Issue 7, 2022

Interpretation of anomalously long crosslinks in ribosome crosslinking reveals the ribosome interaction in stationary phase E. coli

Abstract

Crosslinking mass spectrometry (XL-MS) of bacterial ribosomes revealed the dynamic intra- and intermolecular interactions within the ribosome structure. It has been also extended to capture the interactions of ribosome binding proteins during translation. Generally, XL-MS often identified the crosslinks within a cross-linkable distance (<40 Å) using amine-reactive crosslinkers. The crosslinks larger than cross-linkable distance (>40 Å) are always difficult to interpret and remain unnoticed. Here, we focused on stationary phase bacterial ribosome crosslinking that yields ultra-long crosslinks in an E. coli cell lysate. We explain these ultra-long crosslinks with the combination of sucrose density gradient centrifugation, chemical crosslinking, high-resolution mass spectrometry, and electron microscopy analysis. Multiple ultra-long crosslinks were observed in E. coli ribosomes for example ribosomal protein L19 (K63, K94) crosslinks with L21 (K71, K81) at two locations that are about 100 Å apart. Structural mapping of such ultra-long crosslinks in 70S ribosomes suggested that these crosslinks are not potentially formed within one 70S particle and could be a result of dimer and trimer formation as evidenced by negative staining electron microscopy. Ribosome dimerization captured by chemical crosslinking reaction could be an indication of ribosome–ribosome interactions in the stationary phase.

Graphical abstract: Interpretation of anomalously long crosslinks in ribosome crosslinking reveals the ribosome interaction in stationary phase E. coli

Supplementary files

Article information

Article type
Paper
Submitted
14 Apr 2022
Accepted
15 May 2022
First published
16 May 2022
This article is Open Access
Creative Commons BY license

RSC Chem. Biol., 2022,3, 886-894

Interpretation of anomalously long crosslinks in ribosome crosslinking reveals the ribosome interaction in stationary phase E. coli

S. A. Misal, B. Zhao and J. P. Reilly, RSC Chem. Biol., 2022, 3, 886 DOI: 10.1039/D2CB00101B

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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