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MIMM 324 > Lecture 6 > Flashcards

Lecture 6 Flashcards

1
Q

What type of RNA do all viruses have to make so that it can be translated by host ribosome?

A

+mRNA

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2
Q

What is the 5’ cap structure important for?

A

-translation
-initiation
-processing
-transport
-stability

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3
Q

what is the 5’utr?

A

-3-1000 nt in lenght
-often structures (must be unwound to allow passage of ribosomes)
-length and 2nd structure influence translation efficiency

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4
Q

WHAT IS THE 3’ UTR?

A

-CAN REGULATE TRANSLATION INITIATION, efficiency and mRNA stability
-Poly(A) tail (stability, translation)

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5
Q

5’ dependant initiation

A

40S subunit-> initiation factor binding -> eIF1A and eIF3 bind eIF3 is associated with the 40S ribosomal subunit and plays a role in keeping the large (60S) ribosomal subunit from prematurely binding. eIF3 also interacts with the eIF4F complex, which consists of three other initiation factors: eIF4A (helicase that unwinds rna), eIF4E, and eIF4G -> binding of tertiary complex = 43s preinitiation complex -> binding of eIF4G eIF4G is a scaffolding protein that directly associates with both eIF3 and the other two components. eIF4E is the cap-binding protein. Binding of the cap by eIF4E is often considered the rate-limiting step of cap-dependent initiation, and the concentration of eIF4E is a regulatory nexus of translational control -> binding to eIF4E aka cap binding protein -> 48 initiation complex

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6
Q

What is juxtaposition of mRNA ends

A

-we need the 3’ end to be near the 5’ end for good translation efficiency
-for the 5’ end the 3’ end to be close, the cells achieve with an interaction between the Pabp (wich interacts with the poly a tail) and the eIF4G (wich interacts with the eIF4E aka the cap binding protein)
-it makes like this loop

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7
Q

What is the special thing that pea enation mosaic virus and barley yellow dwarf virus do?

A

they have these CITE elements (cap independant translation elements)
-they can bind to some of the translation factors and recruit 40S
-they make this kissing loop and they can directly load the ribosome onto the ribosomal rna

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8
Q

What happens during the 60S subunit joining

A

-once you have the 40s ribosomal unit bound to the cap in cells through the eIF4E protein
-you get scanning of the first ribosome looking for the first AUG, when found the 60S binds= trabnslation of proteins

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9
Q

WHat are the other mechanisms for decoding that have been discovered in virus infected cells^

A

-ribosome shunting
-internal initiation
-IRES elements
-Methionine independant initiation
-poly proteins
-leaky scanning
-re-initiation
-readthrough
-ribosomal frameshifting

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10
Q

Ribosome shunting

A

-the 40S just skips a stable stem loop
-shunting is predicted to decrease dependence of mRNAs for the eIF4F complex during initiation by reducing the need for mRNA unwinding
-ex: adenovirus late mRNA

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11
Q

Internal initiation

A

-ex: polio +strand
-the 5’ utr is big and highly structured
there is a bunch of AUGs before it starts normally
-proteins get choppeddd

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12
Q

Internal initiation: IRES

A

-they are structures RNA that can directly recruit the ribosome and some translation initiation factors to an internal site on the RNA
-used by polio. hep c and others
-there are multiple types

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13
Q

What are the different requirements for eIFs

A

-5’ dependant initiation: all e IFs
-Type 1 or 2 IRES: all eLFs except eIF4E
-Hep c IRES: eIF2 and eIF3

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14
Q

Methionine independant initiation

A

-Can assemble 80S ribosomes without any eIFs of Met-tRNAi
-RNA mimics tRNAi
-Cricket Paralysis virus: sticks itself into the P site of the 80S ribosome aka it mimics the initiator tRNA and places the ribosome right at a site where it can start initiating a translation
-Turnip yellow mosaic virus: does the same as cricket but with a valine molecule instead of a tRNAi

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15
Q

true or false: eukaryotic mRNAs are monocistronic

A

true it means 1 mRNA= 1 protein

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16
Q

What are polyproteins^

A

-long proteins that can be cut up into mature proteins
-ex: picornaviruses and flavivirus

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17
Q

What is leaky scanning

A

-some start codons are in good context and some are in a bad spot
-the ribosome scans and sometimes it misses an AUD because it is in a bad context
-ex: paramyxoviruses: it is how they encode their cap proteins

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18
Q

RE-initiation

A

There is something about the viral mRNA or there is a viral protein whcih keeps the 40S ribosomal subunit after it finishes and ORF
It keeps it associated with the mRNA and so therefore4 it can start translation of a downstream ORF because it sort of held on the rna somehow
-ex: herpes and paramyxoviruses

