The RNA chaperone protein CspA stimulates translation during cold acclimation by promoting the progression of the ribosomes

CspA is an RNA binding protein expressed during cold-shock in Escherichia coli, capable of stimulating translation of several mRNAs - including its own - at low temperature. We used reconstituted translation systems to monitor the effects of CspA on the different steps of the translation process and probing experiments to analyze the interactions with its target mRNAs. We specifically focused on cspA mRNA which adopts a cold-induced secondary structure at temperatures below 20°C and a more closed conformation at 37°C. We show that at low temperature CspA specifically promotes the translation of the mRNA folded in the conformation less accessible to the ribosome (37°C form). CspA interacts with its mRNA without inducing large structural rearrangement, does not bind the ribosomal subunits and is not able to stimulate the formation of the translation initiation complexes. On the other hand, CspA promotes the progression of the ribosomes during translation of its mRNA at low temperature and this stimulation is mRNA structure-dependent. A similar structure-dependent mechanism may be responsible for the CspA-dependent translation stimulation observed with other probed mRNAs, for which the transition to the elongation phase is progressively facilitated during cold acclimation with the accumulation of CspA.

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Dissecting the Roles of Cuticular Wax in Plant Resistance to Shoot Dehydration and Low-Temperature Stress in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22041554 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1554

Author(s):

Tawhidur Rahman ◽

Mingxuan Shao ◽

Shankar Pahari ◽

Prakash Venglat ◽

Raju Soolanayakanahally ◽

...

Keyword(s):

Fatty Acids ◽

Low Temperature ◽

Cold Acclimation ◽

Water Loss ◽

Cuticular Wax ◽

Dehydration Stress ◽

Wax Deposition ◽

Cuticular Waxes ◽

Gas Chromatography Mass Spectroscopy

Cuticular waxes are a mixture of hydrophobic very-long-chain fatty acids and their derivatives accumulated in the plant cuticle. Most studies define the role of cuticular wax largely based on reducing nonstomatal water loss. The present study investigated the role of cuticular wax in reducing both low-temperature and dehydration stress in plants using Arabidopsis thaliana mutants and transgenic genotypes altered in the formation of cuticular wax. cer3-6, a known Arabidopsis wax-deficient mutant (with distinct reduction in aldehydes, n-alkanes, secondary n-alcohols, and ketones compared to wild type (WT)), was most sensitive to water loss, while dewax, a known wax overproducer (greater alkanes and ketones compared to WT), was more resistant to dehydration compared to WT. Furthermore, cold-acclimated cer3-6 froze at warmer temperatures, while cold-acclimated dewax displayed freezing exotherms at colder temperatures compared to WT. Gas Chromatography-Mass Spectroscopy (GC-MS) analysis identified a characteristic decrease in the accumulation of certain waxes (e.g., alkanes, alcohols) in Arabidopsis cuticles under cold acclimation, which was additionally reduced in cer3-6. Conversely, the dewax mutant showed a greater ability to accumulate waxes under cold acclimation. Fourier Transform Infrared Spectroscopy (FTIR) also supported observations in cuticular wax deposition under cold acclimation. Our data indicate cuticular alkane waxes along with alcohols and fatty acids can facilitate avoidance of both ice formation and leaf water loss under dehydration stress and are promising genetic targets of interest.

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RNA Binding Proteins Control Transdifferentiation of Hepatic Stellate Cells into Myofibroblasts

Cellular Physiology and Biochemistry ◽

10.1159/000491987 ◽

2018 ◽

Vol 48 (3) ◽

pp. 1215-1229 ◽

Cited By ~ 5

Author(s):

Sihyung Wang ◽

Youngmi Jung ◽

Jeongeun Hyun ◽

Matthew Friedersdorf ◽

Seh-Hoon Oh ◽

...

