sRNA

Question 1

What is antisense cis RNA?

Answer 1

A piece of RNA that is complementary to the coding strand, and is physically located across from the gene that it’s regulating

Question 2

How large are cis sRNAs?

Answer 2

Can be anywhere from 10s to 1000s of nucleotides long

Question 3

Why do cis sRNAs have extended perfect complementary with their targets?

Answer 3

Being on the antisense strand ensure that their sequence is perfectly complementary to their targets

Question 4

What would be one advantage to a cis sRNA being longer?

Answer 4

It can cover and block several ORFs, or block the ribosome binding site, leading to more regulation

Question 5

What is the typical mechanism of sRNAs?

Answer 5

Destabilizes the target mRNA and causes it to be degraded

Question 6

What are 6 mechanisms by which sRNAs regulate their target genes?

Answer 6

1. Destabilizes the target mRNA and causes it to be degraded (typical mechanism)
2. Transcription attenuation
3. Repression or activation of translation
4. Binding to and inactivating RNA binding proteins
5. Interfere with transcription by their promoters competing with the target’s promoters for RNAP
6. Can also activate mRNA expression (but rarely)

Question 7

How does the aspocR antisense RNA in Listeria work?

Answer 7

Targets pocR mRNA for degradation. It is on the antisense strand and has perfect complementary

Question 8

Why don’t Listeria cells want pocR to be expressed when no B12 is present in the cell?

Answer 8

PocR is a transcription factor that promotes expression of genes that need B12 to function. So if there’s no B12, the cell will waste energy making them

Question 9

What is the sequence of events by which the aspocR antisense RNA in Listeria prevents expression of pocR when there is NO B12 in the cell?

Answer 9

1. The riboswitch in the sRNA 5’ UTR will not be binding to anything
2. The anti-terminator hairpin forms spontaneously
3. aspocR is transcribed
4. aspocR targets pocR mRNA for destruction, and expression of genes that require B12 to function is suppressed

Question 10

What is the sequence of events by which the aspocR antisense RNA in Listeria prevents expression of pocR when there IS B12 in the cell?

Answer 10

1. B12 binds to the riboswitch
2. The terminator hairpin forms
3. Transcription of aspocR is attenuated
4. pocR is allowed to be expressed, and it will allow the genes that need B12 to be expressed

Question 11

What are trans sRNAs?

Answer 11

sRNAs that are not from the same or an overlapping sequence as their targets. Their sequences are elsewhere in the genome

Question 12

How are cis and trans sRNAs different in terms of their complementarity? What does this mean?

Answer 12

Cis sRNAs will have perfect complementarity, and trans sRNAs will most likely be imperfect since they’re elsewhere in the genome. It means that trans sRNAs are able to target multiple mRNA transcripts

Question 13

What is the most common mechanism by which trans sRNAs regulate their target mRNAs?

Answer 13

Repress translation by binding to and blocking the ribosome binding site. Also results in increased degradation of the transcript from a lack of translation

Question 14

What are 4 mechanisms by which trans sRNAs regulate their target mRNAs?

Answer 14

1. Block translation (most common)
2. Bind to the 5’ UTR and stabilize it to promote translation
3. Transcription attenuation
4. Directly destabilize target mRNA

Question 15

What is Hfq?

Answer 15

A highly conserved RNA binding protein (a chaperone) that helps many sRNAs do their function

Question 16

How does Hfq work? (3 ways)

Answer 16

Binds to sRNAs and stabilizes their interactions with their target mRNAs. It also results in the inhibition of translation by blocking the ribosome binding site, and can recruit other proteins to degrade the mRNA