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19
Q

Suppression of termination(readthrough)

A

sometimes there is a stop codon and sometimes this stop codon can be misread or charges with suppressor tRNA aka suppression of the termination so you get continuation of the reading frame
ex: retroviruses and alphaviruses

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20
Q

Ribosomal frameshifting

A

This happens when the ribosome runs into a slippery sequence or a structure and it can cause it to like bounce back and change reading frames and it continues on translating
ex: retroviruses

21
Q

regulation of translation

A

-happens mainly at the recycling of the tertiary complex aka rate limiting
-If you have stress in the ER you wanna turns off translation: eIF2alpha kinases aka perk phosphorylates eIF4, translation is shut iff and eIf2 can’t be recycled
-same goes with amino acid deprivation, you need to turn off translation until you have enough aa. done by GCN2
-PKR senses dsRNA, if lots of it, PKR sounds the alarm and phosphorylates eIF2 and turns off translation

22
Q

how is PKR activated?

A

-PKR is present in an inactive form in the cell
-PRK is induced and activated by virus infection aka when it sees dsrna, it dimerizes and phosphorylates
-Leads to inhibition of translation and apoptosis
-it can activate the interferon response
-different viral mechanisms have evolved to inactivate the PKR pathway

23
Q

How do viruses prevent the activation of PKR?

A

adeno viruses make the virus associated rna and binds to pKR and gums it, so it can’t get phosphorylation of eIF2 and protein synthesis continues

24
Q

What does viral inhibition of cellular translation do?

A

the viruses do that so that the cell can’t establish an antiviral response
-with polio it completely runs off host translation so it stops our cells from making proteins that are cap dependant.
-only thing that is made are the viral proteins

25
Q

Modulation of cap recognition: polio edition

A

-does viral inhibition by cutting up eLF4E which cleaves the boundaries between the viral proteins. These proteases can also clave eIF4G’s link between it an eIF4E(aka cap binding protein). Now no host protein can be made and polio can make viral proteins because in the case of polio its proteins don

26
Q

Modulation of cap recognition: adenovirus and influenza ed:

A

they dephosphorylates eIF4E and this sequesters the cap-binding protein

27
Q

true or false: viruses can’t regulate protein synthesis

A

they can regulate protein synthesis and inhibit cellular protein synthesis

28
Q

Common set of assembly reactions =

A

-formation of individual structural units of the protein shell from one or several viral proteins
-assembly of the protein shell by appropriate and sometimes variable, interactions among structural units
-selective packaging of the nucleic acid genome and other essential virion components
-some viruses will aquire an envelope
-realse from host cell
-some viruses will have maturation of virus particles

29
Q

Assembly is dependant on…

A

host cell machinery
the viruses might need:
-cellular chaperones
-transport systems
-secretory pathwats
-nuclear import and export machinery

30
Q

true or false: proteins have addresses that localize them to specific places in the cell and viral proteins have these too

A
31
Q

viral replication and assembly often take place in…

A

factories or inclusions
-it concentrate viral proteins to accelerate reactions
-in positive start RNA virus these are often sorts of membranous inclusions and these concentrate viral proteins to accelerate reactions. membrane targeting can happen through signal sequences

32
Q

what are the types of targeting signals

A

-membrane targeting: can happen through signal sequences, fatty acid modifications, membrane retention signals
-nuclear localization sequences (NLS)
-nuclear export signals: to make sure that the virus gets out of the nucleus

33
Q

Where are usually the viral proteins^

A

-THE NUCLEUS: easier to pack there
-the viruses all bring the packing material to the nucleus
-for most it happens in the viruses because you don’t want it to be found in the cytoplasm by the immune system

34
Q

Sub-assemblies

A

Virus particles are complicates
-they are not all made at once
-sub assemblies ensure ordely formation of viral particles and virion subunits
-formation of discrete intermediate structures
-aka quality control

35
Q

What are the strategies to make sub assemblies

A

-Assembly from individual protein molecules:
you produce the individual proteins and they have high affinity with each other and they will automatically find each other and form some kind of assembly in the cell

-Assembly from a polyprotein precursor:
the proteins could be made as polyproteins and so they associate and then they get cleaved into their mature viral protein

-Chaperone assisted assembly:
you can make a protein and then it needs to be folded properly by a chaperone from host to take on its mature form

36
Q

Sequential and concerted assembly

A

-Sequential
ex: polio
virus attaches, uncoating, translation, structural unid is made, capsid assembly and then genome is incomporated in the capsid, stuff gets cleaved and then it yeets out of the cell

