scholarly journals Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression

RNA ◽  
2013 ◽  
Vol 19 (10) ◽  
pp. 1317-1326 ◽  
Author(s):  
A. Brummer ◽  
S. Kishore ◽  
D. Subasic ◽  
M. Hengartner ◽  
M. Zavolan
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Binding Specificity ◽  
Translational Repression ◽  
Coding Region

scholarly journals Regulation of Motility in Erwinia carotovora subsp. carotovora: Quorum-Sensing Signal Controls FlhDC, the Global Regulator of Flagellar and Exoprotein Genes, by Modulating the Production of RsmA, an RNA-Binding Protein

2010 ◽  
Vol 23 (10) ◽  
pp. 1316-1323 ◽  
Author(s):  
Asita Chatterjee ◽  
Yaya Cui ◽  
Pranjib Chakrabarty ◽  
Arun K. Chatterjee
Keyword(s):  
Quorum Sensing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Erwinia Carotovora ◽  
Translational Repression ◽  
Global Regulator ◽  
Acylhomoserine Lactone ◽  
Σ Factor ◽  
Regulatory Effects

Erwinia carotovora subsp. carotovora causes soft-rotting (tissue-macerating) disease in many plants and plant organs. Although pectinases are the primary determinants of virulence, several ancillary factors that augment bacterial virulence have also been identified. One such factor is bacterial motility. Flagellum formation and bacterial movement are regulated in many enterobacteria, including E. carotovora subsp. carotovora, by FlhDC, the master regulator of flagellar genes and FliA, a flagellum-specific σ factor. We document here that motility of E. carotovora subsp. carotovora is positively regulated by the quorum-sensing signal, N-acylhomoserine lactone (AHL), and negatively regulated by RsmA, a post-transcriptional regulator. RsmA, an RNA-binding protein, causes translational repression and promotes RNA decay. Our data show that RsmA negatively regulates flhDC and fliA expression. Moreover, the chemical stabilities of transcripts of these genes are greater in an RsmA– mutant than in RsmA+ bacteria. These observations contrast with positive regulation of flhDC and motility by CsrA (= RsmA) in Escherichia coli. In the absence of AHL, the AHL receptors ExpR1/ExpR2 (= AhlR) in Erwinia carotovora subsp. carotovora negatively regulate motility and expression of flhDC and fliA by activating RsmA production. In the presence of AHL, regulatory effects of ExpR1/ExpR2 are neutralized, resulting in reduced levels of rsmA expression and enhanced motility.

scholarly journals Multiple Mechanisms Inactivate the LIN-41 RNA-Binding Protein to Ensure A Robust Oocyte-to-Embryo Transition in Caenorhabditis elegans

2018 ◽  
Author(s):  
Caroline A. Spike ◽  
Gabriela Huelgas-Morales ◽  
Tatsuya Tsukamoto ◽  
David Greenstein
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Adaptor Protein ◽  
Protein Translation ◽  
Translational Repression ◽  
Meiotic Maturation ◽  
Oocyte Growth ◽  
Translational Repressor

ABSTRACTIn the nematode Caenorhabditis elegans, the conserved LIN-41 RNA-binding protein is a translational repressor that coordinately controls oocyte growth and meiotic maturation. LIN-41 exerts these effects, at least in part, by preventing the premature activation of the cyclin-dependent kinase CDK-1. Here we investigate the mechanism by which LIN-41 is rapidly eliminated upon the onset of meiotic maturation. Elimination of LIN-41 requires the activities of CDK-1 and multiple SCF-type ubiquitin ligase subunits, including the conserved substrate adaptor protein SEL-10/Fbw7/Cdc4, suggesting that LIN-41 is a target of ubiquitin-mediated protein degradation. Within the LIN-41 protein, two non-overlapping regions, Deg-A and Deg-B, are individually necessary for LIN-41 degradation; both contain several potential phosphodegron sequences, and at least one of these sites is required for LIN-41 degradation. Finally, Deg-A and Deg-B are sufficient, in combination, to mediate SEL-10-dependent degradation when transplanted into a different oocyte protein. Although LIN-41 is a potent inhibitor of protein translation and M-phase entry, the failure to eliminate LIN-41 from early embryos does not result in the continued translational repression of LIN-41 oocyte mRNA targets. Based on these observations, we propose a molecular model for the elimination of LIN-41 by SCFSEL-10 and suggest that LIN-41 is inactivated before it is degraded. Furthermore, we provide evidence that another RNA-binding protein, the GLD-1 tumor suppressor, is regulated similarly. Redundant mechanisms to extinguish translational repression by RNA-binding proteins may both control and provide robustness to irreversible developmental transitions, including meiotic maturation and the oocyte-to-embryo transition.

FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline

Development ◽  
2000 ◽  
Vol 127 (24) ◽  
pp. 5265-5276 ◽  
Author(s):  
R. Clifford ◽  
M.H. Lee ◽  
S. Nayak ◽  
M. Ohmachi ◽  
F. Giorgini ◽  
...  
Keyword(s):  
Sex Determination ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Translational Repression ◽  
Specific Substrate ◽  
Interaction Domain ◽  
C Elegans ◽  
Male Sex ◽  
F Box Protein

Male sex determination in the Caenorhabditis elegans hermaphrodite germline requires translational repression of tra-2 mRNA by the GLD-1 RNA binding protein. We cloned fog-2 by finding that its gene product physically interacts with GLD-1, forming a FOG-2/GLD-1/tra-2 3′untranslated region ternary complex. FOG-2 has an N-terminal F-box and a novel C-terminal domain called FTH. Canonical F-box proteins act as bridging components of the SCF ubiquitin ligase complex; the N-terminal F-box binds a Skp1 homolog, recruiting ubiquination machinery, while a C-terminal protein-protein interaction domain binds a specific substrate for degradation. However, since both fog-2 and gld-1 are necessary for spermatogenesis, FOG-2 cannot target GLD-1 for ubiquitin-mediated degradation. We propose that FOG-2 also acts as a bridge, bringing GLD-1 bound to tra-2 mRNA into a multiprotein translational repression complex, thus representing a novel function for an F-box protein. fog-2 is a member of a large, apparently rapidly evolving, C. elegans gene family that has expanded, in part, by local duplications; fog-2 related genes have not been found outside nematodes. fog-2 may have arisen during evolution of self-fertile hermaphroditism from an ancestral female/male species.

scholarly journals Spnr, a murine RNA-binding protein that is localized to cytoplasmic microtubules.

1995 ◽  
Vol 129 (4) ◽  
pp. 1023-1032 ◽  
Author(s):  
J M Schumacher ◽  
K Lee ◽  
S Edelhoff ◽  
R E Braun
Keyword(s):  
Translational Control ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Translational Repression ◽  
Rna Transport ◽  
Binding Domains ◽  
Cytoplasmic Microtubules ◽  
Pachytene Spermatocytes ◽  
Expression Libraries

Previous studies in transgenic mice have established the importance of the 3' untranslated region (UTR) of the spermatid-specific protamine-1 (Prm-1) mRNA in its translational control during male germ cell development. To clone genes that mediate the translational repression or activation of the Prm-1 mRNA, we screened cDNA expression libraries made with RNA from pachytene spermatocytes and round spermatids, with an RNA probe corresponding to the 3' UTR of Prm-1. We obtained six independent clones that encode Spnr, a spermatid perinuclear RNA-binding protein. Spnr is a 71-kD protein that contains two previously described RNA binding domains. The Spnr mRNA is expressed at high levels in the testis, ovary, and brain, and is present in multiple forms in those tissues. Immunolocalization of the Spnr protein within the testis shows that it is expressed exclusively in postmeiotic germ cells and that it is localized to the manchette, a spermatid-specific microtubular array. Although the Spnr protein is expressed too late to be directly involved in the translational repression of Prm-1 specifically, we suggest that the Spnr protein may be involved in other aspects of spermatid RNA metabolism, such as RNA transport or translational activation.

scholarly journals Translational repression by an RNA-binding protein promotes differentiation to infective forms in Trypanosoma cruzi

2018 ◽  
Vol 14 (6) ◽  
pp. e1007059 ◽  
Author(s):  
Maria Albertina Romaniuk ◽  
Alberto Carlos Frasch ◽  
Alejandro Cassola
Keyword(s):  
Trypanosoma Cruzi ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Translational Repression

scholarly journals Bovine Coronavirus Nonstructural Protein 1 (p28) Is an RNA Binding Protein That Binds Terminal Genomic cis-Replication Elements

2009 ◽  
Vol 83 (12) ◽  
pp. 6087-6097 ◽  
Author(s):  
Kortney M. Gustin ◽  
Bo-Jhih Guan ◽  
Agnieszka Dziduszko ◽  
David A. Brian
Keyword(s):  
Rna Binding ◽  
Nonstructural Protein ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Coding Region ◽  
Bovine Coronavirus ◽  
Stem Loop ◽  
Nonstructural Protein 1 ◽  
Gel Shift ◽  
Rna Levels

