An Alarmone is an intracellular signal molecule that is produced due to harsh environmental factors. They regulate the gene expression at transcription level. A riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA, it works as a way to sense eviromental changes.

I've been reading some papers ("ZTP 5-Amino 4-lmidazole Carboxamide Riboside S-Triphosphate): A Proposed Alarmone for 1O-Formyl-Tetrahydrofolate Deficiency" , Bochner 1982; "An Ancient Riboswitch Class in Bacteria Regulates Purine Biosynthesis and One-Carbon Metabolism" Kim 2015) which study how ZTP can bring changes upon 10f-THF deficiency. Bochner (1982) through several experiments proposes ZTP as an alarmone for 10f-THF; some assumptions of Bochner might not have been entirely correct and a later paper fails to replicate some experiments. Later Kim (2015) propose ZTP as a riboswitch.

I'm not fully aware of the differences between the concept of "alarmone" and "riboswitch". Seems to me that both Bochner and Kim propose virtually the same thesis.

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    $\begingroup$ I don't really consider myself qualified to answer, but sounds to me like alarmone is a functional category whereas riboswitch is a structural category. Thus, they're not mutually exclusive - a riboswitch can act as an alarmone but not all riboswitches do, and vice versa an alarmone might be a riboswitch but not all alarmones are. At least that's my impression. $\endgroup$
    – Armatus
    Apr 13 '18 at 18:01
  • $\begingroup$ Your first paragraph answers it! $\endgroup$
    Apr 20 '18 at 12:16

First time I actually hear the word alarmone so bear with me okay?

"An Alarmone is an intracellular signal molecule that is produced due to harsh environmental factors. They regulate the gene expression at transcription level" <- this probably refers to activating/inhibiting transcription factors and stuff like that. Looking at bit further into the wikipedia article from whence you copied the description, we see that ppGpp is considered an alarmone.

According to the wikipedia article on ppGpp (https://en.wikipedia.org/wiki/Guanosine_pentaphosphate) we see e.g. this line "When (p)ppGpp associates with the promoter it affects the RNA polymerase enzyme's ability to bind and initiate transcription", so this alarmone can act by inhibiting RNA polymerase's ability to bind to the promoter.

A riboswitch on the other hand is a structural element INSIDE an RNA molecule that causes a conformational change upon binding a ligand. This conformational change then has an effect on transcription or translation etc. Thus, an alarmone could probably bind to a riboswitch to exert its effect, but a riboswitch is a quite specific thing. You can read about some of the mechanisms in the wikipedia article https://en.wikipedia.org/wiki/Riboswitch

So basically, think of alarmones as signalling molecules and riboswitches as structural elements in transcripts that regulate gene expression upon ligand binding.


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