SEA-PHAGES | General Question on RBS scores and start selection

Link to this post \| posted 30 Apr, 2020 04:33
fbaliraine	I am inclined to change a start from that called by GM, in favor of the next one which definitely has a better RBS score, but then this question of curiosity comes to my mind: Often, we annotators will scan the sequence to look for the best RBS score. However, ribosomes are “machines” which I would expect to bind at the earliest strong binding site they can find along their path down the sequence. It is understandable for places with z values below 2, but from the resource guide, “A Z-value higher than 2 is getting good”. If ribosomes do not go back and forth, first taking a “dry run” through the sequence like us humans to choose the best RBS score, what would then make a ribosome to skip start 2 in the attached figure (z= 2.018, Fs -5.536, called by GM in MrMiyagi at position 35962 bp), for example, and go several bases down the road to choose start 3, which has a better RBS score (Z = 3.053, -2.645)? 175Kb

Link to this post | posted 30 Apr, 2020 04:33

I am inclined to change a start from that called by GM, in favor of the next one which definitely has a better RBS score, but then this question of curiosity comes to my mind: Often, we annotators will scan the sequence to look for the best RBS score. However, ribosomes are “machines” which I would expect to bind at the earliest strong binding site they can find along their path down the sequence. It is understandable for places with z values below 2, but from the resource guide, “A Z-value higher than 2 is getting good”. If ribosomes do not go back and forth, first taking a “dry run” through the sequence like us humans to choose the best RBS score, what would then make a ribosome to skip start 2 in the attached figure (z= 2.018, Fs -5.536, called by GM in MrMiyagi at position 35962 bp), for example, and go several bases down the road to choose start 3, which has a better RBS score (Z = 3.053, -2.645)?

Link to this post \| posted 30 Apr, 2020 09:22
debbie	Hi Fred, My recommendation is to not take any one piece of data when making this decision. I believe the best start can most easily be derived from the Starterator report. Take a look. comparative data is always useful. Let me know if you have additional questions. debbie PS There is a lot of biology in the answer to your general question. The ribosome loves to treat the sequence like one big operon, but that isn't what happens. Starts and stops along the way have to do with regulation, most of which falls into the 'I don't know why' category.

Link to this post | posted 30 Apr, 2020 09:22

debbie

Hi Fred,
My recommendation is to not take any one piece of data when making this decision. I believe the best start can most easily be derived from the Starterator report. Take a look. comparative data is always useful.
Let me know if you have additional questions.
debbie

PS There is a lot of biology in the answer to your general question. The ribosome loves to treat the sequence like one big operon, but that isn't what happens. Starts and stops along the way have to do with regulation, most of which falls into the 'I don't know why' category.

Link to this post \| posted 04 May, 2020 04:53
fbaliraine	I am settling for start #3 in MrMiyagi, which has a better RBS score (Z = 3.053, -2.645)and is present in all members of the pharm, called 2/3 of the annotated genomes so far (see attached). Thanks. 18Kb

Link to this post \| posted 04 May, 2020 11:17
debbie	Fred, Good choice! debbie

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General Question on RBS scores and start selection