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Glossary of Microbiology 7

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penicillin MOR
enzymatic inactivation
polymyxin MOR
dec permeability
macrolides, tetracycline MOR
efflux
macrolides, streptogramins, tetracycline, aminoglycosides MOR
altered target (ribosome)
vancomycin MOR
altered target (cell wall precursor)
lysostaphin
disrupts S. aureus biofilms and eradicates extracellular matrices
what can furanone be used for?
to disrupt quorum sensing
T/F (according to Wenzel)

Antibiotic resistant S. aureus is the most daunting challenge on the near horizon for the Infectious Diseases community
T
what is the one characteristic that can distinguish viruses from other organisms (Cabral)?
have DNA or RNA for genetic material, but not both
T/F All icosahedra have two, three, or five-fold symmetry
T
what are the three major structural components of the simple virion?
(1) genome

(2) capsid

(3) envelope (not present in some viruses)
nucleocapsid
capsid + genome
what are the two types of nucleocapsids?
(1) icosahedral (cubic)

(2) helical (radial)
desc the envelope of orthomyxoviridae (2)
(1) neuraminidase (sialidase)

- cleaves neuraminic acid and disrupts the mucin barrier, exposing the sialic acid binding sites beneath

(2) Hemagglutinin

- can attach to host sialic acid receptors, needed for adsorption
desc the envelope of paramyxoviridae (2)
(1) HA and NA are a part of the same glycoprotein spike

(2) possess a fusion protein (F protein) that causes the infected host cells to fuse together into multinucleated giant cells
orthomyxoviridae i.e.
influenza virus
paramyxoviridae i.e.
parainfluenza virus, respiratory syncytial virus, mumps virus, and measles virus
what type of nucleic acid does adenoviridae have?
linear, dsDNA; can form circle

- also has terminal protein on each 5' end, helps in replication
what type of nucleic acid does parvoviridae have?
linear, single-stranded DNA, with terminal inverted repeat
what type of nucleic acid does papovaviridae have?
circular, double-stranded DNA
what type of nucleic acid does poxviridae have?
linear, double-stranded DNA
what type of nucleic acid does herpetoviridae have?
linear, double-stranded DNA
T/F Complex viruses have a nucleocapsid?
F, only simple viruses do
T/F Complex virus is composed of a genome and of a complex protein/lipid material which serves as a protective coat
T
what is the generalization for animal viruses concerning DNA viruses?
All DNA viruses have dsDNA except Parvoviridae (ssDNA)
what is the generalization for animal viruses concerning RNA viruses?
All RNA viruses have ssDNA with except Rheoviridae (dsRNA)
Rheoviridae, Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Retroviridae have _____ RNA
segmented
All helical animal viruses have what type of genome?
RNA
All animal DNA viruses have linear nucleic acid except?
papovaviridae and hepdnaviridae which have circular DNA
all animal DNA viruses lack an envelope except for what?
herpetoviridae, hepadnavirus, and poxviridae
Poxviridae
- simple or complex?
- reactive to ether?
- 2 important pathogens
complex

resistant to ether

Variola virus (smallpox), Vaccinia virus
Adenoviridae
- presence of envelope?
naked
Papoviridae
- presence of envelope?
- e.g.
naked

Papilloma virus (warts)
Parvoviridae e.g.
human parvovirus (bone marrow aplasia, erythema infectiosum)
Togaviridae, Flaviviridae, and Retroviridae
- envelope?
- site of envelopment?
- reaction to ether?
enveloped, surface/cytoplasm, sensitive to ether
Togaviridae
- important pathogens
rubella virus, equine encephalitis
Flaviviridae
- important pathogens (4)
dengue virus, st. louis encephalitis, yellow fever virus, hepatitis C virus
retroviridae
- important pathogens
HTLV*
Rheoviridae, Picornaviridae, Caliciviridae
- envelope?
naked
rheoviridae
- reaction to ether?
- important pathogens
partially resistant

rheovirus, colorado tick fever virus, rotavirus
Picornaviridae
- reaction to ether?
- important pathogens (6)
resistant to ether

Poliovirus, Coxsackievirus, Echovirus, Rhinovirus, Hepatitis A virus, Enterovirus
Calciviridae
- important pathogens
Norwalk agent
Togaviridae, Flaviviridae, Retroviridae, Rheoviridae, Picornaviridae, Caliciviridae
- capside symmetry?
icosahedral
Bunyaviridae, Coronaviridae, Filoviridae, Arenaviridae, Paramyxoviridae, Orthomyxoviridae, Rhabdoviridae
- capsid symmetry
- envelope
helical, enveloped
Bunyaviridae
- important pathogens
California encephalitis virus, Hantavirus
Coronaviridae
- important pathogens
Coronavirus, SARS
Filviridae
- important pathogens
Ebola virus
Arenaviridae
- important pathogens
Lymphocytic chriomeningitis virus, Lassa virus, Machupo virus
Paramyxoviridae
- important pathogens
Parainfluenza virus, Mumps virus, Measles virus, Respiratory Syncytial virus
Orthomyxoviridae
- important pathogens
Influenza A, B, and C
Rhabdoviridae
- important pathogens
rabies virus
what is the peak season for influenza?
Jan - March
Some viruses can code for anti-inflammatory cytokines. Comment on this statement using HIV-1 as an example.
HIV-1 can infect macs, codes for anti-inflammatory cytokine IL-10, which has two main fxns:

