Abstract:
:The GIR1 branching ribozyme constitutes a separate class of naturally occurring ribozymes. Most studies have been performed with the single GIR1 known from the myxomycete Didymium iridis whereas the large number of GIR1s found in the amoeboflagellate Naegleria has remained largely uncharacterized. Here, we investigate ribozyme cleavage properties of a collection of Naegleria GIR1 ribozymes and define the variant from N. pringsheimi as a suitable model due to its superior activity in vitro. We identify the minimal ribozyme by deletion analysis applying a new RNase R based assay for the branching reaction, and by mutational analysis we demonstrate a surprising effect on the activity of structural elements J2/10 and L9 located outside the core of the ribozyme. These elements are located in regions that differ mostly from the Didymium ribozyme and illustrate the usefulness of comparative ribozyme studies.
journal_name
RNA Bioljournal_title
RNA biologyauthors
Tang Y,Nielsen H,Birgisdottir AB,Johansen Sdoi
10.4161/rna.8.6.16027subject
Has Abstractpub_date
2011-11-01 00:00:00pages
997-1004issue
6eissn
1547-6286issn
1555-8584pii
16027journal_volume
8pub_type
杂志文章相关文献
RNA Biology文献大全abstract::Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism across the eukaryotic domain. Recent computational and structural studies have provided new insights into how they recognize RNA, and show that the recognition is sequence-specific and modular. The modular code for RNA-binding by PPR pro...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.24769
更新日期:2013-01-01 00:00:00
abstract::How have the branchpoint motifs evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R1C2T3R4A5Y6, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G4/A4 ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by ...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2019.1697548
更新日期:2020-03-01 00:00:00
abstract::Epithelial-mesenchymal interactions are required to coordinate cell proliferation, patterning, and functional differentiation of multiple cell types in a developing organ. This exquisite coordination is dependent on various secreted molecules that provide developmental signals to mediate these tissue interactions. Rec...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.1080/15476286.2017.1361098
更新日期:2017-12-02 00:00:00
abstract::Enzymes of the cytosine-5 RNA methyltransferase Trm4/NSun2 family methylate tRNAs at C48 and C49 in multiple tRNAs, as well as C34 and C40 in selected tRNAs. In contrast to most other organisms, fission yeast Schizosaccharomyces pombe carries two Trm4/NSun2 homologs, Trm4a (SPAC17D4.04) and Trm4b (SPAC23C4.17). Here, ...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2019.1568819
更新日期:2019-03-01 00:00:00
abstract::All organisms must keep their DNA intact and free of lesions to obtain faithful transmission of genetic information, and many cellular proteins are involved in genome maintenance. However, also other macromolecules may be subject to repair. Deleterious lesions in proteins can be reversed by several mechanisms, and thi...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.2.1.1602
更新日期:2005-01-01 00:00:00
abstract::Earlier we have demonstrated the presence of internal ribosome entry site (IRES) within tumor suppressor p53 mRNA. Here we have mapped the putative secondary structure of p53- IRES RNA using information from chemical probing and nuclease mapping experiments. Additionally, the secondary structure of the IRES element of...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.8.1.14260
更新日期:2011-01-01 00:00:00
abstract::In the last years, a number of nuclear genes restoring cytoplasmic male sterility (CMS) have been cloned in various crop species. The majority of these genes have been shown to encode pentatricopeptide repeat proteins (PPR) that act by specifically suppressing the expression of sterility-causing mitochondrial transcri...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.25568
更新日期:2013-01-01 00:00:00
abstract::RNase J is a prokaryotic 5'-3' exo/endoribonuclease that functions in mRNA decay and rRNA maturation. Here, we report a novel duplex unwinding activity of mpy-RNase J, an archaeal RNase J from Methanolobus psychrophilus, which enables it to degrade duplex RNAs with hairpins up to 40 bp when linking a 5' single-strande...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1777379
更新日期:2020-10-01 00:00:00
abstract::The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activi...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1860376
更新日期:2020-12-23 00:00:00
abstract::Proper base-pairing of a miRNA with its target mRNA is a key step in miRNA-mediated mRNA repression. RNA remodelling by RNA-binding proteins (RBPs) can improve access of miRNAs to their target mRNAs. The largest isoform p45 of the RBP AUF1 has previously been shown to remodel viral or AU-rich RNA elements. Here, we sh...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1822637
更新日期:2020-09-29 00:00:00
abstract::Altered expression levels of protein-coding genes and microRNAs have been implicated in the pathogenesis of Huntington's disease (HD). The involvement of other ncRNAs, especially long ncRNAs (lncRNA), is being realized recently and the related knowledge is still rudimentary. Using small RNA sequencing and PCR arrays w...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2018.1534524
更新日期:2018-01-01 00:00:00
abstract::The chromatoid body is a large perinuclear ribonucleoprotein particle of germ cells. The chromatoid body is also present in stem cells from planarians. This particle shares markers specific to protein aggresomes and P-bodies, and concentrate several RNA pathways. The assembly mechanism of chromatoid bodies is unknown,...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.2.8049
更新日期:2009-04-01 00:00:00
abstract::Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.5.3.6876
更新日期:2008-07-01 00:00:00
abstract::Transcriptional regulation of microRNA (miRNA) expression is one of the least understood aspects of miRNA biogenesis. In C. elegans the list of miRNAs whose transcriptional control has been described in some detail is currently limited to four: let-7, lin-4, lsy-6, and mir-61. Each of these genes has been shown experi...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.1.7574
