Interactions of the RNA-Binding Protein Hfq with cspA mRNA, Encoding the Major Cold Shock Protein

ABSTRACT CspA, a small protein that is highly induced by cold shock, is encoded by a monocistronic mRNA of 428 nucleotides (nt) whose half-life and abundance are greatly increased following cold shock. We show here that in vitro cspA mRNA can bind multiple copies of Hfq, a hexameric Sm-like protein which promotes a variety of RNA-RNA interactions. Binding of the first Hfq hexamer occurs with an apparent Kd (dissociation constant) of <40 nM; up to seven additional hexamers can bind sequentially at higher concentrations. Known ligands of Hfq, including the small regulatory RNA, RyhB, compete with cspA mRNA. Several experiments suggest that the first binding site to be occupied by Hfq is located at or near the 3′ end of cspA mRNA. The consequences of limited Hfq binding in vitro include nearly total inhibition of RNase E cleavage at a site ∼35 nt from the 3′ end of the mRNA, stimulation of polyadenylation by poly(A) polymerase 1, and subsequent exonucleolytic degradation by polynucleotide phosphorylase. We propose that Hfq may play a facilitating role in the metabolism of cspA mRNA.

Download Full-text

A Temperature-Independent Cold-Shock Protein Homolog Acts as a Virulence Factor in Xylella fastidiosa

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-11-15-0260-r ◽

2016 ◽

Vol 29 (5) ◽

pp. 335-344 ◽

Cited By ~ 11

Author(s):

Lindsey P. Burbank ◽

Drake C. Stenger

Keyword(s):

Deletion Mutant ◽

Cold Shock ◽

Rna Binding ◽

Xylella Fastidiosa ◽

Cold Shock Protein ◽

Plant Colonization ◽

Wild Type ◽

Cold Temperatures ◽

Mrna Stabilization

Xylella fastidiosa, causal agent of Pierce’s disease (PD) of grapevine, is a fastidious organism that requires very specific conditions for replication and plant colonization. Cold temperatures reduce growth and survival of X. fastidiosa both in vitro and in planta. However, little is known regarding physiological responses of X. fastidiosa to temperature changes. Cold-shock proteins (CSP), a family of nucleic acid–binding proteins, act as chaperones facilitating translation at low temperatures. Bacterial genomes often encode multiple CSP, some of which are strongly induced following exposure to cold. Additionally, CSP contribute to the general stress response through mRNA stabilization and posttranscriptional regulation. A putative CSP homolog (Csp1) with RNA-binding activity was identified in X. fastidiosa Stag’s Leap. The csp1 gene lacked the long 5′ untranslated region characteristic of cold-inducible genes and was expressed in a temperature-independent manner. As compared with the wild type, a deletion mutant of csp1 (∆csp1) had decreased survival rates following cold exposure and salt stress in vitro. The deletion mutant also was significantly less virulent in grapevine, as compared with the wild type, in the absence of cold stress. These results suggest an important function of X. fastidiosa Csp1 in response to cellular stress and during plant colonization.

Download Full-text

A cold shock protein promotes high-temperature microbial growth through binding to diverse RNA species

Cell Discovery ◽

10.1038/s41421-021-00246-5 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Zikang Zhou ◽

Hongzhi Tang ◽

Weiwei Wang ◽

Lige Zhang ◽

Fei Su ◽

...

Keyword(s):

High Temperature ◽

Cold Shock ◽

Rna Binding ◽

Cold Shock Protein ◽

Mrna Accumulation ◽

Temperature Resistance ◽

High Temperature Resistance ◽

Biomass Increase

AbstractEndowing mesophilic microorganisms with high-temperature resistance is highly desirable for industrial microbial fermentation. Here, we report a cold-shock protein (CspL) that is an RNA chaperone protein from a lactate producing thermophile strain (Bacillus coagulans 2–6), which is able to recombinantly confer strong high-temperature resistance to other microorganisms. Transgenic cspL expression massively enhanced high-temperature growth of Escherichia coli (a 2.4-fold biomass increase at 45 °C) and eukaryote Saccharomyces cerevisiae (a 2.6-fold biomass increase at 36 °C). Importantly, we also found that CspL promotes growth rates at normal temperatures. Mechanistically, bio-layer interferometry characterized CspL’s nucleotide-binding functions in vitro, while in vivo we used RNA-Seq and RIP-Seq to reveal CspL’s global effects on mRNA accumulation and CspL’s direct RNA binding targets, respectively. Thus, beyond establishing how a cold-shock protein chaperone provides high-temperature resistance, our study introduces a strategy that may facilitate industrial thermal fermentation.