(1) upregulates CCR5 (makes it easier for virus to gain entry)

(2) shuts down immune response
Marburg virus and Ebola virus
- how is the general effect different from e.g. HIV-1
for HIV, you get INC anti-inflammatory cytokines --> shuts down immune system

for Ebola virus and Marburg virus, the immune system is NOT shut down, instead the patient dies from toxic shock syndrome (inc TNF-alpha)
what is the best stage of viral replication to combat infection?
block it at first stage --> attachment
attachment of virus to host cell governed by what type of bond?
adsorption via electrostatic bonding
all animal DNA viruses are naked (i.e. have no envelope) except for ?
Herpetoviridae --> obtain envelope from nuclear membrane of virus-infected cell

Poxviridae --> have a complex lipid-protein mix on their surface

Hepadnaviridae --> have lipoprotein-like material on their surface
viral life cycle
- compare attachment & penetration with regards to pH-dependence, ionic strength-dependence, and temp-dependence
Attachment
- pH-dependent
- Ionic strength-dependent
- temp-independent

Penetration
- pH-independent
- Ionic strength-independent
- temp-dependent
where does assembly occur for adenoviridae, papoviridae, and parvoviridae?
in nucleus
where does assembly occur for Picornaviridae, Poxviridae?
in cytoplasmic "cell factories"
where does assembly occur for Herpetoviridae, Orthomyxoviridae, Paramyxoviridae, Rhabdoviridae?
at cellular membrane
release
- picornaviridae
cell lysis
release
- orthomyxoviridae
budding from cytoplasmic membranes
release
- herpetoviridae
through ER
T/F viruses can imitate every natural ligand in your body
T
Rhinovirus receptor
ICAM-1 interacts in canyon of rhinovirus
ICAM-1
member of Ig superfamily

natural ligand is Lfa-1
PVR
poliovirus receptor

an example of a single type of receptor molecule mediating virus binding and entry
poliovirus genome structure
single-stranded linear RNA (+) strand
reovirus genome structure
double-stranded linear RNA, 10-11 segments
sindbis virus genome structure
single-stranded linear RNA, (+) strand
influenza virus genome structure
single-stranded linear RNA, (-) strand, 7-8 segments
vesicular stomatitis virus genome structure
single-stranded linear RNA, (-) strand
arenavirus genome structure
single-stranded linear RNA, (-) strand, 2 segments
hepatitis delta virus
- genome structure
- RNA polymerase
single-stranded circular RNA, rodlike (-) strand

cellular DNA-dependent RNA polymerase II
most RNA viruses replicate in the cytoplasm. What 4 exceptions instead replicate in the nucleus?
Influenza, Borna, Hepatitis delta, Retroviruses
how do influenza and bunya viruses prime RNA synthesis?
"cap-snatching"

- cellular mRNAs cleaved 10-13 nt from 5' cap by a cap-dependent endonucleolytic activity that is a part of the viral RNA polymerase
- this short host mRNA derived capped RNA is then used as a primer to initiate synthesis of the viral RNA
what type of priming system does poliovirus use?
protein priming system similar to adenovirus
hepatitis delta virus
a "satellite" virus that cannot replicate on its own but is dependent on coinfection of cells with hepatitis B virus to supply proteins necessary for production of infectious particles

RNA is a closed circular ss configuration (only known animal virus with this type of genome)
desc the cap of poliovirus mRNA
poliovirus mRNAs are NOT capped but are translated by a cap-independent mechanism
Reo and arenavirus
- polyadenylation
none

both mRNAs lack a poly(A) tail, but have 3' stem-loop structures that protect the 3' termini from degradation
Vescular stomatitis virus and influenza
- polyadenylation
"stuttering mechanism"

- RNA polymerase reiteratively copies the same stretch of Poly(U) in the (-) strand until several hundred As have been added
constitutive transport elements
retroviruses replicate genomes in nucleus but assemble viral particles in cytoplasm

RNA genomes of simple retroviruses contain constitutive transport elements, cis elements that somehow help to transport the RNA to the cytoplasm by host machinery
Poliovirus / eIF4G / IRES
Poliovirus has not a cap!

