Abstract In order to become bioactive, proteins must be translated and protected from aggregation during biosynthesis. The ribosome and molecular chaperones play a key role in this process. Ribosome-bound nascent chains (RNCs) of intrinsically disordered proteins and RNCs bearing a signal/arrest sequence are known to interact with ribosomal proteins. However, in the case of RNCs bearing foldable protein sequences, not much information is available on these interactions. Here, via a combination of chemical crosslinking and time-resolved fluorescence-anisotropy, we find that nascent chains of the foldable globin apoHmp1–140interact with ribosomal protein L23 and have a freely-tumbling non-interacting N-terminal compact region comprising 63–94 residues. Longer RNCs (apoHmp1–189) also interact with an additional yet unidentified ribosomal protein, as well as with chaperones. Surprisingly, the apparent strength of RNC/r-protein interactions does not depend on nascent-chain sequence. Overall, foldable nascent chains establish and expand interactions with selected ribosomal proteins and chaperones, as they get longer. These data are significant because they reveal the interplay between independent conformational sampling and nascent-protein interactions with the ribosomal surface.
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Mg+2 Ions Mediate the Interaction of Intrinsically Disordered Nascent Chains with the Ribosome
During the last few decades, the ribosome has been regarded primarily as a major cell player devoted to the catalysis of protein biosynthesis during translation [1-5]. It is therefore not surprising that several processes related to translation exploit the ribosome as a central hub. For instance, it is well-known that many events related to translational regulation are mediated by interactions between the ribosome and initiation, elongation or termination factors [6-9]. In addition, the ribosome is involved in mRNA-code recognition and proofreading [10-12] as well as in the control of translation rates via interactions with mRNA codons bearing high- and lowfrequency [13-15] and associated with variable tRNA abundance within the translation machinery [16-18]. Interestingly, the ribosome also assists de novo protein structure formation by minimizing cotranslational aggregation, thus increasing the yield of native-protein production [19,20]. The latter event, however, has not been shown to require -- or even involve -- direct interactions between the ribosome and the nascent protein chain. A notable exception is that of nascent chains bearing either N-terminal signal sequences or translational-arrest tags. These proteins are known to establish short- or long-term contacts with various regions of the ribosome during translation [21-25]. In summary, until recently very little knowledge has been available about direct contacts between the ribosome and nascent polypeptides and proteins that do not carry signal or arrest sequences. Studies based on fluorescence depolarization in the frequency domain [26] and NMR spectroscopy [27-30] provided interesting data that are consistent with, but do not unequivocally establish, the presence of these interactions.
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- PAR ID:
- 10335219
- Date Published:
- Journal Name:
- The neuroscience chronicles
- Volume:
- 3
- ISSN:
- 2767-3405
- Page Range / eLocation ID:
- 3 - 5
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The influence of the ribosome on nascent chains is poorly understood, especially in the case of proteins devoid of signal or arrest sequences. Here, we provide explicit evidence for the interaction of specific ribosomal proteins with ribosome-bound nascent chains (RNCs). We target RNCs pertaining to the intrinsically disordered protein PIR and a number of mutants bearing a variable net charge. All the constructs analyzed in this work lack N-terminal signal sequences. By a combination chemical crosslinking and Western-blotting, we find that all RNCs interact with ribosomal protein L23 and that longer nascent chains also weakly interact with L29. The interacting proteins are spatially clustered on a specific region of the large ribosomal subunit, close to the exit tunnel. Based on chain-length-dependence and mutational studies, we find that the interactions with L23 persist despite drastic variations in RNC sequence. Importantly, we also find that the interactions are highly Mg+2-concentration-dependent. This work is significant because it unravels a novel role of the ribosome, which is shown to engage with the nascent protein chain even in the absence of signal or arrest sequences.more » « less
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N.A. (Ed.)In order to become bioactive, proteins need to be biosynthesized and protected from aggregation during translation. The ribosome and molecular chaperones contribute to both tasks. While it is known that some ribosomal proteins (r-proteins) interact with ribosome-bound nascent chains (RNCs), specific interaction networks and their role within the ribosomal machinery remain poorly characterized and understood. Here, we find that RNCs of variable sequence and length (beyond the 1st C-terminal reside) do not modify the apparent stability of the peptidyl-transferase center (PTC) and r-proteins. Thus, RNC/r-protein interaction networks close to the PTC have no effect on the apparent stability of ribosome-RNC complexes. Further, fluorescence anisotropy decay, chemical-crosslinking and Western blots show that RNCs of the foldable protein apoHmp1-140 have an N-terminal compact region (6394 residues) and interact specifically with r-protein L23 but not with L24 or L29, at the ribosomal-tunnel exit. Longer RNCs bear a similar compact region and interact either with L23 alone or with L23 and another unidentified r-protein, or with molecular chaperones. The apparent strength of RNC/r-protein interactions does not depend on RNC sequence. Taken together, our findings show that RNCs encoding foldable protein sequences establish an expanding specific interaction network as they get longer, including L23, another r-protein and chaperones. Interestingly, the ribosome alone (i.e., in the absence of chaperones) provides indiscriminate support to RNCs bearing up to ca. 190 residues, regardless of nascent-chain sequence and foldability. In all, this study highlights the unbiased features of the ribosome as a powerful nascent-protein interactor.more » « less
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SUMMARY Translation of the chloroplastpsbAmRNA in angiosperms is activated by photodamage of its gene product, the D1 subunit of photosystem II (PSII), providing nascent D1 for PSII repair. The involvement of chlorophyll in the regulatory mechanism has been suggested due to the regulatory roles of proteins proposed to mediate chlorophyll/D1 transactions and the fact that chlorophyll is synthesized only in the light in angiosperms. We used ribosome profiling and RNA‐seq to address whether the effects of light on chloroplast translation are conserved in the liverwort Marchantia (Marchantia polymorpha), which synthesizes chlorophyll in both the dark and the light. As in angiosperms, ribosome occupancy onpsbAmRNA decreased rapidly upon shifting plants to the dark and was rapidly restored upon a transfer back to the light, whereas ribosome occupancy on other chloroplast mRNAs changed very little. The results were similar in aMarchantiamutant unable to synthesize chlorophyll in the dark. Those results, in conjunction with pulse‐labeling data, suggest that light elicits a plastome‐wide activation of translation elongation and a specific increase inpsbAtranslation initiation inMarchantia, as in angiosperms. These findings show that light regulates chloroplast translation similarly in vascular and non‐vascular plants, and that constitutive chlorophyll synthesis does not affect light‐regulatedpsbAtranslation initiation. Additionally, the translational outputs of chloroplast genes are similar inMarchantiaand angiosperms but result from differing contributions of mRNA abundance and translational efficiencies. This adds to the evidence that chloroplast mRNA abundance and translational efficiencies co‐evolve under selection to maintain protein outputs.more » « less
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