scholarly journals Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS

2017 ◽  
Author(s):  
Maksym Bobrovskyy ◽  
Jane K. Frandsen ◽  
Jichuan Zhang ◽  
Anustup Poddar ◽  
Muhammad S. Azam ◽  
...  
Keyword(s):  
Small Rna ◽  
Binding Sites ◽  
Sugar Transport ◽  
Enteric Bacteria ◽  
Sugar Uptake ◽  
Rna Chaperone ◽  
Target Mrnas ◽  
Mrna Targets ◽  
Molecular Features ◽  
Response To Stress

ABSTRACTThe mechanisms by which small RNA (sRNA) regulators select and prioritize target mRNAs remain poorly understood, but serve to promote efficient responses to environmental cues and stresses. We sought to uncover mechanisms that establish regulatory hierarchy for a model sRNA, SgrS, found in enteric bacteria and produced under conditions of metabolic stress when sugar transport and metabolism are unbalanced. SgrS post-transcriptionally controls a nine-gene regulon to restore growth and homeostasis under stress conditions. An in vivo reporter system was used to quantify SgrS-dependent regulation of target genes and established that SgrS exhibits a clear preference for certain targets, and regulates those targets efficiently even at low SgrS levels. Higher SgrS concentrations are required to regulate other targets. The position of targets in the regulatory hierarchy is not well-correlated with the predicted thermodynamic stability of SgrS-mRNA interactions or the SgrS-mRNA binding affinity as measured in vitro. Detailed analyses of SgrS interaction with asd mRNA demonstrate that SgrS binds cooperatively to two sites and remodels asd mRNA secondary structure. SgrS binding at both sites increases the efficiency of asd mRNA regulation compared to mutants that have only a single SgrS binding site. Our results suggest that sRNA selection of target mRNAs and regulatory hierarchy are influenced by several molecular features. The sRNA-mRNA interaction, including the number and position of sRNA binding sites on the mRNA and cofactors like the RNA chaperone Hfq, seem to tune the efficiency of regulation of specific mRNA targets.IMPORTANCETo survive, bacteria must respond rapidly to stress and simultaneously maintain metabolic homeostasis. The small RNA (sRNA) SgrS mediates the response to stress arising from imbalanced sugar transport and metabolism. To coordinate the stress response, SgrS regulates genes involved in sugar uptake and metabolism. Intrinsic properties of sRNAs such as SgrS allow them to regulate extensive networks of genes. To date, sRNA regulation of targets has largely been studied in the context of “one sRNA-one target”, and little is known about coordination of multi-gene regulons and sRNA regulatory network structure. Here, we explore the molecular basis for regulatory hierarchy in sRNA regulons. Our results reveal a complex interplay of factors that influence the outcome of sRNA regulation. The number and location of sRNA binding sites on mRNA targets and the participation of an RNA chaperone dictate prioritized regulation of targets to promote an efficient response to stress.

scholarly journals Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli

2021 ◽  
Vol 7 (4) ◽  
pp. 64
Author(s):  
David Lalaouna ◽  
Karine Prévost ◽  
Seongjin Park ◽  
Thierry Chénard ◽  
Marie-Pier Bouchard ◽  
...  
Keyword(s):  
Complex Formation ◽  
Super Resolution ◽  
Rnase E ◽  
Rna Chaperone ◽  
Target Mrnas ◽  
Mrna Targets ◽  
Super Resolution Microscopy

Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.

scholarly journals Novel mRNA Targets for Tristetraprolin (TTP) Identified by Global Analysis of Stabilized Transcripts in TTP-Deficient Fibroblasts

2006 ◽  
Vol 26 (24) ◽  
pp. 9196-9208 ◽  
Author(s):  
Wi S. Lai ◽  
Joel S. Parker ◽  
Sherry F. Grissom ◽  
Deborah J. Stumpo ◽  
Perry J. Blackshear
Keyword(s):  
Binding Sites ◽  
Zinc Finger Protein ◽  
Global Analysis ◽  
Fibroblast Cell ◽  
Decay Rates ◽  
Physiological Control ◽  
Necrosis Factor Alpha ◽  
Target Mrnas ◽  
Mrna Targets ◽  
Serum Stimulation

ABSTRACT Tristetraprolin (TTP) is a tandem CCCH zinc finger protein that was identified through its rapid induction by mitogens in fibroblasts. Studies of TTP-deficient mice and cells derived from them showed that TTP could bind to certain AU-rich elements in mRNAs, leading to increases in the rates of mRNA deadenylation and destruction. Known physiological target mRNAs for TTP include tumor necrosis factor alpha, granulocyte-macrophage colony-stimulating factor, and interleukin-2β. Here we used microarray analysis of RNA from wild-type and TTP-deficient fibroblast cell lines to identify transcripts with different decay rates, after serum stimulation and actinomycin D treatment. Of 250 mRNAs apparently stabilized in the absence of TTP, 23 contained two or more conserved TTP binding sites; nine of these appeared to be stabilized on Northern blots. The most dramatically affected transcript encoded the protein Ier3, recently implicated in the physiological control of blood pressure. The Ier3 transcript contained several conserved TTP binding sites that could bind TTP directly and conferred TTP sensitivity to the mRNA in cell transfection studies. These studies have identified several new, physiologically relevant TTP target transcripts in fibroblasts; these target mRNAs encode proteins from a variety of functional classes.