ABSTRACT Nonstructural protein 1 (nsp1), a 28-kDa protein in the bovine coronavirus (BCoV) and closely related mouse hepatitis coronavirus, is the first protein cleaved from the open reading frame 1 (ORF 1) polyprotein product of genome translation. Recently, a 30-nucleotide (nt) cis-replication stem-loop VI (SLVI) has been mapped at nt 101 to 130 within a 288-nt 5′-terminal segment of the 738-nt nsp1 cistron in a BCoV defective interfering (DI) RNA. Since a similar nsp1 coding region appears in all characterized groups 1 and 2 coronavirus DI RNAs and must be translated in cis for BCoV DI RNA replication, we hypothesized that nsp1 might regulate ORF 1 expression by binding this intra-nsp1 cistronic element. Here, we (i) establish by mutation analysis that the 72-nt intracistronic SLV immediately upstream of SLVI is also a DI RNA cis-replication signal, (ii) show by gel shift and UV-cross-linking analyses that cellular proteins of ∼60 and 100 kDa, but not viral proteins, bind SLV and SLVI, (SLV-VI) and (iii) demonstrate by gel shift analysis that nsp1 purified from Escherichia coli does not bind SLV-VI but does bind three 5′ untranslated region (UTR)- and one 3′ UTR-located cis-replication SLs. Notably, nsp1 specifically binds SLIII and its flanking sequences in the 5′ UTR with ∼2.5 μM affinity. Additionally, under conditions enabling expression of nsp1 from DI RNA-encoded subgenomic mRNA, DI RNA levels were greatly reduced, but there was only a slight transient reduction in viral RNA levels. These results together indicate that nsp1 is an RNA-binding protein that may function to regulate viral genome translation or replication but not by binding SLV-VI within its own coding region.

scholarly journals The Protease Lon and the RNA-Binding Protein Hfq Reduce Silencing of the Escherichia coli bgl Operon by H-NS

2004 ◽  
Vol 186 (9) ◽  
pp. 2708-2716 ◽  
Author(s):  
Sudhanshu Dole ◽  
Yvonne Klingen ◽  
V. Nagarajavel ◽  
Karin Schnetz
Keyword(s):  
Escherichia Coli ◽  
Transcription Initiation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Specific Effect ◽  
Receptor Protein ◽  
Coding Region ◽  
Genes Encoding ◽  
Pleiotropic Regulators

ABSTRACT The histone-like nucleoid structuring protein H-NS represses the Escherichia coli bgl operon at two levels. H-NS binds upstream of the promoter, represses transcription initiation, and binds downstream within the coding region of the first gene, where it induces polarity of transcription elongation. In hns mutants, silencing of the bgl operon is completely relieved. Various screens for mutants in which silencing of bgl is reduced have yielded mutations in hns and in genes encoding the transcription factors LeuO and BglJ. In order to identify additional factors that regulate bgl, we performed a transposon mutagenesis screen for mutants in which silencing of the operon is strengthened. This screen yielded mutants with mutations in cyaA, hfq, lon, and pgi, encoding adenylate cyclase, RNA-binding protein Hfq, protease Lon, and phosphoglucose isomerase, respectively. In cyaA mutants, the cyclic AMP receptor protein-dependent promoter is presumably inactive. The specific effect of the pgi mutants on bgl is low. Interestingly, in the hfq and lon mutants, the downstream silencing of bgl by H-NS (i.e., the induction of polarity) is more efficient, while the silencing of the promoter by H-NS is unaffected. Furthermore, in an hns mutant, Hfq has no significant effect and the effect of Lon is reduced. These data provide evidence that the specific repression by H-NS can (directly or indirectly) be modulated and controlled by other pleiotropic regulators.

scholarly journals Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP

2008 ◽  
Vol 181 (4) ◽  
pp. 639-653 ◽  
Author(s):  
Hironori Kawahara ◽  
Takao Imai ◽  
Hiroaki Imataka ◽  
Masafumi Tsujimoto ◽  
Ken Matsumoto ◽  
...  
Keyword(s):  
Stem Cells ◽  
Neural Stem Cells ◽  
Translation Initiation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Stress Granules ◽  
Translational Repression ◽  
Rna Recognition Motifs ◽  
Recognition Motifs

Musashi1 (Msi1) is an RNA-binding protein that is highly expressed in neural stem cells. We previously reported that Msi1 contributes to the maintenance of the immature state and self-renewal activity of neural stem cells through translational repression of m-Numb. However, its translation repression mechanism has remained unclear. Here, we identify poly(A) binding protein (PABP) as an Msi1-binding protein, and find Msi1 competes with eIF4G for PABP binding. This competition inhibits translation initiation of Msi1's target mRNA. Indeed, deletion of the PABP-interacting domain in Msi1 abolishes its function. We demonstrate that Msi1 inhibits the assembly of the 80S, but not the 48S, ribosome complex. Consistent with these conclusions, Msi1 colocalizes with PABP and is recruited into stress granules, which contain the stalled preinitiation complex. However, Msi1 with mutations in two RNA recognition motifs fails to accumulate into stress granules. These results provide insight into the mechanism by which sequence-specific translational repression occurs in stem cells through the control of translation initiation.

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