KH domain proteins: Another family of bacterial RNA matchmakers?

Olejniczak, Mikołaj; Basczok, Maciej M; Storz, Gisela

doi:10.1111/mmi.14842

Cited by 33 publications

(45 citation statements)

References 60 publications

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“…Interestingly, we also observed that the putative RBPs KhpA and KhpB (Olejniczak et al, 2021) showed strong tailing towards the RNAP and 30S fractions (Fig. 5A).…”

Section: The Emerging Rna-binding Protein Khpb Is Conserved In Entero...mentioning

confidence: 59%

Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens

Michaux

Gerovac

Hansen

et al. 2022

Preprint

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Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).

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“…Interestingly, we also observed that the putative RBPs KhpA and KhpB (Olejniczak et al, 2021) showed strong tailing towards the RNAP and 30S fractions (Fig. 5A).…”

Section: The Emerging Rna-binding Protein Khpb Is Conserved In Entero...mentioning

confidence: 59%

Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens

Michaux

Gerovac

Hansen

et al. 2022

Preprint

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“…Previous results and those reported here show that Δ pbp1a suppresses the requirement for MreC, MreD, and RodZ (Table 1) (Fenton et al ., 2016, Land & Winkler, 2011, Tsui et al ., 2016). Likewise, Δ khpA and Δ khpB mutations, which result in the absence of the major KhpAB RNA-binding regulatory protein (Hor et al ., 2020, Olejniczak et al ., 2022), suppress Δ mreCD and Δ rodZ mutations (Table 1) (Zheng et al ., 2017). These results are reiterated by Tn-seq analysis (Fig.…”

Section: Resultsmentioning

confidence: 99%

Roles of RodZ and Class A PBP1b in the Assembly and Regulation of the Peripheral Peptidoglycan Elongasome in Ovoid-Shaped Cells ofStreptococcus pneumoniaeD39

Lamanna

Manzoor

Joseph

et al. 2022

Preprint

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RodZ of rod-shaped bacteria functions to link MreB filaments to the Rod peptidoglycan (PG) synthase complex that moves circumferentially perpendicular to the long cell axis, creating hoop-like sidewall PG. Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus; Spn) that lack MreB, use a different modality for peripheral PG elongation that emanates from the midcell of dividing cells. Yet, S. pneumoniae encodes a RodZ homolog similar to RodZ in rod-shaped bacteria. We show here that the helix-turn-helix and transmembrane domains of RodZ(Spn) are essential for growth at 37°C. ΔrodZ mutations are suppressed by Δpbp1a, mpgA(Y488D), and ΔkhpA mutations that suppress ΔmreC, but not ΔcozE. Consistent with a role in PG elongation, RodZ(Spn) co-localizes with MreC and aPBP1a throughout the cell cycle and forms complexes and interacts with PG elongasome proteins and regulators. Depletion of RodZ(Spn) results in aberrantly shaped, non-growing cells and mislocalization of elongasome proteins MreC, PBP2b, and RodA. Moreover, Tn-seq reveals that RodZ(Spn), but not MreCD(Spn), displays a specific synthetic-viable genetic relationship with aPBP1b, whose function is unknown. We conclude that RodZ(Spn) acts as a scaffolding protein required for elongasome assembly and function and that aPBP1b, like aPBP1a, plays a role in elongasome regulation and possibly peripheral PG synthesis.

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“…The structures studied here may also provide a clue as to the mechanism for other effector complexes known to engage RNase E. For instance, the regulatory protein CsrD, which is required for specific turnover of the sRNAs CsrB and CsrC by RNase E (Vakulskas et al, 2016;Potts et al, 2018), may present those RNAs for structure-based recognition in analogy to the RapZ/GlmZ complex studied here. A similar scenario could also apply to recently identified RNA-binding proteins in non-model bacteria such as CcaF1, which modulates degradation of selected transcripts by RNase E in Rhodobacter sphaeroides (Grützner et al, 2021), or to the emerging class of KH proteins that may act as sRNA chaperones in Gram-positive bacteria (Olejniczak et al, 2021). It can even be envisaged that the global RNA chaperone Hfq may form encounter complexes analogous to RapZ to facilitate degradation of base-paired sRNA/target RNAs by RNase E (Figure 5a, right panel).…”

Section: Discussionmentioning

confidence: 95%

Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis

Luisi

Islam

Hardwick

et al. 2022

Preprint

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The biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled through intricate post-transcription networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthetase in Escherichia coli, but when bound by the protein RapZ, it becomes inactivated through cleavage by the endoribonuclease RNase E. Here we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the protein tetrameric quaternary structure to an imperfect structural repeat in the RNA. The RNA is contacted mostly through a highly conserved domain of RapZ that shares deep evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a pre-cleavage encounter intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised for cleavage. The structures suggest how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors are recognised for processing.

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KH domain proteins: Another family of bacterial RNA matchmakers?

Cited by 33 publications

References 60 publications

Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens

Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens

Roles of RodZ and Class A PBP1b in the Assembly and Regulation of the Peripheral Peptidoglycan Elongasome in Ovoid-Shaped Cells ofStreptococcus pneumoniaeD39

Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis

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