更新日期:2009-01-01 00:00:00
abstract::tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, met...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.1080/15476286.2015.1008358
更新日期:2015-01-01 00:00:00
abstract::The tight gene expression regulation controls the development and pathogenesis of human malaria parasite Plasmodium falciparum throughout the complex life cycle. Recent studies have revealed the pervasive nascent transcripts in the genome of P. falciparum, suggesting the existence of a hidden transcriptome involved in...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1732032
更新日期:2020-06-01 00:00:00
abstract::Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common dementia among the elderly. The pathophysiology of AD is characterized by two hallmarks: amyloid plaques, produced by amyloid β (Aβ) aggregation, and neurofibrillary tangle (NFT), produced by accumulation of phosphorylated tau. Th...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1788848
更新日期:2020-07-14 00:00:00
abstract::In metazoan organisms, alternative splicing is a central mechanism for the regulation of gene expression. However, many questions remain about the underlying molecular mechanisms. Our recent work suggests that U1 snRNP-independent premRNA splicing occurs in humans, which contributes to the regulation of alternative sp...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.4.9318
更新日期:2009-09-01 00:00:00
abstract::The endoribonuclease RNase-L requires 2',5'-linked oligoadenylates for activation, and mediates antiviral and antiproliferative activities. We previously determined that RNase-L activation induces senescence; to determine potential mechanisms underlying this activity, we used microarrays to identify RNase-L-regulated ...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.6.3.8526
更新日期:2009-07-01 00:00:00
abstract::MicroRNAs are small, non-coding RNAs that are increasingly appreciated to play critical roles in the modulation of gene expression. In mammalian cells, our knowledge regarding the full impact of microRNAs on cellular behavior remains fragmentary. This has been due, in significant part, to the limited availability of e...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.5.10081
更新日期:2009-11-01 00:00:00
abstract::We previously showed that miR-122 was frequently downregulated in hepatocellular carcinoma (HCC) and C/EBPα transactivated miR-122 expression. In this study, we found that Sp1 bound to the miR-122 promoter at two different sites. Interestingly, either inhibition or overexpression of Sp1 could decrease the miR-122 prom...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2019.1673656
更新日期:2020-02-01 00:00:00
abstract::One of the many important consequences that temperature down-shift has on cells is stabilization of secondary structures of RNAs. This stabilization has wide-spread effects, such as inhibition of expression of several genes due to termination of their transcription and inefficient RNA degradation that adversely affect...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.7.6.13482
更新日期:2010-11-01 00:00:00
abstract::Regulation of protein synthesis is an essential step of gene expression. This process is under the control of cis-acting RNA elements and trans-acting factors. Gemin5 is a multifunctional RNA-binding protein organized in distinct domains. The protein bears a non-canonical RNA-binding site, designated RBS1, at the C-te...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1762054
更新日期:2020-09-01 00:00:00
abstract::We had previously proposed that the post-transcriptional regulation through microRNA as a mechanism for incomplete penetrance and variable expressivity, leads to lack of correlation between genotype and phenotype. Here we report the validation of miRNA-target interactions we predicted earlier and demonstrate the regul...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.19318
更新日期:2012-03-01 00:00:00
abstract::Differential mRNA stability is an important mechanism for regulation of virulence factors in Streptococcus pyogenes (group A streptococcus, GAS), a serious and prevalent human pathogen. We have described 2 Classes of mRNA in GAS that are distinguishable by 1) stability in the stationary phase of growth, 2) kinetics of...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.7.5.13097
更新日期:2010-09-01 00:00:00
abstract::Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process remain poorly understood. For a long time, small rRNA sequences have been widely treated as non-specific degradation products and neglected as garbage sequences. Recently, we identified a new class of antisense ribosoma...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.1080/15476286.2017.1341034
更新日期:2017-11-02 00:00:00
abstract::Bacteria, like mammals, have to constantly defend themselves from viral attack. Like mammals, they use both innate and adaptive defense mechanisms. In this point of view we highlight the commonalities between defense systems of bacteria and mammals. Our focus is on the recently discovered bacterial adaptive immune sys...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.20177
更新日期:2012-05-01 00:00:00
abstract::The ribosome binding site of Escherichia coli rpoS mRNA, encoding the stationary sigma-factor RpoS, is sequestered by an inhibitory stem-loop structure (iss). Translational activation of rpoS mRNA at low temperature and during exponential growth includes Hfq-facilitated duplex formation between rpoS and the small regu...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.7.6.13768
更新日期:2010-11-01 00:00:00
abstract::Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differen...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1733800
更新日期:2020-06-01 00:00:00
abstract::Staphylococcus aureus is one of the major human pathogens, which causes numerous community-associated and hospital-acquired infections. The regulation of the expression of numerous virulence factors is coordinated by complex interplays between two component systems, transcriptional regulatory proteins, and regulatory ...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.20103
更新日期:2012-04-01 00:00:00