Svens MiBi

16s rRNA sequencing?

Bacteria: Cytoplasm

Archaea: Cytoplasm

Eukaryotes: Nukleus

Bacteria: usually circular

Archaea: usually circular

Eukaryotes: usually linear

Bacteria: yes

Archaea: mostly

Eukaryotes: yes

Bacteria: no

Archaea: yes

Eukaryotes: yes

Bacteria: frequent

Archaea: frequent

Eukaryotes: rare

Topoisomerase 2

Bacteria: yes

Archaea: yes

Eukaryotes: no

Bacteria: no

Archaea: no

Eukaryotes: Capping and poly A Tail

Bacteria: very rare

Archaea: very rare

Eukaryotes: most genes

sigma factor -> recognises promoter region

rho factor -> releases the RNA pol

special sigma factrors in both compartments

Initiantion F

Elongation F

Release F

Rescue Factor

yes (in bacteria?)

β-lactams (penicillins, cephalosporins, vancomycin): bind to or inhibit proteins involved in peptidoglycan synthesis → prevent cell wall formation

Aminosides: promote the misfolding of proteins that can decrease membrane stability

Metabolism (Iron), Antimicrobial resistaance (efflux pumps), Biofilm formation, virulence (Exotoxin secretion)

• In transformation, a bacterium takes up a piece of DNA floating in its environment.

• In transduction, DNA is accidentally moved from one bacterium to another by a virus.

• In conjugation, DNA is transferred between bacteria through a tube between cells. (Pilus)

artificial surfaces (Biofilms, implants)

extracellular matrix (wounds, damaged tissues)

Endothelial cells (endocvascoular infections)

epithelial cells (nasal, skin)

FLOW (e.g. in Lungs, bladder, Intestine)

done by mucin secretion, ciliated cells, and smooth muscle shaping epithelium

Supramolecular protein structures

• Pili

• flagella

• curli fibres

Auto transporters

• trimeric autotransporter adhesins (TAA)

surface adhesins

• microbial surface components recognizing adhesive matrix Molecules (MSCRAMM)

• Outer membrane proteins (OMP)

pilin subunits

Pilus: conjungtion or trasfer pilus

fimbriae

• typ 1: adhesion via FimH

• Type P: adhesion via PapG

• TYpe IV pili: twithcig motility

• curly: biofilm formation

catch bonds enhance by tensile mechanical force

shown for blood proteins (selectins) and bacterial proteins (FimH and PilY)

found in the OM of Gramm negative bacteria

cell wall anchored adhesins in gramm negative bacteria

adhesion and entry into host cell,…

anchoring in the peptidoglycan (in the cell wall)

adhesions for biofilm formation and exponantial growth

toxins for infecting and spreading

-> switches stages

SREC Scavanger receptor (on nasal epithel)

via hydrophobuc interactions

or

binding to fibronectin coated plastic or metal surfaces via fibroonectin binding proteins

• termperature

• oxidative stress

• antimicrobial peptides

• low O2, high CO2

• iron resitriction

dont produce the signal to save energy

FliM (rotor protein) is triggered in absence of signal

colonizes stomach mucous membrane

-> senses urea to move toward stomach mucosa

Free iron ions -> complexed by transferrin and lactoferrin

free heme -> complexed by hemopexin

free hemoglobin -> complexed by haptoglobin

siderophores bind free iron more efficiently than transferrin and lactoferrin

highly efficient heme uptake systems in s.aureus

borellia gurgendorferi uses Mn for Fe

Chemoheterorophs (chemical energy source, organic substances as Carbon and electron source)

in respiratory you have oxygen -> electrons are transferred to Oxygen products (O2, NO3-, SO42-)

in fermentation there is no oxygen -> electron tarnsfer directly back to organic products (Pyruvate, Acetyl CoA) —> NO ATP from electron transport phosphoreliation only by substrate level phosphorelation

SCFA and other products can be sensed by scavaner receptors of leucocytes

harder to detect but slower reproduction (less variants)

only Gramm negative

SecA=???

SecB= chaperon, prevents folding of protein and transports prottein to membrane

SecYEG=Translocon (pore)

Alpha helices (they saitsfy the H-Bonds)

positive charges are always on the inside

(can be removed to flip the protein)

they have two sides: one faces the inside (polar) one the outside (hydrophobic) of the pore.

Gly and Ala, because the have a short side chain.