To get around this problem it encodes a protease which lops off the host eIF4G (a protein in the cap-binding complex that is critical for ribosome initiation)

But it's got an IRES (internal ribosome entry sequence) which helps initiation of translation work
Describe polyprotein expression and processing and recognize that both viral and host proteases can be involved.
One large polyprotein is expressed and then cleaved into several smaller peptides by one or more viral-encoded proteases (both cis and trans acting).

For poliovirus: viral RNA is translated into a long precursor polyprotein that is processed by two VIRAL proteases to form viral proteins

For flavivirus: processing of the flavivirus precursor polyprotein is carried out either by the HOST signal peptidase, which occurs in the lumen of the ER, or by the VIRAL protease NS3
Leaky scanning
Leaky scanning

The first start codon in the Sendai virus mRNA is an ACG (very inefficient, frequently passed over). Followed by three in-frame AUG codons that have progressively better "context". So you can get several different products depending on which start codon is used.
Reinitiation
Reinitiation

At the stop codon of an "upstream ORF" (Open Reading Frame) the ribosome stops translation but fails to fall off the mRNA. Rather, it reinitiates at a "downstream AUG". In INFLUENZA, the UAA stop codon of the upstream ORF overlaps the AUG start of the downstream ORF (UAAUG). The downstream ORF is translated 25% of the time relative to the upstream ORF.
Suppression
The gag gene stop codon is misread and an AA is inserted so that translation continues to make a Gag-Pol polyprotein that is later cleaved proteolytically by the viral protease. Can result in more proteins!
Frame Shifting
Frame Shifting

Some retroviruses (e.g. HIV). Gag and Pol are encoded by different overlapping reading frames with gag first, then pol. Before translation reaches the gag stop codon, sometimes a frame shift within gag results in translation of a somewhat truncated Gag fused to Pol sequences in a polyprotein.
lentiviruses
distinguished from other retroviruses by a long incubation period prior to onset of disease (months to years) and by chronic progression of disease in the face of host immunity
genes of the retrovirus
Genes:

gag -- "group specific antigens": structural proteins that make up the virion (matrix MA, capsid CA, and nucleic acid binding proteins NC)

pro -- protease (PR), cleaves the gag-pro-pol polyprotein

pol -- reverse transcriptase (RT) and integrase (IN)

env -- envelope glycoprotein that is cleaved into two subunits that form a complex (transmembrane TM, surface SU)
List the enzymatic activities of RT: RNA- and DNA-directed DNA polymerase, RNase H
RT first copies the ssRNA to make a RNA/DNA hybrid, then removes the template RNA while copying the DNA to make dsDNA. Thus, the enzyme has both RNA- and DNA-directed DNA polymerase activity as well as RNase H activity (digestion of RNA from an RNA/DNA hybrid)
List the DNA virus families; describe their genome structures and site of genome replication (nuclear vs cytoplasmic).
DNA viruses are sometimes referred to as the HHAPPPy viruses:

Herpes
Hepadna
Adeno
Papova
Parvo
Pox

Most replicate in the nucleus (Pox replicates in the cytoplasm)
GP 120
- which virus
- what does it do?
- do antibodies help?
GP 120 is the glycoprotein on HIV that recognizes CD4 on macs, microglia in the brain and T helper cells

antibodies to it do not neutralize infection since select domains on it are undergoing constant mutation
desc how HIV goes from monotropic --> t-tropic
During early infection (i.e., primary viremia) the HIV targets macrophages and uses the chemokine receptor CCR5 on macrophages along with the receptor CD4. Thus, these HIV strains are referred to as "monotropic" (i.e., they have a tropism for monocytes). During the second viremia phase the HIV targets T cells. It recognizes CD4 as the receptor, but in the context of the CxCR4 co-receptor. This latter receptor is found on T helper cells. Thus, the HIV strain now is referred to as a T-tropic strain. Recognition of the appearance of T-tropic strains is important since their appearance augers incipient AIDS.
discuss the differences b/t viruses and bacteria as it relates to transmission of specimens in lab
If one wants to decontaminate any waste that potentially has viral material, one must heat for a minimum of 30 minutes at 100 degress centigrade or higher. This is important in the clinical lab (or in any other area where there is virus material) to prevent contamination to personnel.

If one wants to store virus material, it should be stored at minus 70 degrees centigrade. This is important if (for example) you are collecting virus swabs for later testing in the laboratory. A classical scenario would be where you are obtaining vaginal swabs from a patient with a history of genital herpes who will be delivering soon and you want to know if she is an asymptomatic "shedder". Because the herpes simplex virus 2 (and HSV-1 also) are labile, your sample would degrade if you stored at minus 20 degrees centigrade. So, the results would come back from the lab as your patient being negative for herpesvirus infection while all along she was positive. This confound could have serious sconsequences since the newborn acquire herpes simplex virus infection while undergoing passage through the birth canal.