Opportunistic heterotrophy in gametophytes of the homosporous fern Ceratopteris richardii

Botany ◽  
2009 ◽  
Vol 87 (8) ◽  
pp. 799-806 ◽  
Author(s):  
Deborah A. Alongi ◽  
Jeffrey P. Hill ◽  
Matthew J. Germino
Keyword(s):  
Sugar Transport ◽  
Light Limitation ◽  
Sugar Uptake ◽  
Growth Media ◽  
Ceratopteris Richardii ◽  
Glucose Depletion ◽  
Homosporous Fern ◽  
Preferential Uptake ◽  
Underlying Mechanisms ◽  
Exogenous Sugar

Fern gametophytes are extremely shade-tolerant, potentially existing for long periods under conditions of extreme light limitation. Many previous studies have demonstrated an increase in gametophyte growth and incidence of spontaneous transition to sporophyte morphology (apogamy) under culture on media containing exogenous sugar. However, these studies did not verify sugar uptake or quantify relative growth on media containing different sugar types. Here, we examine the extent of heterotrophy and underlying mechanisms of sugar transport in photosynthetic gametophytes of the fern Ceratopteris richardii Brongn. Exogenous sugar uptake, growth, and sugar transport were evaluated with assays of exogenous glucose depletion, experimental culture of gametophytes under different sugar and light conditions, and bioinformatic approaches. The glucose from the growth media was significantly depleted by gametophytes growing under all conditions, especially those in the dark compared with those exposed to higher light. Gametophyte area increased similarly when cultured on equimolar concentrations of either glucose or the disaccharide sucrose, likely due to preferential uptake of one of the monomers of sucrose. Although at least one gene with similarity to sucrose transporters is expressed in germinating spores, our results suggest a reliance on monosaccharide transport for exogenous sugar uptake. Glucose assimilation in both light and dark conditions constitutes nutritional opportunism and may enhance gametophyte survival in very low light.

scholarly journals The Importance of the Small RNA Chaperone Hfq for Growth of Epidemic Yersinia pestis, but Not Yersinia pseudotuberculosis, with Implications for Plague Biology

2010 ◽  
Vol 192 (16) ◽  
pp. 4239-4245 ◽  
Author(s):  
Guangchun Bai ◽  
Andrey Golubov ◽  
Eric A. Smith ◽  
Kathleen A. McDonough
Keyword(s):  
Yersinia Pestis ◽  
Small Rna ◽  
Small Rnas ◽  
Yersinia Pseudotuberculosis ◽  
Etiologic Agent ◽  
Growth Restriction ◽  
Rna Chaperone ◽  
Unique Biology ◽  
Severe Growth

ABSTRACT Yersinia pestis, the etiologic agent of plague, has only recently evolved from Yersinia pseudotuberculosis. hfq deletion caused severe growth restriction at 37°C in Y. pestis but not in Y. pseudotuberculosis. Strains from all epidemic plague biovars were similarly affected, implicating Hfq, and likely small RNAs (sRNAs), in the unique biology of the plague bacillus.

scholarly journals Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association

2021 ◽  
Vol 22 (18) ◽  
pp. 9980
Author(s):  
Ganesh R. Koshre ◽  
Feba Shaji ◽  
Neeraja K. Mohanan ◽  
Nimmy Mohan ◽  
Jamshaid Ali ◽  
...  
Keyword(s):  
Rna Binding ◽  
Coding Region ◽  
High Association ◽  
Target Mrnas ◽  
Mrna Metabolism ◽  
Mrna Targets ◽  
Genome Wide ◽  
Global Profile ◽  
Specific Mrna

Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3′-UTR processing, we observed a high association of Star-PAP at the 3′-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3′-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.