Gramm negative (because its only in the OM)

IM= every AA must be in contact with the membrane (hydrophobic)

OM=only ever second AA must be hydrophobic (enegetically bad to insert into IM)

mitochondria and chloroplasts

Sec —> SurA (and skp?) —> BamABCDE complex

BamA-hybrid barrel

they get a lipid anker attached (Diacylglycerol)

LolCDE complex (ATPase —> inside the cell, reahces through the membrane) —> LolA (Chaperone) —> LolB (implements lipoprotein in the OM)

having an Asp next to the Cys, where the lipid is attached prohibits this shuttel

Inner membrane ABC Transporter

Periplasmic adapter protein

OM pore

Pili

IM Sec translocon -> co translational transport of Pilin Subunits into the membrane -> get cut of and asseblmed in the base complex -> piston pushing mode -> secretion of folded proteins -> double walled beta barrel that is big enough

once the pili is attached to something in can reverse the ATPase direction and retrackt the pilus for movement

Or toxins are attached to the tip of the pilus

needle

ruler

chaperons -> unfoldet proteins

ATPase

self secreting

“a mess”

does a lot of things

• conjungtion

• DNA release

• DNA uptake

• Toxin delivery

• effector molecule delivery

two classes A & B (one DNA + proteins, one only Proteins)

one or two step secretion process into host cell

ATPase

build from outside to inside

most simple

two steps

one protein that builds its own membrane

trough IM via Sec translocon

trough OM via BamA and its own pore

part thats supposed to be secreted then gets cut from the pore

often ashesins

spring loaded spike

phage derived

to kill eukariotic or prokaryotic victims

ATPase

found in almost all bacteria

largest beta barrel

transport of folded proteins across the OM

folded C-terminal secretion signal

proton motive force driven

two openings: one the side and the bottom -> Schleuse

less complex

but dense cell wall (possibly ExPortals -> channels in cell wall

Type 3,4,7 also found in Gramm positive (but only IM components)

Exotoxins= aprotein toxin secreted by bacteria that kills or damages host cells

Endotoxins= a lipopolysaccharide in the OM of Gramm negative bacteria that becomes toxic to the host after the bacteria cell has lysed

membrane

cytoskeleton

protein synthesis

cellc cycle

signal transduction

cell-cell adhesion

vesicular trafficking

exocytosis

—> 9 classes

A: active toxin

B: mediated uptake (endocytosis or pore formation)

-> gets activated once split

pore forming toxin of streptococci

ologomerize and form huge openings

staph aureus

forms a seven member pore

Repeates in ToXin motife

secreted by T1SS

four functional entities

• Cystein protease domain

• actin crosslinking domain

• Rho activating domain

• alpha/beta hydolase (cleaves itself)

secreted by T3SS

• guanine exchange factor

• GPase activating protein

causes membrane ruffeling and invagination

reversable to keep the cell alive

Shiga toxin

Diphteria toxin

cytolethal distending toxins

DNAse triggering G2 cell cycle arrest

leads to enlarged or distended (aufblähed) cells

e.g. typoid toxin

exfoliative toxins of s.aureus

acts on outside of the cells

to get deeper in the tissue

bridege TCR and MHC calss 2 Moleküle

zytokinsturm

e.g. toxic shock syndrom toxin of s.aureus

• inner parts of the body (Blood, tissue, cerebrospinal fluid)

• eyes

• respiratory trakt (mostly)

lactobacillus (98% after puperty)

cancer

diabetes, obesity

MS, Autism, Alzheimer, Parkinson

Chrons disease, ulcerative solitis

allergies, asthma, atherosclerosis

exfoliatin A, B and D -> cleave cadherins (desmosome) -> deattachement of the upper epidermis

mucus rinses bacteria off

steady state of producting mucus and bacteria rying to break through -> Germ free mice overproduce mucus -> colon gets huge

small

• single, thinner layer of mucus (beacuse nutrients need to be absorbable

• protection via antimicrobial modulators

large

• two, thicker layer

• outer layer is colonized

Short chain fatty acids!

vitamins

diversity and abundance varies widely amogst healthy subjects

but functional capacity is conserved!

imfalmmation kills sommensals while pathogens are resitant

-> high diversity -> health

-> low diversity -> disease

bacteria that improve xour mood

bacteria can produce neurotransmitters?

innate: all

adaptive: only vertebrata

antimicrobial

• lipids (damage bacteria membrane) -> in sebaceous glands (Talgdrüsen)

• peptides (damage membrane)

• enzymes (detruct cell wall and membrane)

Myeloperoxidase (production of toxic oxygen and nitrogen compounds)

terminal complement components (membrane attack complex)

all are cationic -> Cationic Antimicrobial peptides (CAMPs)

e.g. alpha defensins, HIstatins, beta defensins

alpha defensins -> to protect epithelial stem cells

lysozyme (cleaves peptidoglycan) -> s.aureus is resistnt because it has an O-Acetylation at the cleavesite

elastase (cleaves bacterial proteins)

phospholipase PLAII (cleaves bacterial phosphoolipids)

O2 —> NADPH Oxidase —> O2- —> Superoxid mutase —> H2O2 Myeloperoxidase —> HOCl or —> Fenton reaction (Fe+) —> HO

Arginin -> NO Synthase -> NO -> ONOO- -> NO2 + HO

redness, warmth, pain, swelling, altered function

TNF alpha

IL-1beta

IL-6

produced by activated macrophages, endothelial and epithelial cells

effects: secretion of defensins

endothelial pereability

activation of macrophages and lymphocytes

systemic efffects: fever

relase of acute phase proteins

schock if to much

same pathway as IL-1

-> MyD88 -> kinase kaskade -> NF-kB -> transkribtion

Lipopolsaccaride (LPS)

sensed by TLR4 -> senses lipid anchor

chlamydia can “inactivate” its LPS (only express 4-5 instead of 6 fatty acids?) so it stays unrecognized

pseudomonas also changes the number of fatt acids depending on its environment (at the cost of being more sensitive for defensins)

depending on the methylation patterns of CpG sequences

GPCR

bacterial peptides (formyl peptides) or fermentation products (short chain fatty acids)