Keyword(s):

Hepatic Stellate Cells ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Stellate Cells ◽

Fibrous Matrix ◽

Rna Immunoprecipitation ◽

Physical Interactions ◽

Β Receptor ◽

Dependent Mechanism

Background/Aims: Myofibroblasts (MF) derived from quiescent nonfibrogenic hepatic stellate cells (HSC) are the major sources of fibrous matrix in cirrhosis. Because many factors interact to regulate expansion and regression of MF-HSC populations, efforts to prevent cirrhosis by targeting any one factor have had limited success, motivating research to identify mechanisms that integrate these diverse inputs. As key components of RNA regulons, RNA binding proteins (RBPs) may fulfill this function by orchestrating changes in the expression of multiple genes that must be coordinately regulated to affect the complex phenotypic modifications required for HSC transdifferentiation. Methods: We profiled the transcriptomes of quiescent and MF-HSC to identify RBPs that were differentially-expressed during HSC transdifferentiation, manipulated the expression of the most significantly induced RBP, insulin like growth factor 2 binding protein 3 (Igf2bp3), and evaluated transcriptomic and phenotypic effects. Results: Depleting Igf2bp3 changed the expression of thousands of HSC genes, including multiple targets of TGF-β signaling, and caused HSCs to reacquire a less proliferative, less myofibroblastic phenotype. RNA immunoprecipitation assays demonstrated that some of these effects were mediated by direct physical interactions between Igf2bp3 and mRNAs that control proliferative activity and mesenchymal traits. Inhibiting TGF-β receptor-1 signaling revealed a microRNA-dependent mechanism that induces Igf2bp3. Conclusions: The aggregate results indicate that HSC transdifferentiation is ultimately dictated by Igf2bp3-dependent RNA regulons and thus, can be controlled simply by manipulating Igf2bp3.

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A Calcium-Dependent Mechanism Responsible for Increasing the Freezing Tolerance of the Bivalve Mollusc Modiolus Demissus

Journal of Experimental Biology ◽

10.1242/jeb.69.1.13 ◽

1977 ◽

Vol 69 (1) ◽

pp. 13-21

Author(s):

DENNIS J. MURPHY

Keyword(s):

Low Temperature ◽

Freezing Tolerance ◽

Time Course ◽

Cell Membranes ◽

Contractile Response ◽

Temperature Acclimation ◽

Freezing Injury ◽

Total Change ◽

Calcium Dependent ◽

Dependent Mechanism

1. A time course of the changes in blood Ca2+ and freezing tolerance of Modiolus demissus (Dillwyn) demonstrated that increases in freezing tolerance parallel increases in blood Ca2+. The increases in freezing tolerance occurred rapidly, suggesting that Ca2+ affects freezing tolerance directly by its presence in the blood. 2. The presence of La3+ reduced the freezing tolerance of isolated foot muscle. Thus, Ca2+ appears to increase freezing tolerance directly by binding to cell membranes. 3. The loss of the contractile response of freeze-thawed foot muscle to Ach, KCl and caffeine and the continued response to CaCl2 suggested that cell membranes are the primary sites of freezing injury. 4. The increase in blood Ca2+ following low-temperature acclimation accounted for only 40% of the total change in freezing tolerance. Therefore, other mechanisms responsible for increasing the freezing tolerance of M. demissus following low temperature acclimation also exist.

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Metabolic and Tissue Solute Changes Associated With Changes in the Freezing Tolerance of the Bivalve Mollusc Modiolus Demissus

Journal of Experimental Biology ◽

10.1242/jeb.69.1.1 ◽

1977 ◽

Vol 69 (1) ◽

pp. 1-12

Author(s):

DENNIS J. MURPHY

Keyword(s):

