BIMM 120 - Midterm 2 (Saier) - week 4

F-type ATPase architecture

F-type = found in all domains of life

F0 subunit - hydrophobic, in membrane, rotor, contains c-ring

F1 subunit - hydrophilic, alpha-beta subunits form a hexamer, beta subunit catalyzes ATP, alpha subunit supports beta

F-type ATPase function

uses the proton motive force (H+ concentration gradient) to synthesize ATP

transports 12 H+/3 ATP/rotation

3 major components of bacterial flagellum

basal body - anchors to envelope, contains the motor

hook - connects basal body to filament

filament - the “tail”, extends many cell lengths and acts like a propeller to move microbe

bacterial flagella rotation is driven by _____, and its direction of rotation depends on _______

proton motive force, chemotactic signal transduction that monitors the environment (aka detection of chemical gradients in the environment)

bacterial flagellum - flagellar motor composition

5 proteins total:

MotA and Mot B act as proton channels and proton movement causes conformational changes in MotA leading to the power stroke that turns the motor

bacterial flagellum - flagella order of assembly/assembly process

basal body —> hook —> filament

flagellum tail is made by having the components travel through the hollow tube and added to the end, is eventually capped by HAP2

type III secretory system (T3SS) = important for this assembly of components outside the membrane

bacterial flagellum - FliK

FliK - filament-type protein, acts as a internal ruler to regulate hook length in prokaryotes

hook-basal body completion = crucial checkpoint

types of motility in prokaryotes

swimming, gliding, swarming, and twitching

bacterial flagellum - swarming

when the cell moves because there’s numerous flagella

bacteria that can swarm can also swim, but to switch between these, there’s a change in cell morphology (swarming cells = more elongated and flagellated)

bacterial flagellum - where flagella grows can depend on _____

environmental signals like the presence of a surface or change in viscosity can cause more flagella to grow on the sides of the bacteria (lateral)

key differences in archaeal vs bacterial flagella

archaeal flagella = slower, thinner, lacks a hollow interior that’s large enough for flagellin monomers to go through, new subunits are assembled at the base, share structural homology with type IV pili (T4P), powered by ATP hydrolysis (more environment-independent)

bacterial flagella = new subunits are assembled at the tip, share homology with T3SS, powered by PMF (environment-based)

archaea have different cell walls and don’t have peptidoglycan

flagella rings - M ring

“membrane”, made of FliF proteins, have different copies of the same protein with the same sequence but multiple conformations

location - inner membrane

flagella rings - M ring associates

associates with transmembrane export gate complex, is chemiosmotically powered (H+ or Na+ antiport —> protein export), substrate-specific chaperones are generally required to export working flagellin/components

flagella rings - S ring

“secretory”, uses FliF protein

location - inner membrane, tied to M ring

flagella rings - C ring

“cytoplasm”, uses FliG, FliM, FliN

location - cytoplasm (inside cell)

function - supplies force generation, direction regulation, and serves as rotor

exists different number of FliM-FliN depending on direction —> CW has fewer than CCW mode (default mode)

CheY-P (phosphoryl CheY) binds to C ring to switch to CW motion

MFXF motif = “reverse gear” of motor

flagella rings - P ring

“peptidoglycan-associated”, uses FlgI

location - peptidoglycan cell wall

function - almost water tight, only 1-2 molecules can fit in the gap

salmonella FliC vs FlgB switching

FliC - good for invading/colonizing tissue and tumbling

FlgB - good for straight movement

can only express either or, not both

FliC and FlgB = used for filament assembly, up to 15 µm (bacterial cell lengths are only 1-3 µm)

bacterial flagella - flagella cap

HAP2 - made of FliD proteins, stops flagellum growth

power sources of bacterial flagellum

MotA-MotB = H+ driven in E. Coli and salmonella

Na+ driven in some species like marine vibrio PomA-PomB and hyperalkalophilic bacillus MotP-MotS, because more Na+ in environment

bacterial flagellum - motor process: stator and rotor

stator - MotAB = ion selector, produces power stroke that powers flagella movement, interacts with FliG+FliM+FliN complex

rotor - the flagellum - the C-terminal domain of FliG interacts with MotAB to produce the torque

bacterial flagella turning CCW vs CW (viewing from outside-in)

counterclockwise = coherent swimming, goes forward, all flagella move together (bundling)

clockwise = tumbling, backwards movement

flagella expression are within 3 promoter classes - class 1

aka flhDC (makes flhD and flhC transcription factors)

controlled solely by global regulators (master operon), are strictly required to express subsequent promoters

flagella expression are within 3 promoter classes - class 2

supplies hook-basal body (HBB), includes TFs FliA (turns on class 3 genes) and FlgM (turns off class 3 genes until hook is ready)

hook completion —> FlgM secretion —> active FliA —> trigger class 3 promoters

flagella expression are within 3 promoter classes - class 3

filament but also some regulatory proteins

importance of oligomerization/polymerization in genome economy

oligomerization = combining a few identical/similar subunits into a functional complex

polymerization = combining many repeating subunits into a long structure

need to make many various structures but limited to a small genome so solve by expressing lots of one thing (1 monomer) that can aggregate easily and form various structures quickly

swimming without flagella method

cells with a helical shape lack cell walls to maintain their morphology by internal cytoskeletal filaments, believe use contractile cytoskeleton as linear motor instead

form multiple kinks on the surface and move liquid inside cell past itself, using the sodium motive force

bacterial flagella has about ___ flagella and is powered by ____

10 flagella, proton motive force

1000 flagella allows swarming but other flagella also exist (can use PMF or sodium motive force, depends on species)

pilus-independent adventurous motility

a type of independent motility, aka A motility - secrete polysaccharides to generate propulsion, leaving a trail of slime

polysaccharides play a role in adhesion to surfaces

centipede/inchworm motility

specifically mycoplasma = type of tiny, asymmetrical bacteria that move with the direction of a “head”

mycoplasma mobile - have large surface Gli proteins that are localized at the “neck” region and function like legs —> centipede/wave-like movement

mycoplasma pneumoniae - exhibit gliding motility in direction of the terminal organelle

type IV pilli (T4P) role in motility

allows microbes to move over surfaces without flagella, provide twitching motility

creates cell propulsion by involving pilus extension, attachment to a surface, and retraction —> “walking”

twitching motility is powered by _____

ATP hydrolysis

gliding is powered by ______

the proton motive force

2 independent forms of motility

T4P-mediated social motility

Pilus-independent adventurous motility

T4P-mediated social motility

a type of independent motility, S-motility, a type of twitching motility

archaeal flagella (archellum) structure

FlaJ = at the base, likely part of the basal body

FlaI = an ATPase

FlaH = an ATP binding protein but doesn’t hydrolyze ATP, interacts with FlaI

homologous to F0/F1 ATPase where FlaH = alpha subunit and FlaI = beta subunit

flavobacterial gliding

uses SprB and Gld proteins, SprB = highly repetitive 669 kDa that is required for movement over agar

Move like centipede legs where legs = SprB adhesins and muscles = Gld motor (proteins)