Download Full-text

The Cold-Shock Protein Ybx1 Is Required for Development and Maintenance of Acute Myeloid Leukemia (AML) in Vitro and In Vivo

Blood ◽

10.1182/blood.v130.suppl_1.792.792 ◽

2017 ◽

Vol 130 (Suppl_1) ◽

pp. 792-792

Author(s):

Florian Perner ◽

Ashok K. Jayavelu ◽

Tina Maria Schnoeder ◽

Nomusa Mashamba ◽

Juliane Mohr ◽

...

Keyword(s):

Mouse Model ◽

Protein Expression ◽

Malignant Transformation ◽

Cell Lines ◽

Median Survival ◽

Cold Shock ◽

Rna Binding ◽

Cold Shock Protein ◽

Significant Delay

Abstract The family of cold shock proteins (CSPs) is highly conserved and consists of 8 members, including Ybx1-3, Csde1 and Lin28. Ybx1 is a multifunctional DNA/RNA binding protein that modulates gene transcription and translation during inflammation and malignant transformation. Recently, our group identified Ybx1 as a mediator of Jak2 signaling in MPN that protects Jak2-mutated cells from Jak-inhibitor induced apoptosis. In a recently published genome wide CRISPR-Cas9 dropout screen in AML cell lines, depletion of Ybx1 resulted in the highest dropout indices compared to other CSP members, with strongest dependencies in cell lines harboring MLL-rearrangements. Protein expression of Ybx1 in healthy individuals (n=10), primary MDS (n=54) and AML (n=58) bone marrow (BM) biopsies, revealed high protein expression in the majority of AML and MDS cases. Consistently, gene expression data revealed high mRNA expression of Ybx1 in AML samples compared to normal controls. Genetic inactivation of Ybx1 in human AML cell lines by RNAi resulted in reduced proliferative capacity. Therefore, we sought to investigate the requirement for Ybx1 in malignant transformation. We used BM cells from a previously published conventional knockout (ko) mouse model (Lu et al., 2005) in which homozygous deletion is embryonically lethal due to brain malformation. We sorted Lineage-Sca1+Kit+ (LSK-) cells from the BM of heterozygous (Ybx1+/-) and wildtype (Ybx1+/+) mice. Cells were retrovirally infected with either MLL-AF9 (MA9) or HoxA9 and Meis1a (HA9M1) to assess for disease development by serial plating in methylcellulose. Haploinsufficiency for Ybx1 in MA9- or HA9M1 transformed cells limited re-plating capacity to 2-4 rounds. When we injected 2,5x 104 MA9-infected LSK cells into sublethally irradiated recipient mice, recipients of MA9-Ybx1+/- cells (n=8) and MA9-Ybx1+/+ (n=10) showed development of AML. However, recipients of MA9-Ybx1+/- cells had a significant delay in AML development (median survival 67.5 days for Ybx1+/+ versus 101.5 days for Ybx1+/- animals, p=0.0078**). This effect appeared even more pronounced when 1x 106 whole BM cells were transplanted into sublethally irradiated secondary recipients. Besides a significant delay in AML development (median survival 37.5 days for recipients of MA9-Ybx1+/+ versus 79 days for MA9-Ybx1+/- BM, p=0.0042**), disease penetrance was reduced by 40%, indicating that haploinsufficiency for Ybx1 impairs development of MA9 driven AML. In contrast, immunophenotypic abundance of stem- and progenitor cells in Ybx1+/+ versus Ybx1+/- animals revealed comparable numbers in all relevant subpopulations. Serial competitive transplantation of Ybx1+/+ and Ybx1+/- BM into primary and secondary recipient animals showed no competitive disadvantage or lack of self-renewal capacity of Ybx1+/- cells. To address the question whether Ybx1 may also be essential for maintenance of AML, we used RNAi to deplete Ybx1 in already established MA9 driven AML. LSK cells from BL/6 mice transformed with MA9 were injected into primary recipient mice. After AML onset, MA9-LSK cells were sorted and infected with either one of 3 shRNAs against Ybx1 or non-targeting (NT-) control. Lentiviral knockdown of 40% reduced colony formation by more than 50% but did not limit the re-plating capacity in vitro. When injected into sub-lethally irradiated recipient mice, lentiviral knockdown (kd) of Ybx1 resulted in a significant delay in AML development (median survival 39.5 days for NT-control versus 53 days for Ybx1 kd, p=0.0446*). To validate our findings, we used a newly generated conditional ko mouse model for Ybx1, in which exon 3 coding for the cold-shock domain is deleted by activation of an Mx1-Cre-recombinase following pIpC administration. Preliminary results provide first evidence that genetic deletion of Ybx1 after onset of MA9 driven leukemia resulted in improved survival of primary recipient (median survival 73 versus 83 days) and a reduced penetrance in secondary recipient mice. Taken together our results may provide first evidence for a functional role of Ybx1 in MLL-AF9 driven AML. As Ybx1 seems to be dispensable for normal hematopoietic cells, these findings may offer a potential therapeutic index. Experiments to assess for the requirement for Ybx1 in maintenance of murine and human AML as well as analysis on proteomic and transcriptional changes following Ybx1 deletion are currently under way. Disclosures No relevant conflicts of interest to declare.

