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1.
Protein Sci ; 32(9): e4737, 2023 09.
Article in English | MEDLINE | ID: mdl-37497650

ABSTRACT

Methicillin-resistant Staphylococcus aureus (MRSA) causes life-threatening human infections. Bacteriophage-encoded endolysins degrade the cell walls of Gram-positive bacteria by selectively hydrolyzing the peptidoglycan layer and thus are promising candidates to combat bacterial infections. PlyGRCS, the S. aureus-specific bacteriophage endolysin, contains a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Here, we show the crystal structure of full-length PlyGRCS refined to 2.1 Å resolution. In addition, a serendipitous finding revealed that PlyGRCS binds to cold-shock protein C (CspC) by interacting with its CHAP and SH3_5 domains. CspC is an RNA chaperone that plays regulatory roles by conferring bacterial adaptability to various stress conditions. PlyGRCS has substantial lytic activity against S. aureus and showed only minimal change in its lytic activity in the presence of CspC. Whereas the PlyGRCS-CspC complex greatly reduced CspC-nucleic acid binding, the aforesaid complex may downregulate the CspC function during bacterial infection. Overall, the crystal structure and biochemical results of PlyGRCS provide a molecular basis for the bacteriolytic activity of PlyGRCS against S. aureus.


Subject(s)
Bacterial Proteins , Cold Shock Proteins and Peptides , Endopeptidases , Heat-Shock Proteins , Methicillin-Resistant Staphylococcus aureus , Staphylococcus Phages , Humans , Cold Shock Proteins and Peptides/chemistry , Endopeptidases/chemistry , Endopeptidases/genetics , Endopeptidases/metabolism , Methicillin-Resistant Staphylococcus aureus/virology , Bacterial Proteins/chemistry , Heat-Shock Proteins/chemistry , Staphylococcus Phages/enzymology
2.
Int J Biol Macromol ; 220: 743-753, 2022 Nov 01.
Article in English | MEDLINE | ID: mdl-35987358

ABSTRACT

Cold shock proteins (CSPs) are an ancient and conserved family of proteins. They are renowned for their role in response to low-temperature stress in bacteria and nucleic acid binding activities. In prokaryotes, cold and non-cold inducible CSPs are involved in various cellular and metabolic processes such as growth and development, osmotic oxidation, starvation, stress tolerance, and host cell invasion. In prokaryotes, cold shock condition reduces cell transcription and translation efficiency. Eukaryotic cold shock domain (CSD) proteins are evolved form of prokaryotic CSPs where CSD is flanked by N- and C-terminal domains. Eukaryotic CSPs are multi-functional proteins. CSPs also act as nucleic acid chaperons by preventing the formation of secondary structures in mRNA at low temperatures. In human, CSD proteins play a crucial role in the progression of breast cancer, colon cancer, lung cancer, and Alzheimer's disease. A well-defined three-dimensional structure of intrinsically disordered regions of CSPs family members is still undetermined. In this article, intrinsic disorder regions of CSPs have been explored systematically to understand the pleiotropic role of the cold shock family of proteins.


Subject(s)
Cold Shock Proteins and Peptides , Cold-Shock Response , Intrinsically Disordered Proteins , Bacterial Proteins/chemistry , Cold Shock Proteins and Peptides/chemistry , Cold Temperature , Humans , Intrinsically Disordered Proteins/chemistry , Protein Structure, Secondary , RNA, Messenger/genetics
3.
EMBO J ; 41(4): e109175, 2022 02 15.
Article in English | MEDLINE | ID: mdl-34994471

ABSTRACT

Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo-EM structure determination to show that folding of a ß-barrel protein begins with formation of a dynamic α-helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N-terminal part of the nascent chain refolds to a ß-hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α-helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl-transferase center suggest that protein folding could modulate ribosome activity.


Subject(s)
Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Circular Dichroism , Cold Shock Proteins and Peptides/genetics , Cryoelectron Microscopy , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Models, Molecular , Protein Biosynthesis , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Folding , Protein Processing, Post-Translational , Ribosomes/genetics , Ribosomes/metabolism
4.
Protein J ; 39(5): 487-500, 2020 10.
Article in English | MEDLINE | ID: mdl-33094361

ABSTRACT

Prokaryotic 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 ß-strands 1 and 2, the loop ß1-ß2 as well as the loops connecting ß3 with ß4 and ß4 with ß5. 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.


