Are you feeling a chill?

One of the interesting aspects of RNA biology is the functioning of structured RNAs as regulatory elements, in particular as sensors that detect changes in environment and transduce the information into a change in gene expression.  One interesting class of such RNAs are the so-called riboswitches.  These are RNAs that typically bind to a ligand, much as an in vitro-selected RNA may bind to a chemical (such as an amino acid). Binding changes the structure of the RNA, leading to changes in transcription, stability of the RNA, or translatability of the RNA.

Riboswitches may bind small molecule ligands.  Alternatively, they may sense temperature.  This occurs because many RNA structures can be rather sensitive to changes in temperature, owing to the tendency of some secondary structures to become disrupted at physiologically meaningful temperatures.  A recent study extends the realm of RNA thermometers to include the sensing of cold temperatures, and adds a new twist to the nature of the riboswitch.  In this study, the authors studied the regulatory motif of the E. coli cspA gene; this gene is a cold-shock gene, whose expression increases with lower temperature.  This regulation may be attributed to in part to the 5′-untranslated part of the cspA mRNA. This work showed that low temperature promotes an RNA fold that enhances translation and RNA stability. Interestingly, this fold requires much (most) of the cspA mRNA; in other words, the whole mRNA is a sort of RNA thermometer that senses low temperature. The authors propose that the structural variations reflect co-transcriptional folding of the RNA, and that two different pathways (and end products) are traversed in cells growing at normal and low temperatures.

From the summary of the paper:

Highlights
  • cspA mRNA adopts different conformations before and after cold shock
  • The cold-shock structure results from stabilization of a folding intermediate
  • The cold-shock structure is more efficiently translated than the 37°C structure
Summary
Cold induction of cspA, the paradigm Escherichia coli cold-shock gene, is mainly subject to posttranscriptional control, partly promoted by cis-acting elements of its transcript, whose secondary structure at 37°C and at cold-shock temperature has been elucidated here by enzymatic and chemical probing. The structures, which were also validated by mutagenesis, demonstrate that cspA mRNA undergoes a temperature-dependent structural rearrangement, likely resulting from stabilization in the cold of an otherwise thermodynamically unstable folding intermediate. At low temperature, the “cold-shock” structure is more efficiently translated and somewhat less susceptible to degradation than the 37°C structure. Overall, our data shed light on a molecular mechanism at the basis of the cold-shock response, indicating that cspA mRNA is able to sense temperature downshifts, adopting functionally distinct structures at different temperatures, even without the aid of trans-acting factors. Unlike with other previously studied RNA thermometers, these structural rearrangements do not result from melting of hairpin structures.

The citation:

Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, Romby P, Galerzi CO, Pon CL. 2010. The cspA mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA. Mol. Cell 37, 21-33. 10.1016/j.molcel.2009.11.033

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5 Responses to Are you feeling a chill?

  1. Dave Wisker says:

    Are there any riboswitches that respond to more subtle changes in temperature, like day-night fluctuations?

  2. Arthur Hunt says:

    Are there any riboswitches that respond to more subtle changes in temperature, like day-night fluctuations?

    Not that I know of. I’m not sure where one would look. Most microbes grow in ways (aquatic or in soil) where these variations are probably buffered, so any diurnal temperature fluctuations aren’t going to be very great (if any). I would guess that no one has even thought to look for this in land plants or animals, although temperatures in plants, at least, may fluctuate wildly enough such that such a thermometer may be able to work.

    Interesting question.

  3. Clem Weidenbenner says:

    Dave, Art:
    Here’s an abstract from Nakaminami et al. in PNAS (PNAS 103, 10123 – June ’06). So not only does it look like wheat is into this sort of thermal reg but even seems to tackle the problem in much the same way.

    Abstract:
    In Escherichia coli, a family of cold shock proteins (CSPs) function as transcription antiterminators or translational enhancers at low temperature by destabilizing RNA secondary structure. A wheat nucleic acid-binding protein (WCSP1) was found to contain a cold shock domain (CSD) bearing high similarity to E. coli cold shock proteins. In the present study, a series of mutations were introduced into WCSP1, and its functionality was investigated by using in vivo and in vitro assays in the context of functional conservation with E. coli CSPs. Constitutive expression of WT WCSP1 in an E. coli cspA, cspB, cspE, cspG quadruple deletion mutant complemented its cold-sensitive phenotype, suggesting that WCSP1 shares a
    function with E. coli CSPs for cold adaptation. In addition, transcription antitermination activity was demonstrated for WCSP1 by using an E. coli strain that has a hairpin loop upstream of a chloramphenicol resistance gene. In vitro dsDNA melting assays
    clearly demonstrated that WCSP1 melts dsDNA, an activity that was positively correlated to the ability to bind ssDNA. When mutations were introduced at critical residues within the consensus RNA binding motifs (RNP1 and RNP2) of WCSP1, it failed to melt
    dsDNA. Studies with WCSP1-GFP fusion proteins documented patterns that are consistent with ER and nuclear localization. In vivo and in vitro functional analyses, coupled with subcellular localization data, suggest that WCSP1 may function as a RNA chaperone to destabilize secondary structure and is involved in the regulation of translation under low temperature.

  4. Dave Wisker says:

    Interesting, Clem. Thanks!

  5. Dov Henis says:

    Life IS INDEED An RNA World

    Genomes Are RNAs’-Made Patterns-Manuals

    “Repeats protect DNA”
    http://www.the-scientist.com/blog/display/57135/

    “More On Evolution In The Still RNA World”
    http://www.the-scientist.com/community/posts/list/260/122.page#4818

    Fitting together the pieces of the “still an RNA world” puzzle ?

    – Rational probability and possibility that the initial, independent pre-biometabolism direct sunlight-fueled genes (life) were RNAs, who evolved their DNA-images as operational patterns-manuals libraries, and celled and genomed them. They most probably synthesized (and nucleusized) their DNAs manual libraries as their functional organs, to serve as their environmentally stabler than RNA, than themselves, works memory cores.

    – Rational possibility that ALL RNAs represent the original archae-genes that since their (life) genesis have been and still are the primary actors, assessors, messengers, operators of all life processes.

    – Rational possibility that the RNAs are the environmental feedback communicators to, and modifiers of, the genomes, that the RNAs are the effectors of the desirable biased genes expressions modifications, of enhanced energy constraining for survival.

    Dov Henis
    (Comments From The 22nd Century)
    28Dec09 Implications Of E=Total[m(1 + D)]
    http://www.the-scientist.com/community/posts/list/184.page#4587
    Cosmic Evolution Simplified
    http://www.the-scientist.com/community/posts/list/240/122.page#4427

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