Co-Expression and Co-Purification of Archaeal and Eukaryal Box C/D RNPs

Yu, Peng; Yu, Ge; Tian, Shaoxiong

doi:10.1371/journal.pone.0103096

Cited by 14 publications

(11 citation statements)

References 43 publications

(46 reference statements)

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“…Fibrillarin forms a complex with Nop56, Nop58, a guide RNA and 15.5k, we postulate that the fibrillarin ribonuclease activity is directed by the complex to selective sites. Currently, we and others have been unsuccessful to form an active eukaryotic ribonucleoprotein complex with fibrillarin ( Peng et al, 2014 ). These complexes have been successfully carried out in Archaea that lack the GAR domain, but not with any of the eukaryotic counterparts ( Peng et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana

et al. 2017

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Fibrillarin is one of the most important nucleolar proteins that have been shown as essential for life. Fibrillarin localizes primarily at the periphery between fibrillar center and dense fibrillar component as well as in Cajal bodies. In most plants there are at least two different genes for fibrillarin. In Arabidopsis thaliana both genes show high level of expression in transcriptionally active cells. Here, we focus on two important differences between A. thaliana fibrillarins. First and most relevant is the enzymatic activity by AtFib2. The AtFib2 shows a novel ribonuclease activity that is not seen with AtFib1. Second is a difference in the ability to interact with phosphoinositides and phosphatidic acid between both proteins. We also show that the novel ribonuclease activity as well as the phospholipid binding region of fibrillarin is confine to the GAR domain. The ribonuclease activity of fibrillarin reveals in this study represents a new role for this protein in rRNA processing.

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Section: Discussionmentioning

confidence: 99%

Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana

et al. 2017

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“…In addition, the target RNA species could be released on demand by corresponding RNases or ribozyme for further studies. As the tRNA scaffold has been used for the successful production of various forms of target RNAs, e.g., viral RNAs and aptamers (Ponchon et al 2009;Ponchon and Dardel 2007), hammerhead riboswitch RNAs (Nelissen et al 2012), pre-miRNAs (Li et al 2015;Li et al 2014;Wang et al 2015), and snoRNAs (Peng et al 2014), the efficiency in heterogenous expression truly depends upon the structure of chimeric RNAs and resistance to bacterial RNase (Chen et al 2015;Ho et al 2018;Li et al 2014).…”

Section: Stable Rna Carriers For Fermentation Production In Vivomentioning

confidence: 99%

Novel approaches for efficient in vivo fermentation production of noncoding RNAs

Batra

et al. 2020

Appl Microbiol Biotechnol

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Genome-derived noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs), play an essential role in the control of target gene expression underlying various cellular processes, and dysregulation of ncRNAs is involved in the pathogenesis and progression of various diseases in virtually all species including humans. Understanding ncRNA biology has opened new avenues to develop novel RNA-based therapeutics. Presently, ncRNA research and drug development is dominated by the use of ncRNA mimics that are synthesized chemically in vitro and supplemented with extensive and various types of artificial modifications and thus may not necessarily recapitulate the properties of natural RNAs generated and folded in living cells in vivo. Therefore, there are growing interests in developing novel technologies for in vivo production of RNA molecules. The two most recent major breakthroughs in achieving an efficient, large-scale, and cost-effective fermentation production of recombinant or bioengineered RNAs (e.g., tens of milligrams from 1 L of bacterial culture) are (1) using stable RNA carriers and (2) direct overexpression in RNase III-deficient bacteria, while other approaches offer a low yield (e.g., nano-to microgram scales per liter). In this article, we highlight these novel microbial fermentation-based technologies that have shifted the paradigm to the production of true biological ncRNA molecules for research and development.

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“…In eukaryotes, FIB forms a ribonucleoprotein (RNP) complex with Nop56, Nop58, and 15.5ka proteins, and one of several C/D box small nucleolar RNAs (snoRNA); the latter guides the whole complex to the target rRNA for methylation [ 1 , 4 , 5 ]. Archaeal FIB proteins can form a similar RNP complex with L7Ae, Nop5, and a guide RNA to methylate pre-rRNA sequences [ 6 ]. Also, FIB can independently carry out the methylation of histone H2A in ribosomal promoters [ 7 – 9 ].…”

Section: Introductionmentioning

confidence: 99%

Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin

Pereira-Santana¹,

Gamboa-Tuz²,

Zhao³

et al. 2020

PLoS Comput Biol

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Fibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and high conservation of fibrillarins, there little is known about the evolutionary dynamics of this small gene family. We applied a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins across the Tree of Life. We identified 1063 non-redundant FIB sequences across 1049 completely sequenced genomes from Viruses, Bacteria, Archaea, and Eukarya. FIB is a highly conserved single-copy gene through Archaea and Eukarya lineages, except for plants, which have a gene family expansion due to paleopolyploidy and tandem duplications. We found a high conservation of the FIB genomic context during plant evolution. Surprisingly, FIB in mammals duplicated after the Eutheria split (e.g., ruminants, felines, primates) from therian mammals (e.g., marsupials) to form two main groups of sequences, the FIB and FIB-like groups. The FIB-like group transposed to another genomic context and remained syntenic in all the eutherian mammals. This transposition correlates with differences in the expression patterns of FIB-like proteins and with elevated Ks values potentially due to reduced evolutionary constraints of the duplicated copy. Our results point to a unique evolutionary event in mammals, between FIB and FIB-like genes, that led to non-redundant roles of the vital processes in which this protein is involved.

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Co-Expression and Co-Purification of Archaeal and Eukaryal Box C/D RNPs

Cited by 14 publications

References 43 publications

Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana

Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana

Novel approaches for efficient in vivo fermentation production of noncoding RNAs

Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin

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