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In prokaryotes, if there is an mRNA with a good (almost the consensus sequence) Shine-Dalgarno (SD) sequence, ribosome proteins will bind to it.

In eukaryotes, ribosome binds to the 5' cap, then start sliding until it finds a good Kozak sequence and translation initiates.

  1. Why will a good sequence (SD & Kozak) greatly enhance translation efficiency in both cases? I can't understand this since translation is about the bases downstream of those sequences, I have no idea how they can exert effects on overall efficiency.

  2. in eukaryotes, how can ribosome 'foresee' which is the best Kozak in a mRNA? E.g. there are 2 'AUG' in that mRNA and the first one has a better Kozak consensus. So how can ribosome 'know' the second Kozak is worse than the first, and start translation at first 'AUG', but not continue sliding towards the second Kozak?

Thanks

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  • $\begingroup$ While this is a good question with plenty of detail, it's often helpful to cite sources (e.g. links to journal articles, textbooks, wikipedia, or other resources) to maximize clarity and reliability. $\endgroup$ Jan 17 at 18:26
  • $\begingroup$ Ribosomes cannot “know” or “see” anything. Please edit your question to remove anthropomorphic language. It is sloppy and encourages sloppy thinking such as the ridiculous suggestion that the ribosome compares the environments of different AUGs, including those not yet encountered. $\endgroup$
    – David
    Jan 17 at 20:06
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I would strongly recommend looking in more detail into available resources for SD and Kozak sequences, wikipedia basically answers these questions and has plenty of further reading if you desire to explore these questions.

At the same time, remember that these are statistical processes involving thousands of molecules, rather than deterministic processes happening at a single molecule. Thus, what changes with different sequences is a rate at which some step occurs (e.g. rate of ribosome assembly, rate of translation initiation, rate of start recognition); none of these steps will occur with 100% probability on every mRNA molecule.

What this means is that you can write down equations for kinetic models of translation, allowing us to apply principles of mass action and rates of reaction from elementary chemistry. Having a higher rate of ribosome affinity for a sequence is therefore similar in effect to just having more mRNA, in the sense that in both cases you will do more translation and make more protein.

Thus, it might be easier to use the terminology of "strong" and "weak" SD/Kozak sequences. A strong sequence has a high rate of reaction and a weak sequence has a low rate of reaction. Here, the "reaction" in question is ribosome binding, or translation initiation, or whatever process we're currently studying.

Now, as to the specific questions:

  1. Sequences alter the rate at which downstream processes occur. So, e.g. a weak Kozak sequence will often simply not initiate translation, and the ribosome will fall off without translating anything. This will almost never happen with a strong Kozak sequence, so a strong Kozak is more "efficient" in the sense of more reliably leading to translation. A strong Shine-Dalgarno sequence increases the rate at which ribosome binding occurs.

Both ribosome binding and translation initiation are necessary for protein production, so if you increase the rate at which these processes occur, you increase translational efficiency in each case.

  1. There is no "foreseeing". Think about this mechanistically. The ribosome scans 3' along the mRNA, starting at the point of attachment. Also, each ribosome attachment to an mRNA can only start one translation event. Once a ribosome stops scanning and starts translating, it does not recognize subsequent Kozaks.

Thus, if there is a strong Kozak sequence, then translation will almost always start at the strong sequence, and will never have the opportunity to start at a sequence further 3'. It is mostly only when a 5' Kozak is weak that further Kozaks get recognized at all ("leaky scanning"):

The first start codon closest to the 5′ end of the strand is not always recognized if it is not contained in a Kozak-like sequence. Lmx1b is an example of a gene with a weak Kozak consensus sequence.[22] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. Exceptions to the first AUG rule may occur if it is not contained in a Kozak-like sequence. This is called leaky scanning and could be a potential way to control translation through initiation.[23] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. (Wikipedia)

So it's not that Kozaks are required, necessarily. You just need some set of circumstances which increase the probability that the ribosome starts translating next to a start codon. The Kozak simply happens to be an efficient way to get a ribosome to start translating. The closer a sequence is to the consensus Kozak sequence, the more efficient it is, because the probability of translation initiation is higher.

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  • $\begingroup$ Oh thanks! So to clear my understanding, for q1: 'efficiency' means how strong are the interactions between the ribosome and the SD sequence. If it is stronger, the ribosome will less likely to detach during translation (i.e. higher processibility), hence a better efficiency? (i.e. higher efficiency = stronger ribosome binding) $\endgroup$
    – Questions
    Jan 18 at 6:17
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    $\begingroup$ for q2: when the ribosome slides to a strong Kozak sequence, it will start translation there no matter if there are even stronger Kozaks downstream? But sometimes when the first Kozak is too weak, leak scanning occurs i.e. subseuent Kozaks are selected? $\endgroup$
    – Questions
    Jan 18 at 6:19
  • $\begingroup$ @Questions comment 1: I would say that "efficiency" is a very high-level term that just means "how much protein do I make for a fixed concentration of all reactants". I would agree that higher affinity of sequence for the ribosome (what you seem to call "interaction") does lead to higher efficiency, but efficiency is a much larger outcome, really the product of (ribosome affinity of mRNA) * (strength of translation start site/kozak) * (ability to recruit co-translational helper complexes) * (...a lot of other stuff). A sequence on its own is not "efficient", it doesn't do anything. $\endgroup$ Jan 18 at 21:37
  • $\begingroup$ @Questions comment 2: I believe that is approximately correct. There is always a small chance that the ribosome fails to start translation, and therefore downstream Kozaks get a chance. Likely there is some weird mechanism by which a downstream Kozak can conformationally constrain upstream Kozaks; for example viral translation is weird and there are often internal ribosome entry sites (IRES) and weird stuff like that. But for normal canonical translation, I think that a strong first Kozak dominates everything else. Though I could be wrong in some detail, biology is weird! $\endgroup$ Jan 18 at 21:41
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    $\begingroup$ @Maxiilian Press Thanks a lot for the clear explanation :) $\endgroup$
    – Questions
    Jan 19 at 4:07

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