-Concerted
ex: influenza
it brings in its nucleocaspsid protein and its matrix into the nucleus where it assembles the viral genome segments. Those can zip through the nuclear pore and when they arrive at the surface of the cell they interact with the envelope glycoproteins and that drives budding from the plasma membrane

37
Q

How do viruses distinguish viral genomes from cellular DNA or RNA molecules^

A

packaging signals in the viral genome
these are discrete sequences that are typically recognized by viral proteins
-to know if a particular sequence is a packaging sequence insert it in a cell and see if it is gonna get packaged

38
Q

Herpesvirus packaging

A

herpesvirus replication produces concatemers with head-to-tail copies of viral genome

39
Q

HSV-1 packaging signals

A

aka pac 1 and 2 are needed for recognition of viral RNA and cleavage
-there are these motor proteins that wind up the DNA into the capsid and when they hit pac 2 then iy cleaves the DNA
-this ensures that the right size of DNA is in the capsid

40
Q

packaging signals: RNA genomes retroviruses edition

A

structures RNA which are packaging signals
-in the case of retroviruses it is the SL element, it recognizes 2 viral genomes because retrovitruses put 2 genomes in their viral protein
-this is because the packaging signal that is recognized is actually the kissing loop interaction between the 2 genomes that gets recognized by the viral protein and then it drags it into the virion particle

41
Q

Packaging segmented genomes

A

-evidence for specific packaging sequence on each RNA segment
ex: influenza virus always has 8 rna segments and each has its own packaging signal and that ensures that you get the right number of segments into the viral particle
-serial dependance of packaging
ex: bacteriophage smth 6: they always put the small segment first, then the medium and then the large in virion, if the small is nit there the medium can’t get in

42
Q

Aquiring an envelope

A

-envelope glycoproteins and capsids drive budding ex: alphaviruses
-internal matrix (internal leaflet of viral envelope) or capsid proteins drive budding ex: retroviruses
-Envelope proteins drive budding ex: influenza virus
-matrix proteins drive budding but additional components needed for efficiency and accuracy ex: ebolavirus

Afetr assembly of internal structures (most enveloped viruses)
-can occur at many cellular membranes (nuclear membrane, ER, Golgi, plasma membrane, etc)

43
Q

Internal assembly: influenza virus: example of how a virus might spetially and temporally regulate assembly reaction

A

-Internal structures are assembled in the nucleus and they are transported to the membrane where the matrix proteins drives budding to produce the viral particle
-the genome segments are associated with the nucleocapsid and matrix proteins in the zip out the nuclear pore and they are transported on microtubules onto the surface of the cell where the viral glycoproteins are waiting.
-internal structure assembly and budding are spatially and temporally separated
-matric protein targeted to the membrane (hydrophobic region)

44
Q

Retroviruses budding requires the …

A

ESCRT pathway
-retroviruses undergo a maturation step after they are released from the cell
-the retroviral RNA is produced in the nucleus, they get exported and they dimerize and bind to the structural proteins that target it to the cell membrane=budding
-maturation happens after the viral particle has left the cell by a protease cleavage event within the virion aka they mature once they leave the cell
Late (L) domains bind cellular proteins involved in vesicle trafficking, needed for virus release (found in + and - enveloped RNA viruses)

45
Q

True or false: viral envelope envelope can be derived from any membranes

A

true

46
Q

Viral assembly and egress: herpes

A

DNA virus: they replicate in the nucleus, they bud out of the nucleus into the ER, then bud out into the golgi where they are decorated with their envelope glycoprotens. they bud out of the golgi into a secretory vesicle and they undergo exocytosis
they are only infectious when they have their envelope from golgi

47
Q

maturation: dengue ed:

A

Dengue created its virion in the ER and passes through the trans golgi network and the change in pH and the exposure to the furin molecule causes a cleavage event that cleaves the PR protein and then the viral proteins are released and the PR proteins are also release and then the viral proteins are mature

48
Q

vaccinia virus special quirk

A

-a lot of proteins sometimes they don’t wanna infect the cell that they just came from
-they’ll down-regulate the receptor for the virus so that no other virus can reinfect
- vaccinia builds these actin tails and propels the virion away from the cell to prevent it from coming back and reinfecting it

49
Q

Release of non-enveloped viral particles

A

Cell lysis:
-apoptosis, necroptosis
-viral protein can induce rupture of cell membranes (ex: viroporins)
-loss of membrane integrity with inhibition of protein synthesis

Non-lytic release
-vesicular release ex: polio
-exocytosis/exosomes (some virus can gain transient envelopes)

MIMM 324 (26 decks)

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