Formylated peptides because baceteria use formyl-Met as protein synthesis start

PROBLEM: Mitochondria us that as well

produces CHIPS (Chemotaxis inhibitor protein of S.aureus) that inhibits RPR1 (Formyl peptide receptor -> GPCR

Neutrophil granulocytes (=polymorphonuclear leukocytes =

PMN)

resident macrophages

• Phagocytosis

• Degranulation (release toxins against bacteria)

• NETs (neutrophil extracellular traps)

Non-opsonic phagocytosis (direct recognition)

• C-type lectin receptors -> carbohydrates

• Scavanger receptors -> charges molecules such as LPS, LTA, WTA

• Adhesins -> sialylated glycans

Opsonic Phagocytosis (labeling, marking by others)

• complement system (C4b,…)

• Collectins

• antibodies

• activation via one of three pathways (Classic (C1 binds to Antibody), lectin (MBL binds to carbohydrates), alternative(spontaneus hydrolysis of C3 -> if bacterial surface present its not reversed?)

• C3 convertase formation

• C5 convertase formation

• Membrane attack complex

-> MLB deficiency ist the most common inherited immune deficiency

express mannose -> MLB binds to mannose and activates complement system -> macrophages phagocyte bacteria -> bacteria inhibits phagosomal degredation -> persist in the macrophage (hides)

MLB deficiency gives resitstance against mycobacteria (e.g. tuberculosis)

Factor H binds to sialic acid (modified sugar) to prevent C3 conversion

Neisseria incorporates sialic acid into its LPS

split products =Anaphylatoxins have pro Inflammatory activity

C4a, C3a, C5a -> chemotaxis, vasodilation, histamine release,…

Type 3 effector proteins -> inhibit cytosceleon rearengement

can produce leukocidins -> e.g streptolysin I -> formes pore in membrane -> kills leucocyte

the effectiveness by which and antigen elicts an immune response

proteins (form more diverse chemical forms ad maintain tertiary structure)

firstt: IgM then IgG

second: mostly IgG

monomeric IgM and IgD

when they encounter the antigen on thei own there is no calss switch -> IgM

if they get help by a ThCell they can switch classes

Differences in the constant regions may lead to:

- Isotypes: same person, different AB classes (IgE and IgM)

- Allotypes: my IgG againsts Spike protein and Annikas IgG against spike protein (same class, same antigen but still different)

- Idiotypes: my IgG against spike protein and my IgG against Influenza (same, person, same class, different antigen)

parts between the VDJ regions that enable the recombination of the different parts

-> regulated by T-helper cells with the help of cytokines

quick replication time

strong selective pressure

switch antigens! e.g. tryoanosoma brucei

salmonella enterica -> two versions of flagellin

neisseria -> different variations of pilin protein

produces Protein A which binds to FC part of the AB -> immune cells cant bind the AB anymore

Aluminiumhydroxid

sepcific lipid/water mix

-> epigenetic modifications

people with vaccine against BCG also dies less from tuberculosis

T cell receptor is Ig like heterodimer in membran bound form

TCR bind antigen if presented by MHC2

needs CD3 as coreceptor

MHC I = intracellular antigens

MHC II = extracellular antigens

BUT: Distinction between antigen processing

pathways for loading peptides on class I and

class II MHC is not absolute  cross

presentation

if antigen is presented -> secretes perforin -> forms pore

secretes granzymes -> enters cell trough pores -> induces apoptosis

OR binds to fas ligand -> induces caspases -> apoptosis

TH0 binds MHC II on antigen-presenting cell.

 If T-cell receptor binds antigen . . .

- Activation to become TH2 cell

- Proliferation of TH2 cells

 B cells bind antigen with antibodies:

- Endocytoses and presents antigen on MHC II

- TH2 CD40L binds CD40

- Recognition of B cell

- CD4 binds MHC II

 If T-cell receptor binds to antigen . . .

Activated TH2 activates B cell:

- Secretes Il-4, IL-6

- Stimulates B-cell proliferation, differentiation

 B cells undergo class switching:

- Form plasma cells

- Secreted antibodies coat extracellular antigens.

- Prevent virus binding to target cells

 Form memory B cells

- Reactivate if binds antigen again

- Fast response—no need for TH2 binding

the present cytokines

yes with CD1

shielding or inhibition of MAMPS

Antigenic variantion

inhibition of psonation

inhibition of ROS

resistance to antimicrobial peptides

inhibition of fusion of phagosome with lysosome —> altering of membrane trafficking is common (e.g tubercolosis, salmonella

survival within phagosome

escape from phagosome

Modulation of T cell response

superantigen -> cytokin storm -> overreaction