In terms of being more resistant to chemicals than bacteria: The point here is that most disinfection and sterility that is conducted is done so with bacteria in mind. Things that "kill" bacteria rarely have an effect on viruses. Generally, one has to use strong oxidizers and phenols to kill viruses. Oxidizers target the virus nucleic acids and renders them incapable of replicating. Use of oxidizers such as "bleach" is often recommended for disinfection where medical personnel or researchers are exposed to large volumes of blood. A classical examples are accidental spills in research labs, spilling of blood in blood banks, the necropsy/autopsy room,etc.
understand the hazards of transmission of viruses between personnel
viruses are relatively easy to
transmit? In lecture you mentioned about using chlorox to clean a big
blood spill, autoclaving instruments to 100C for 30 min, and X-ray and
gamma rays for fluids
what effect does Marburg virus have on the immune response?
Marburg virus hyper-elevates the immune response by causing a hyperproduction of pro-inflammatory cytokines...particularly tumor necrosis factor (TNF) alpha. SO, the affected patient suffers froma toxic shock-like syndrome associated with enlargement of the spaces between the endothelial cells lining the blood vessels (etc) resulting in bleeding from orifices and pores...as well as other problems such as liver failure.
what general effect does HIV have on the immune response?
HIV causes immune suppression...essentially by wiping out the helper T cell population late in the HIV infection process (i.e., via the action of T-tropic HIV)
how does papova virus (e.g. SV40) solve the end replication problem?
Bidirectional replication forks with both leading a lagging strand synth migrate away from the origin in opposite directions in this ds circular DNA. At about the half-way point the molecule resembles the greek letter theta, so this DNA replication is called "theta replication". This strategy solves the end replication problem by never having any ends to replicate (the viral DNA always remains circular).
regarding SV40 DNA replication, what fxn does host topoisomerase II play?
following rounds of replication you get a bunch of interlocked circular molecules (a catenane); topoisomerase II is required to decatanate individual genomes prior to packaging
how does adenovirus get around the end replication problem?
Uses protein priming. Cis-acting origins lie within the inverted terminal repeats. DNA synthesis begins when the preterminal protein (attached to each 5' end) associates with the origin sequences. The viral DNA polymerase then covalently attaches a template-directed C to the B-OH of a serine residue within the preterminal protein and leading strand synth by the viral DNA polymerase proceeds the full length of the genome (no lagging strand)
how does parvovirus get around the end replication problem?
Uses hairpin priming. The 3' OH at the end of this hairpin serves to prime DNA synth. A nick created near the elongated hairpin serves to prime additional synth. By alternating between hairpin priming and nick priming, the genome is replicated. As RNA primers are not used, the end replication problem is skirted.
what drug to use for small pox infection and why?
pox virus, big 'ol dsDNA replicates in cytoplasm, uses only viral-encoded DNA replication factors

viral DNA polymerase is relatively sensitive to CIDOFOVIR
how does Pox virus get around the end replication problem?
Hairpin priming to form "head-to-head/"tail-to-tail" concatemers. Replication initiated at a nick formed near one loop (similar to parvovirus). Entire genome is replicated twice, once down one strand, around the other loop, then back up the other strand. Result is a "head-to-head" dimer, or two copies of the viral genome linked together in inverted orientation to one another. Can do it again to get a tetramer -- tail-to-tail/head-to-head orientation. Eventually individual genomes are separated -- cleavage likely occurs at the Holiday jxns.
acyclovir
used against herpes virus (inhibits viral DNA polymerase)

remarkably non-toxic. Why? must be first monophosphorylated by virally-encoded thymidine kinase (host doesn't have it); also host is less likely to use this
name three drugs used to treat cytomegalovirus. which one needs to be converted to monophosphorylated form first by viral kinase?
gangiclovir (mono-P needed), foscarnet, cidofovir
HSV & Varicella zoster virus
- what general type of virus
- where do they establish latency?
Herpes viruses

latency in neurons
EBV & Kaposi's sarcoma
- what general type of virus
- where do they establish latency?
Herpes viruses

latency in B cells
Describe herpesviral latency using EBV as a model: latent genome structure, location, origin of replication, dependence on host factors, and requirement for and functions of EBNA-1.
Latent EBV genome resides in the B cell nucleus as a large circular dsDNA "episome". Unlike lytic replication, latent replication is linked to the cell cycle, restricted to one replication of the viral genome per round of host cell DNA replication, and limited to very low copy numbers per cell. Viral components: oriP and EBNA-1. EBNA-1 bound to oriP serves to recruit host replicative machinery to this site and also "tethers" the episome to segregating host chromosomes to ensure that both daughter cells receive one copy of the episome.

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