Oxygen Consumption ◽

Low Temperature ◽

Freezing Tolerance ◽

Anaerobic Metabolism ◽

Arrhenius Plot ◽

Physiological Mechanism ◽

Temperature Acclimation ◽

Anaerobic Conditions ◽

Rate Of Oxygen Consumption ◽

Dependent Mechanism

1. A physiological mechanism responsible for increasing the freezing tolerance of the bivalve Modiolus demissus (Dillwyn) following low-temperature acclimation was demonstrated. 2. The rates of oxygen consumption of M. demissus acclimated to temperatures between 0 and 24 °C were presented as an Arrhenius plot. A change in slope occurred at 10 °C, suggesting that temperature alone was not responsible for the increased decline in the rate of oxygen consumption below 10 °C. 3. Low-temperature acclimation had no effect on blood Na+ or K+ concentrations but did reduce the concentration of blood Mg2+ and, in addition, resulted in the accumulation of end-products characteristic of anaerobic metabolism - tissue alanine and proline, and blood Ca2+. Furthermore, maintenance of M. demissus under anaerobic conditions increased freezing tolerance. 4. Taken together, these data indicate that the increased freezing tolerance of M. demissus acclimated to low temperatures involves a conversion to anaerobic metabolism. 5. The increase in blood Ca2+ following low-temperature acclimation was associated with the increased freezing tolerance. Finally, Mg2+ simulated the effect of Ca2+ on freezing tolerance, but was only 20% as effective. 6. These results suggest that a Ca2+-dependent mechanism responsible for increasing the freezing tolerance of M. demissus exists, and that the increase in blood Ca2+ is due to a conversion to anaerobic metabolism.

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Low Temperature Induced Biochemical Mechanisms: Implications for Cold Acclimation and De-Acclimation

Interacting Stresses on Plants in a Changing Climate ◽

10.1007/978-3-642-78533-7_42 ◽

1993 ◽

pp. 647-657 ◽

Cited By ~ 9

Author(s):

C. Stushnoff ◽

R. L. Remmele ◽

V. Essensee ◽

M. McNeil

Keyword(s):

Low Temperature ◽

Cold Acclimation ◽

Biochemical Mechanisms

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FUS-dependent loading of SUV39H1 to OCT4 pseudogene-lncRNA programs a silencing complex with OCT4 promoter specificity

Communications Biology ◽

10.1038/s42003-020-01355-9 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Michele Scarola ◽

Elisa Comisso ◽

Massimo Rosso ◽

Giannino Del Sal ◽

Claudio Schneider ◽

...

Keyword(s):

Rna Binding ◽

Biological Function ◽

Rna Binding Protein ◽

Evolutionary Conservation ◽

Epigenetic Silencing ◽

Site Specificity ◽

Sequence Element ◽

Regulatory Circuits ◽

Promoter Specificity ◽

Dependent Mechanism

Abstract The resurrection of pseudogenes during evolution produced lncRNAs with new biological function. Here we show that pseudogene-evolution created an Oct4 pseudogene lncRNA that is able to direct epigenetic silencing of the parental Oct4 gene via a 2-step, lncRNA dependent mechanism. The murine Oct4 pseudogene 4 (mOct4P4) lncRNA recruits the RNA binding protein FUS to allow the binding of the SUV39H1 HMTase to a defined mOct4P4 lncRNA sequence element. The mOct4P4-FUS-SUV39H1 silencing complex holds target site specificity for the parental Oct4 promoter and interference with individual components results in loss of Oct4 silencing. SUV39H1 and FUS do not bind parental Oct4 mRNA, confirming the acquisition of a new biological function by the mOct4P4 lncRNA. Importantly, all features of mOct4P4 function are recapitulated by the human hOCT4P3 pseudogene lncRNA, indicating evolutionary conservation. Our data highlight the biological relevance of rapidly evolving lncRNAs that infiltrate into central epigenetic regulatory circuits in vertebrate cells.