Download Full-text

Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system

The EMBO Journal ◽

10.1093/emboj/20.5.1144 ◽

2001 ◽

Vol 20 (5) ◽

pp. 1144-1152 ◽

Cited By ~ 109

Author(s):

T. Hirose

Keyword(s):

Rna Editing ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Site Specific ◽

A Site

Download Full-text

Critical role for cold shock protein YB-1 in cytokinesis

10.1101/2020.03.18.997817 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sunali Mehta ◽

Michael Algie ◽

Tariq Al-Jabri ◽

Cushla McKinney ◽

Srinivasaraghavan Kannan ◽

...

Keyword(s):

Cell Division ◽

Cancer Progression ◽

Cold Shock ◽

Binding Protein ◽

Critical Role ◽

Confocal Imaging ◽

Cold Shock Protein ◽

Microtubule Organization ◽

Atomistic Modelling

ABSTRACTHigh levels of the cold shock protein Y-box-binding protein-1, YB-1, are tightly correlated with increased cell proliferation and cancer progression. However, the precise mechanism by which YB-1 regulates proliferation is unknown. Here, we found that YB-1 depletion in several cell lines resulted in cytokinesis failure, multinucleation and an increase in G1 transit time. Rescue experiments indicated that YB-1 was required for completion of cytokinesis. Using confocal imaging of cells undergoing cytokinesis both in vitro and in zebrafish embryos, we found that YB-1 was critical for microtubule organization during cytokinesis. Using mass spectrometry we identified multiple novel phosphorylation sites on YB-1. We show that phosphorylation of YB-1 at multiple serine residues was essential for its function during cytokinesis. Using atomistic modelling we show how multiple phosphorylations alter YB-1 conformation, allowing it to interact with protein partners. Our results establish phosphorylated YB-1 as a critical regulator of cytokinesis, defining for the first time precisely how YB-1 regulates cell division.SUMMARYY-box-binding protein-1, YB-1, is essential for cell division, but it is not clear how it functions. Using live imaging and confocal microscopy we show that YB-1 functions only in the last step of division, specifically being required to initiate cytokinesis.

