multiple start codons (virus)

[theonlytycrane]

I came across a question describing a virus with multiple start codons, A, B, and C, for a gene encoding a surface antigen.

To clarify, the surface antigen may vary slightly depending on which start codon is used, correct? The question was saying how if a mutation occured at A, then B or C could still be used.

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[----x----]

I don't think the question is fully given in your post, but I'll address two things which may be the question.

1. If 3 different codon sequences can be "start", it doesn't matter which codon sequence it is - it will have the same function.

2. If there are 3 different start codons: A, B, and C - which are found at different areas of the sequence, then a knockout of one of the start codons will mean the transcription will not start until the next start codon. Let's say for example they are found in order on the gene: A -> B -> C.

If A is knocked out, anything between A and B will no longer be transcribed. Everything from B to the next stop codon will still be transcribed. If there is anything between A and B which is vital to the function, this would be a loss of function mutation. Perhaps it will change the tertiary structure of the surface antigen (may change function as well), or any other variety of things from losing that part of the transcript.

If the question wants anything more complex than that, I don't have enough info to elaborate

 

[theonlytycrane]

@----x----

Also from the passage: Gene S encodes the surface antigen which is used to recognize and enter liver cells. It has three in-frame start codons referred to as pre-S1, pre-S2, and S.

The correct answer is (C). I interpreted "pre-S1" to mean before the start codon, but I think by "in-frame" I was incorrect.

 

[----x----]

This question is essentially asking you what is the most significant mutation (what will have the highest likelihood of knocking out of the function of gene S).

Going through the options:

A) Missense mutation in pre-S2

This will change a single codon in the pre-s2 region to a different amino acid. This may or may not affect the start codon S2 (it could code even for a different start codon, for example) - and it's unclear if pre-s2 is required for transcription, given S1 is also a start codon located upstream. Let's see if there's a more severe mutation as an option.

B) Nonsense mutation late in S
S will be transcribed - but late in the sequence there was a mutation which created a "stop" codon. This could be bad, but as it's late in the sequence it's possible the function of S will be unaffected. This isn't clearly going to knock out the function, let's continue to other options.

C) Single base pair insertion in pre-S1
This will cause a frame shift in the entire sequence from pre-S1 onward. This shift could do any number of things to each codon in S, and is one of the most serious as it's possible that nearly all the coded amino acids will be different - or that a stop codon is coded for prematurely (like B), or any number of things. This sounds pretty bad.

D) Three nucleotide deletion early in S

A deletion can be just as problematic as an insertion, causing a frame shift just like we saw in C. However, 3 base pairs were deleted. This means that one entire codon will be removed - so all the subsequent codons will be unaffected. This is much less severe than C.


So, the answer is C.

 

[theonlytycrane]

For (C) are you interpreting the single base insertion before the start codon(s), after, or both cases?

 

[----x----]

"pre-S1" is the name of one start codon.

For answer C, one base pair is inserted in the pre-s1 codon. Not before or after, but in the codon, per the question answer.

Assuming they are in the order of pre-s1, pre-s2, then s - it would affect pre-s1 from the inserted base, and due to the frame shift also anything after that.

The most important thing is that this causes a frameshift mutation, not that it occurs in pre-s1. It is significant that it occurs in pre-s1 because the whole strand will be affected since pre-s1 is at the beginning, but remember we're not just knocking out the "start" function of pre-s1 - we are potentially changing every single amino acid thereafter because the reading frame shifted over one base pair.

For example, instead of

pre-s1
ACG GCC GCG GGG

A base was inserted (A in this example, between C and G) at pre-s1 so it would read

ACA GGC CGC GGG G...

You can see how this shift in reading frame has the potential to change every single amino acid (AA) coded for thereafter, and even if a few are the same, the AA sequence will be different enough that the original function will almost certainly not be maintained.

 

[theonlytycrane]

Thanks for the continued help. The interpretation for "in-frame" start codon is that the codons described are the ones being translated, correct?

I was thinking that a mutation in pre-s1 (the start codon) would prevent translation entirely. But by "in-frame", I think I should be thinking about the a.a. sequence being changed as you described, not the start codon itself which would prevent translation.

 

[----x----]

There are 3 start codons, so knocking one out won't stop the gene from translating. (I do wonder if you misstyped some information from the passage, and if there are really 2 start codons pre-s1 and pre-s2, and S is simply the gene - otherwise the answer options don't make sense, early vs late in S for example).

One "reading frame" is from a start codon to the next stop codon. It is broken into a series of nucleotide triplets which code for their respective amino acids, or start/stop. In some genomes, reading frames can overlap (more often in viral, prokaryotic, or bacterial/mitochondrial genomes). In this question's example, it is viral DNA with what seems to be 3 (2?) overlapping reading frames starting at pre-s1, pre-s2 and terminating at the stop codon. As was discussed above, knocking one out may or may not affect the function of gene S - but a frameshift mutation certainly will.

However, thinking of these reading frames is likely spending too long on this question. I simply looked at:
A - missense in 1 start codon, gene could still be fine since the other start codon is present.
B - stop codon late in gene S, gene is mostly translated so may still function.
C - insertion of a single nucleotide, whole thing will be off.
D - deletion, but it's 3 nucleotides so reading frame isn't shifted.

C it is.