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Cold Acclimation Proteome Analysis Reveals Close Link between the Up-Regulation of Low-Temperature Associated Proteins and Vernalization Fulfillment

Journal of Proteome Research ◽

10.1021/pr100475r ◽

2010 ◽

Vol 9 (11) ◽

pp. 5658-5667 ◽

Cited By ~ 41

Author(s):

Elham Sarhadi ◽

Siroos Mahfoozi ◽

Seyed Abdollah Hosseini ◽

Ghasem Hosseini Salekdeh

Keyword(s):

Low Temperature ◽

Cold Acclimation ◽

Proteome Analysis ◽

Close Link ◽

Associated Proteins

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Association of Nonribosomal Nucleolar Proteins in Ribonucleoprotein Complexes during Interphase and Mitosis

Molecular Biology of the Cell ◽

10.1091/mbc.10.1.77 ◽

1999 ◽

Vol 10 (1) ◽

pp. 77-90 ◽

Cited By ~ 66

Author(s):

Serafı́n Piñol-Roma

Keyword(s):

Ribosomal Proteins ◽

Rna Binding ◽

Rrna Synthesis ◽

28S Rrna ◽

Ribosomal Subunits ◽

Interphase Cell ◽

Ribonucleoprotein Complexes ◽

Nucleolar Proteins ◽

M Phase ◽

Nucleolar Rna

rRNA precursors are bound throughout their length by specific proteins, as the pre-rRNAs emerge from the transcription machinery. The association of pre-rRNA with proteins as ribonucleoprotein (RNP) complexes persists during maturation of 18S, 5.8S, and 28S rRNA, and through assembly of ribosomal subunits in the nucleolus. Preribosomal RNP complexes contain, in addition to ribosomal proteins, an unknown number of nonribosomal nucleolar proteins, as well as small nucleolar RNA-ribonucleoproteins (sno-RNPs). This report describes the use of a specific, rapid, and mild immunopurification approach to isolate and analyze human RNP complexes that contain nonribosomal nucleolar proteins, as well as ribosomal proteins and rRNA. Complexes immunopurified with antibodies to nucleolin—a major nucleolar RNA-binding protein—contain several distinct specific polypeptides that include, in addition to nucleolin, the previously identified nucleolar proteins B23 and fibrillarin, proteins with electrophoretic mobilities characteristic of ribosomal proteins including ribosomal protein S6, and a number of additional unidentified proteins. The physical association of these proteins with one another is mediated largely by RNA, in that the complexes dissociate upon digestion with RNase. Complexes isolated from M-phase cells are similar in protein composition to those isolated from interphase cell nuclear extracts. Therefore, the predominant proteins that associate with nucleolin in interphase remain in RNP complexes during mitosis, despite the cessation of rRNA synthesis and processing in M-phase. In addition, precursor rRNA, as well as processed 18S and 28S rRNA and candidate rRNA processing intermediates, is found associated with the immunopurified complexes. The characteristics of the rRNP complexes described here, therefore, indicate that they represent bona fide precursors of mature cytoplasmic ribosomal subunits.

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A systems theory perspective on the translation process

Translation Cognition & Behavior ◽

10.1075/tcb.00026.car ◽

2019 ◽

Vol 2 (2) ◽

pp. 211-232

Author(s):

Michael Carl ◽

Andrew Tonge ◽

Isabel Lacruz

Keyword(s):

Systems Theory ◽

Dissipative Structures ◽

Source Text ◽

Translation Process ◽

Gaze Patterns ◽

Word Translation ◽

Time And Energy ◽

Translation Systems ◽

Internal Order

Abstract The translation process has often been described as a sequence of three steps, source text (ST) analysis, source-target transfer, and target text (TT) generation. We propose a radically different view, in which the human translation process consists of a hierarchy of interacting word and phrase translations systems which organize and integrate as dissipative structures. Activation of word (or phrase) translation systems is a non-selective subliminal process in the translator’s mind not restricted to one language. Depending on the entropy (i.e., the internal order) of the word translation systems, a human translator spends more or less time and energy during the translation process, which can be measured in the form of gaze patterns and production duration.

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