Download Full-text

Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E

Nucleic Acids Research ◽

10.1093/nar/gkz1152 ◽

2019 ◽

Vol 48 (2) ◽

pp. 847-861 ◽

Cited By ~ 2

Author(s):

Nida Ali ◽

Jayaraman Gowrishankar

Keyword(s):

Escherichia Coli ◽

Active Site ◽

Rna Binding ◽

Initial Step ◽

Dominant Negative ◽

Rnase E ◽

Wild Type ◽

Catalytic Active Site

Abstract RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5′-sensor pocket that renders enzyme activity maximal on 5′-monophosphorylated RNAs. The protein's non-catalytic C-terminal half (CTH) harbours RNA-binding motifs and serves as scaffold for a multiprotein degradosome complex, but is dispensable for viability. Here, we provide evidence that a full-length hetero-tetramer, composed of a mixture of wild-type and (recessive lethal) active-site mutant subunits, exhibits identical activity in vivo as the wild-type homo-tetramer itself (‘recessive resurrection’). When all of the cognate polypeptides lacked the CTH, the active-site mutant subunits were dominant negative. A pair of C-terminally truncated polypeptides, which were individually inactive because of additional mutations in their active site and 5′-sensor pocket respectively, exhibited catalytic function in combination, both in vivo and in vitro (i.e. intragenic or allelic complementation). Our results indicate that adjacent subunits within an oligomer are separately responsible for 5′-sensing and cleavage, and that RNA binding facilitates oligomerization. We propose also that the CTH mediates a rate-determining initial step for enzyme function, which is likely the binding and channelling of substrate for NTH’s endonucleolytic action.

Download Full-text

RNA and DNA Binding Epitopes of the Cold Shock Protein TmCsp from the Hyperthermophile Thermotoga maritima

The Protein Journal ◽

10.1007/s10930-020-09929-6 ◽

2020 ◽

Vol 39 (5) ◽

pp. 487-500

Author(s):

Konstanze von König ◽

Norman Kachel ◽

Hans Robert Kalbitzer ◽

Werner Kremer

Keyword(s):

Nucleic Acids ◽

Cold Shock ◽

Rna Binding ◽

Dissociation Constants ◽

Thermotoga Maritima ◽

Cold Shock Protein ◽

Binding Motif ◽

Purine Base ◽

High Affinity ◽

Binding Epitope

AbstractProkaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and “RNA chaperones”. They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using heteronuclear 2D NMR spectroscopy. At “physiological” growth temperatures of TmCsp (≥ 343 K), all oligonucleotides studied have dissociation constants between 1.6 ((dT)7) and 25.2 ((dA)7) μM as determined by tryptophan fluorescence quenching. Reduction of the temperature to 303 K leads to a pronounced increase of affinity for thymidylate (dT)7 and uridylate (rU)7 heptamers with dissociation constants of 4.0 and 10.8 nM, respectively, whereas the weak binding of TmCsp to cytidylate, adenylate, and guanylate heptamers (dC)7, (dA)7, and (dT)7 is almost unaffected by temperature. The change of affinities of TmCsp for (dT)7 and (rU)7 by approximately 3 orders of magnitude shows that it represents a cold chock sensor that switches on the cold shock reaction of the cell. A temperature dependent conformational switch of the protein is required for this action. The binding epitope on TmCsp for the ssDNA and RNA heptamers is very similar and comprises β-strands 1 and 2, the loop β1–β2 as well as the loops connecting β3 with β4 and β4 with β5. Besides the loop regions, surprisingly, mainly the RNA-binding motif RNP1 is involved in ssDNA and RNA binding, while only two amino acids, H28 and W29, of the postulated RNA-binding motif RNP2 interact with the uridylate and thymidylate homonucleotides, although a high affinity in the nanomolar range is achieved. This is in contrast to the binding properties of other CSPs or cold shock domains, where RNP1 as well as RNP2 are involved in binding. TmCsp takes up a unique position since it is the only one which possesses a tryptophan residue instead of a usually highly conserved phenylalanine or tyrosine residue at the end of RNP2. NMR titrations suggest that neither (dT)7 nor (rU)7 represent the full binding motif and that non-optimal intercalation of W29 into these oligonucleotides blocks the access of the RNP2 site to the DNA or RNA. NMR-experiments with (dA)7 suggest an interaction of W29 with the adenine ring. Full binding seems to require at least one single purine base well-positioned within a thymine- or uracil-rich stretch of nucleic acids.

Download Full-text