evasion - slippery/polymorphic polysaccharide

pili (aka fimbriae)

extend/retract via ATP hydrolysis, assembled by inserting subunits at the base

spirochetes

periplasmic flagella, enable swimming in viscous fluids and swarming motility (internal flagella)

gas vesicles

protein-bound, permeable to gases not water —> buoyancy

PHB/PHV granules

carbon storage granule, citric acid cycle intermediates redirected to make cytoplasmic granules

glycogen granules

carbon storage granules, glycogenin protein center, surrounded by protein

carboxysomes

protein-bound organelles for carbon fixation in cyanobacteria, done via RuBisCo (most abundant enzyme on Earth but very inefficient)

CO2 can diffuse through its membrane but not its protein shell

cellulosomes

degrade cellulose (most common macromolecule on Earth)

cellulosomes structure

anchoring protein - bind scaffold to cell

scaffoldin - hold enzymes out at a useful distance

CBM - bind carbs

catalytic enzymes - cut cellulose

acidocalcisomes

found in bacteria and euk, universal, contain lots of calcium, H+, and polyphosphate (highly energetic)

anammoxosomes

mitochondria-like, oxidize NH3 using NO2 to make N2 and H2O, done anaerobically

nanowires

broad class of conductive structures with diameters in nm, can be produced by microbes that are peptide-based, low energy required, renewable raw materials

allow miniaturization of high-density integration of components and construction of flexible electronics

3 types of nanowires

pilin-based nanowires/electrically conductive pili (e-pili), curli fibers, protein wires from cable bacteria

e-pili

based on type 4 pili, conductive without native metal cofactors, conduits for long range e- transport from inside cell to extracellular terminal e- acceptors/surface sensors

have high abundance/close packing of aromatic rings —> higher conductivity

can modify C-terminal of exposed peptide ligand to enhance sensory function

curli fibers

poor conductors in native state

can be modify exposed metal-binding peptides to more closely packed aromatic residues to improve conductivity

protein nanowires from cable bacteria

cable bacteria in aquatic sediments form long chains of cells to shuttle e- from sulfide oxidation to O2 rich areas

nanowire applications

can’t be used to power massive things (ie. car batteries, etc)

can be used to make:

sensors (ie. ammonia, hydration, glucose, etc), electricity production, memristors (mimics biological neurons, can increase conductivity with increased duration/frequency of electrical input)

surface sensing and attachment + types

surface adhesion helps with antibiotic resistance, is first stage of biofilm formation

types: flagella, type IV pili

flagella in surface sensing

adhesin+biofilm formation, can be mediated by interference in abcteria flagella’s rotation by proximal surface —> flagella impedance

type IV pili in surface sensing

extend via assembly ATPase polymerization to attach to surface —> retracts via retraction ATPase depolymerization —> twitch motility

bacteria surface sensing examples

P. aeruginosa - polar flagella normally attaches and detaches but if don’t detach, become irreversibly attached —> halt flagella rotation —> T4P attach to signal organelle to retract —> increase cAMP —> increase virulence gene expression

Proteus mirabilis - change from swimmer to swarmer when interact with surface (triggered by flagella impedance), flagella acts as mechanosensory organelle

E. Coli - regulates virulence through mechanosensors, uses type III secretory system, flagella mechanosensing aids in successful host colonization because more flagella in early infection is good for establishing contact on epithelial cells

swimming vs swarmer

swimming - discrete rods, about 10 flagella

swarmer - filamentous cell, could be 1000s of flagella

mechanosensing

ability to detect + respond to mechanical forces/physical stimuli in environment