Ribonucleoprotein multimers and their functions

Bleichert, Franziska; Baserga, Susan J.

doi:10.3109/10409238.2010.496772

Cited by 24 publications

(23 citation statements)

References 231 publications

(337 reference statements)

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“…A di-sRNP with two different sRNAs could bring together distal regions of the rRNA, facilitating long-range interactions in these long substrate RNAs. Although two different sRNAs assembled into a single sRNP is a possibility, this arrangement may also require a higher degree of cellular regulation in order to direct correct incorporation of different sRNAs into a single sRNP (Bleichert and Baserga 2010b).…”

Section: Why a Di-srnp?mentioning

confidence: 99%

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Bower-Phipps

Taylor²,

Wang³

et al. 2012

RNA

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Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 29-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species-Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus-indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

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Section: Why a Di-srnp?mentioning

confidence: 99%

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Bower-Phipps

Taylor²,

Wang³

et al. 2012

RNA

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“…11! regulate the oligomerization state of proteins both positively (Bleichert and Baserga, 2010;Huthoff et al, 2009;Xie et al, 2018) and negatively (Yoshida et al, 2004). Our data suggests that while the majority of RNA-associated proteins form higher-order assemblies with RNA, the oligomerization of 21% is potentially inhibited by RNA.…”

Section: Characterization Of Individual Rna-associated Proteinsmentioning

confidence: 74%

Systematic discovery of endogenous human ribonucleoprotein complexes

Mallam

Sae-Lee

Schaub

et al. 2018

Preprint

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RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. While recent studies have systematically identified individual RBPs, their higher order assembly into Ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that over 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. Importantly, these data also provide specific novel insights into the function of well-studied protein complexes not previously known to associate with RNA, including replication factor C (RFC) and cytokinetic centralspindlin complex. Finally, we use our method to systematically identify cell-type specific RNA-associated proteins in mouse embryonic stem cells. We distribute these data as a resource, rna.MAP (rna.proteincomplexes.org) which provides a comprehensive dataset for the study of RNA-associated protein complexes. Our system thus provides a novel methodology for further explorations across human tissues and disease states, as well as throughout all domains of life. ! 3! ! 4! upon CF-MS by comparing chromatographic separations of cellular lysate under control and RNA degrading conditions ( Figure 1A). A statistical framework is then applied to discover RNP complexes by identifying concurrent shifts of known protein complex subunits upon RNA degradation ( Figure 1A).Analysis of DIF-FRAC data answers important questions as to the role of RNA plays in macromolecular complexes. Specifically, we identify RNP complexes that 1) dissociate, 2) form stable protein-only complexes, and 3) change composition in the absence of RNA suggesting specific roles for RNA in each of these cases. Because DIF-FRAC is independent of UV crosslinking, nucleotide incorporation, genetic manipulation or poly(A) RNA capture efficiency, it can therefore be used to investigate a wide variety of cell types, tissues and species. To demonstrate this versatility, we apply DIF-FRAC to mouse embryonic stem cells (mESCs), identifying 1,165 RNA-associated proteins, to show the method is highly adaptable and can be extended to discover RNP complexes in diverse samples.Finally, we created a system-wide resource of 1,428 RNP complexes, many of which are previously unreported as having an RNA component, representing 20% of known human protein complexes. We provide our resource, rna.MAP, to the community as a fully searchable web database at rna.proteincomplexes.org. Results and Discussion Differential fractionation (DIF-FRAC) identifies RNP complexesThe DIF-FRAC strategy builds upon our previous strategy of Co-Fractionation Massspectroscopy (CF-MS) for identifying protein complexes in cellular lysate (Havugimana et al., 2012;Wan et al., 2015). CF-MS chromatograp...

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“…This may explain why the targets of nucleotide modification of some of the candidate box C/D sRNAs and box H/ACA sRNAs cannot be identified [42, 43, 61–66]. Therefore, some archaeal sRNPs may function in pre-rRNA cleaving or folding [69, 107, 115]. The hypothesis that sRNPs act as chaperones is consistent with the box C/D sRNP di-sRNP model.…”

Section: Other Functions Of Box C/d and Box H/aca Srnpsmentioning

confidence: 90%

“…The existence of many candidate sRNAs discovered using experimental approaches has been confirmed by either northern blots or by primer extension [42, 43, 61–65]. Some predicted sRNAs have been shown experimentally to be able to assemble into sRNPs which are catalytically active [26, 43, 65, 67–69]. In addition, the predicted target sites of some candidate guide sRNAs have been confirmed to be modified [42, 43, 61, 63–65, 67].…”

Section: Discovery Of Archaeal Sno-like Rnasmentioning

confidence: 99%

“…The hypothesis that sRNPs act as chaperones is consistent with the box C/D sRNP di-sRNP model. A dimeric sRNP can potentially allow base-pairing with four segments of pre-rRNAs using the four guide sequences, trapping nearby pre-rRNA sequences and avoiding the formation of premature RNA tertiary structures [16, 69]. The nonmodification functions of archaeal sRNPs are speculative.…”

Section: Other Functions Of Box C/d and Box H/aca Srnpsmentioning

confidence: 99%

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Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification

Yip

Vincent

Baserga

2013

Archaea

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Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.

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Ribonucleoprotein multimers and their functions

Cited by 24 publications

References 231 publications

The box C/D sRNP dimeric architecture is conserved across domain Archaea

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Systematic discovery of endogenous human ribonucleoprotein complexes

Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification

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