structure of pathogens

advantages of symmetry in viruses

genomic efficiency
self-assembly
rapid disassembly

helical symmetry

rod-shaped
open symmetry
length determined by genome length
e.g. TMV

icosahedral symmetry

spherical
60 identical subunits
20 triangular faces with 3-fold symmetry
core fold = jelly roll fold
e.g. canine parvovirus

quasi equivalence

icosahedrons with T>1
identical proteins adopt different conformations - pentamers and hexamers

human rhinovirus capsid structure

pseudo T = 3
3 core proteins VP1/2/3 all have jelly roll fold
quasi equivalent icosahedra

human rhinovirus binding ICAM-1

conserved binding site in canyon stabilised by pocket factors - not accessible to antibodies
rearranges capsid by changing VP4 conf
low pH releases pocket factor and promotes genome release

applications of viral structure

antiviral drug discovery
vaccine development - e.g. FMDV
fundamental biology

rhabdovirus proteins

Nucleoprotein
Phosphoprotein
Matrix protein
Glycoprotein
Polymerase

rhabdovirus - nucleocapsid

RNA binds groove between 2 N domains
each N binds 9 bases
positive residues attract phosphate backbone
unstructured in absence of M

rhabdovirus - M protein

links N and G
condenses N
forms polymers between N and envelope

rhabdovirus - phosphoprotein

CTD binds N+RNA
NTD binds N when no RNA in RNA binding groove
flexible region binds L and recruits into virions
positions N near RNA exit channel ready for binding

HSV proteins

Envelope proteins
Tegument
Major capsid protein
Portal vertex

HSV - capsid

VP5 hexons
VP5/VP26 pentons
VP23/VP19C triplexes stabilise
portal vertex containing UL6
T = 16

HSV - tegument

non symmetric layer between capsid and envelope
contains proteins for assembly and egress

HSV envelope

gD/B/L form fusion machinery
has host proteins derived from budding

dengue virus structure and proteins

icosahedra with protein layer outside envelope
3 structural proteins - C, E, M

dengue - capsid

dimeric alpha helical
basic - binds DNA
no higher order structure

dengue - envelope

dimeric in mature virion
changes conformation during fusion from dimer to trimer in low pH
180 E per virion - 90 dimers

dengue - membrane

expressed as prM which binds E and inhibits fusion when virus is not mature
pr removed in golgi by furin
pH change activates E

HIV-1 structure

enveloped
asymmetrical spherical
proteins = Env, gag, pol

HIV-1 particle maturation

1. cleavage of Gag polyprotein by protease after budding at 5 sites
2. Matrix remains associated with lipid membrane
3. NC+RNA condenses
4. capsid reorganises to mature - surrounds NC+RNA in fullerene core

virus structure and evolution

protein structure is more highly conserved than amino acid sequence

PRD1 family of proteins

hexon proteins with double jelly roll fold
evolved by gene duplication
fold shared by many viruses
arrangement and location of folds is conserved

apicomplexa cell morphology

plastids inherited from red algal symbiont
apicoplast that carries out biosynthesis
mitochondria functions in Fe-S biogenesis
giardia and trichomonas only have mitosomes

evolution of plastids

endosymbiont reduced by losing nucleus

Plasmodium life cycle

Mosquito blood meal releases sporozoites
liver stage - schizogony
erythrocytic stage - ring

Eimeria life cycle

sporulated oocyst ingested by animal
schizogony I-III in gut
gamete
oocyst egested

cryptosporidium life cycle

oocyst contaminates water
ingested by host
asexual and sexual cycles in host gut
thick walled oocyst exits host

toxoplasma life cycle

faecal oocysts from cats
ingested by intermediate host
tachyzoites and bradyzoites formed

apicomplexa life cycles

endodyogeny
schizogony
leukocyte transformation
endopolygeny

endodyogeny

2 daughter cells within mother cell
one round of S and M followed by budding of daughter cells
toxoplasma

schizogony

multiple daughter cells from single parent cell
multiple asynchronous rounds of nuclear division followed by synchronous final mitosis
plasmodium

leukocyte transformation

uses host machinery causing parent cell division
thelieria

endopolygeny

single parent cell divides into multiple daughter cells via internal budding
stage with polyploid nucleus

apicomplexa cell cycle regulation

checkpoints absent or unusual
varies per cycle
global - kinases

kinetoplastid cell morphology

morphology alters after invasion
flagellum for movement and invasion
kinetoplastid organelle is full of DNA - extension of mitochondria

kinetoplastid genome structure

diploid
transcription is polycistronic - no gene specific control

leishmania life cycle

sandfly blood meal injects promastigotes
phagocytosed by macrophages and transforms into amastigotes
amastigotes taken in blood meal
amastigotes transform to promastigotes in gut

leishmania pathology

type depends on parasite and vector species
cutaneous - skin lesion

T.cruzi life cycle

triatomine blood meal releases metacyclics at wound site
metacyclic transform into amastigotes
transform into trypomastigotes which are taken in blood meal
epimastigotes in midgut of bug
metacyclics in hindgut

T.cruzi pathology

chagas disease
chronic infection may by asymptomatic
determinate chronic disease - cardiac or GI muscle patholgy

T.brucei life cycle

Tseste fly injects metacyclic trypomastigotes
transform into blood trypomastigotes
tseste ingests blood trypomastigotes
transform into procyclics in midgut
leave midgyt and transform into epimastigotes and then metacyclics in salivary gland

T.brucei pathology

african sleeping sickness
non-specific acute symptoms
neuropsychiatric symptoms

synthesis of bacterial cell wall

1. make lipid II (disaccharide and pentapeptide)
2. flip lipid II to periplasm
3. polymerise to existing PG - GTase and transpeptidase activity
   class A PBPs = bifunctional
   class B PBPs and SEDs = monofunctional

regulation of PG synthesis

CwlM non phos interacts with MurJ flippase to regulate precursor transport - no synthesis
CwlM phos by PknB activates MurA - first enzyme in synthetic pathway
depletion increases susceptibility to beta lactams

bacterial imaging techniques

super resolution microscopy
total internal reflection microscopy
cryo EM

divisome function

finds centre of cell and recruits PG synthesis enzymes
FtsZ treadmills and brings PG machinery - can be tracked by TIRF which calculates FtsZ velocity

divisome regulation by MInCDE

MinD binds membranes when ATP-bound
MinC binds MinD to prevent FtsZ polymerisation
MinE stimulates MinD ATPase activity causing membrane release
results in oscillation of MinD from pole to pole so less MinD in centre = FtsZ can assemble here

divisome regulation SlmA

SlmA coats DNA to prevent FtsZ assembling before DNA segregation

elongasome function

insert new PG to aid rod-shaped elongation
MreB directly binds membrane and forms antiparallel flat filaments
MreB circumferential motion drives elongation - TIRF