The small RNA chaperone Hfq is a critical regulator for bacterial biosynthesis of selenium nanoparticles and motility in Rahnella aquatilis

2020 ◽  
Vol 104 (4) ◽  
pp. 1721-1735
Author(s):  
Qiaolin Xu ◽  
Yanzhao Song ◽  
Zhiqing Lin ◽  
Gary Bañuelos ◽  
Yanyun Zhu ◽  
...  
Keyword(s):  
Small Rna ◽  
Selenium Nanoparticles ◽  
Rna Chaperone ◽  
Rahnella Aquatilis

scholarly journals Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Cristine R. Casingal ◽  
Takako Kikkawa ◽  
Hitoshi Inada ◽  
Yukio Sasaki ◽  
Noriko Osumi
Keyword(s):  
Brain Development ◽  
Rna Binding ◽  
Fragile X ◽  
Autism Spectrum ◽  
Mtor Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Sequencing Analysis ◽  
Embryonic Brain ◽  
Target Mrnas ◽  
Mrna Targets

AbstractCorticogenesis is one of the most critical and complicated processes during embryonic brain development. Any slight impairment in corticogenesis could cause neurodevelopmental disorders such as Fragile X syndrome (FXS), of which symptoms contain intellectual disability (ID) and autism spectrum disorder (ASD). Fragile X mental retardation protein (FMRP), an RNA-binding protein responsible for FXS, shows strong expression in neural stem/precursor cells (NPCs) during corticogenesis, although its function during brain development remains largely unknown. In this study, we attempted to identify the FMRP target mRNAs in the cortical primordium using RNA immunoprecipitation sequencing analysis in the mouse embryonic brain. We identified 865 candidate genes as targets of FMRP involving 126 and 118 genes overlapped with ID and ASD-associated genes, respectively. These overlapped genes were enriched with those related to chromatin/chromosome organization and histone modifications, suggesting the involvement of FMRP in epigenetic regulation. We further identified a common set of 17 FMRP “core” target genes involved in neurogenesis/FXS/ID/ASD, containing factors associated with Ras/mitogen-activated protein kinase, Wnt/β-catenin, and mammalian target of rapamycin (mTOR) pathways. We indeed showed overactivation of mTOR signaling via an increase in mTOR phosphorylation in the Fmr1 knockout (Fmr1 KO) neocortex. Our results provide further insight into the critical roles of FMRP in the developing brain, where dysfunction of FMRP may influence the regulation of its mRNA targets affecting signaling pathways and epigenetic modifications.

scholarly journals Endogenous Retroviruses Walk a Fine Line between Priming and Silencing

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 792 ◽  
Author(s):  
Harrison Cullen ◽  
Andrea J. Schorn
Keyword(s):  
Small Rna ◽  
Binding Sites ◽  
Small Rnas ◽  
Genome Stability ◽  
Sequence Variation ◽  
Endogenous Retroviruses ◽  
Highly Active ◽  
Trna Primer ◽  
Ltr Retroelements ◽  
Transcription And Replication

Endogenous retroviruses (ERVs) in mammals are closely related to infectious retroviruses and utilize host tRNAs as a primer for reverse transcription and replication, a hallmark of long terminal repeat (LTR) retroelements. Their dependency on tRNA makes these elements vulnerable to targeting by small RNAs derived from the 3′-end of mature tRNAs (3′-tRFs), which are highly expressed during epigenetic reprogramming and potentially protect many tissues in eukaryotes. Here, we review some key functions of ERV reprogramming during mouse and human development and discuss how small RNA-mediated silencing maintains genome stability when ERVs are temporarily released from heterochromatin repression. In particular, we take a closer look at the tRNA primer binding sites (PBS) of two highly active ERV families in mice and their sequence variation that is shaped by the conflict of successful tRNA priming for replication versus evasion of silencing by 3′-tRFs.

scholarly journals Model-assisted analysis of the peach pedicel–fruit system suggests regulation of sugar uptake and a water-saving strategy

2020 ◽  
Vol 71 (12) ◽  
pp. 3463-3474
Author(s):  
Dario Constantinescu ◽  
Gilles Vercambre ◽  
Michel Génard
Keyword(s):  
Sugar Transport ◽  
Water Saving ◽  
Lower Pressure ◽  
Sugar Concentration ◽  
Sugar Uptake ◽  
Pressure Potential ◽  
High Sugar Concentration ◽  
High Sugar ◽  
Diurnal Patterns ◽  
Assisted Analysis

Abstract We develop a model based on the biophysical representation of water and sugar flows between the pedicel, fruit xylem and phloem, and the fruit apoplast and symplast in order to identify diurnal patterns of transport in the pedicel–fruit system of peach. The model predicts that during the night water is mainly imported to the fruit through the xylem, and that fruit phloem–xylem transfer of water allows sugar concentrations in the phloem to be higher in the fruit than in the pedicel. This results in relatively high sugar transport to the fruit apoplast, leading to relatively high sugar uptake by the fruit symplast despite low sugar concentrations in the pedicel. At midday, the model predicts a xylem backflow of water driven by a lower pressure potential in the xylem than in the fruit apoplast. In addition, fruit xylem-to-phloem transfer of water decreases the fruit phloem sugar concentration, resulting in moderate sugar uptake by the fruit symplast, despite the high sugar concentration in the pedicel. Globally, the predicted fruit xylem–phloem water transfers buffer the sugar concentrations in the fruit phloem and apoplast, leading to a diurnally regulated uptake of sugar. A possible fruit xylem-to-apoplast recirculation of water through the fruit phloem reduces water lost by xylem backflow at midday.

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