Backbone and sidechain NMR assignments for the ribosome maturation factor RimP from Escherichia coli
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Backbone and sidechain NMR assignments for the ribosome maturation factor RimP from Escherichia coli Andreas Schedlbauer1 · Borja Ochoa‑Lizarralde1 · Idoia Iturrioz1 · Retina Çapuni1 · Tammo Diercks1 · Elisa de Astigarraga1 · Paola Fucini1,2 · Sean R. Connell1,2 Received: 18 December 2019 / Accepted: 30 March 2020 © Springer Nature B.V. 2020
Abstract Ribosome biogenesis is an energetically expensive and complex cellular process that involves the coordinated folding of the ribosomal RNA and dozens of ribosomal proteins. It proceeds along multiple parallel pathways and is guided by transacting factors called ribosome assembly factors. Although this process has been studied for decades, there are still many open questions regarding the role of the ribosome assembly factors in directing the folding of ribosome biogenesis intermediates. RimP is one of the early acting factors and guides the assembly of the small 30S ribosomal subunit by facilitating the binding of ribosomal proteins uS5 and uS12. Here we report the virtually complete 1H, 15N, and 13C chemical shift assignment of RimP from Escherichia coli. The NMR chemical shift data, deposited in the BMRB data bank under Accession No. 28014, indicates a widely folded protein composed of three alpha helices and eight beta strands. Keywords NMR · Ribosome maturation factors · rimP · Multidimensional NMR spectroscopy Abbreviations IPTG Isopropyl-thio-β-d-galactoside E. coli Escherichia coli RimP Ribosome maturation factor P PIC Protease inhibitor cocktail TCEP Tris(2-carboxyethyl)-phosphine RCI Random coil index
Biological context Bacterial ribosome assembly involves the coordinated and integrated folding of its ribosomal RNA (rRNA) along with diverse ribosomal r-protein components (Wilson and Nierhaus 2007; Shajani et al. 2011; Davis and Williamson * Paola Fucini [email protected] * Sean R. Connell [email protected] 1
Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Bizkaia, Spain
Basque Foundation for Science, IKERBASQUE, 48011 Bilbao, Spain
2
2017). Concurrent with this folding, the rRNA is processed (i.e. trimmed from a larger transcript) while both rRNA and r-proteins are modified post-transcriptionally and -translationally, respectively. This assembly process is guided by a growing number of known assembly factors that include GTPases, modification enzymes (e.g. methylases), helicases, and other chaperones. Although their specific molecular roles are not generally established, these assembly factors are believed to facilitate ribosome assembly by directing r-protein binding to the rRNA and guiding rRNA folding by avoiding kinetic traps, which are alternative RNA conformations that slowly refold to the native structure and derive from a degeneracy of local interactions (Woodson 2000). The assembly factor RimP was first identified from the observation that a rimP chromosomal deletion reduced the amount of translating 70S ri
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