Subject(s)
Bacterial Proteins/chemistry , Cold Shock Proteins and Peptides/chemistry , DNA-Binding Proteins/chemistry , Epitopes/chemistry , RNA-Binding Proteins/chemistry , Thermotoga maritima/chemistry , Amino Acid Motifs , Bacterial Proteins/genetics , Cold Shock Proteins and Peptides/genetics , DNA-Binding Proteins/genetics , Epitopes/genetics , RNA-Binding Proteins/genetics , Thermotoga maritima/genetics
5.
Malar J ; 19(1): 382, 2020 Oct 27.
Article in English | MEDLINE | ID: mdl-33109193

ABSTRACT

The cold shock domain (CSD) forms the hallmark of the cold shock protein family that provides the characteristic feature of binding with nucleic acids. While much of the information is available on bacterial, plants and human cold shock proteins, their existence and functions in the malaria parasite remains undefined. In the present review, the available information on functions of well-characterized cold shock protein members in different organisms has been collected and an attempt was made to identify the presence and role of cold shock proteins in malaria parasite. A single Plasmodium falciparum cold shock protein (PfCoSP) was found in P. falciparum which is reported to be essential for parasite survival. Essentiality of PfCoSP underscores its importance in malaria parasite life cycle. In silico tools were used to predict the features of PfCoSP and to identify its homologues in bacteria, plants, humans, and other Plasmodium species. Modelled structures of PfCoSP and its homologues in Plasmodium species were compared with human cold shock protein 'YBOX-1' (Y-box binding protein 1) that provide important insights into their functioning. PfCoSP model was subjected to docking with B-form DNA and RNA to reveal a number of residues crucial for their interaction. Transcriptome analysis and motifs identified in PfCoSP implicate its role in controlling gene expression at gametocyte, ookinete and asexual blood stages of malaria parasite. Overall, this review emphasizes the functional diversity of the cold shock protein family by discussing their known roles in gene expression regulation, cold acclimation, developmental processes like flowering transition, and flower and seed development, and probable function in gametocytogenesis in case of malaria parasite. This enables readers to view the cold shock protein family comprehensively.


Subject(s)
Cold Shock Proteins and Peptides/genetics , Gene Expression Regulation , Genetic Pleiotropy , Plasmodium falciparum/genetics , Protozoan Proteins/genetics , Amino Acid Sequence , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/metabolism , Gene Expression Profiling , Plasmodium falciparum/metabolism , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism , Sequence Alignment
6.
Biochemistry (Mosc) ; 85(Suppl 1): S1-S19, 2020 Jan.
Article in English | MEDLINE | ID: mdl-32087051

ABSTRACT

This review summarizes the features of cold shock domain (CSD) proteins in the context of their interactions with nucleic acids and describes similarities and differences in the structure of cold shock proteins of prokaryotes and CSD proteins of eukaryotes with special emphasis on the functions related to the RNA/DNA-binding ability of these proteins. The mechanisms and specificity of their interaction with nucleic acids in relation to the growing complexity of protein domain structure are described, as well as various complexes of the mammalian Y-box binding protein 1 (YB-1) with nucleic acids (filaments, globules, toroids). The role of particular amino acid residues in the binding of nitrogenous bases and the sugar-phosphate backbone of nucleic acids is emphasized. The data on the nucleic acid sequences recognized by the Y-box binding proteins are systematized. Post-translational modifications of YB-1, especially its phosphorylation, affect the recognition of specific sequences in the promoter regions of various groups of genes by YB-1 protein. The data on the interaction of Lin28 protein with let-7 miRNAs are summarized. The features of the domain structure of plant CSD proteins and their effect on the interaction with nucleic acids are discussed.


Subject(s)
Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/metabolism , Nucleic Acids/metabolism , Protein Domains , Protein Processing, Post-Translational , Y-Box-Binding Protein 1/metabolism , Amino Acid Sequence , Animals , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cold Shock Proteins and Peptides/genetics , Cold Temperature , Gene Expression Regulation , Humans , Plant Proteins/chemistry , Plant Proteins/genetics , Plant Proteins/metabolism , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Y-Box-Binding Protein 1/chemistry
7.
J Chem Inf Model ; 60(2): 546-561, 2020 02 24.
Article in English | MEDLINE | ID: mdl-31910002

ABSTRACT

Understanding which aspects contribute to the thermostability of proteins is a challenge that has persisted for decades, and it is of great relevance for protein engineering. Several types of interactions can influence the thermostability of a protein. Among them, the electrostatic interactions have been a target of particular attention. Aiming to explore how this type of interaction can affect protein thermostability, this paper investigated four homologous cold shock proteins from psychrophilic, mesophilic, thermophilic, and hyperthermophilic organisms using a set of theoretical methodologies. It is well-known that electrostatics as well as hydrophobicity are key-elements for the stabilization of these proteins. Therefore, both interactions were initially analyzed in the native structure of each protein. Electrostatic interactions present in the native structures were calculated with the Tanford-Kirkwood model with solvent accessibility, and the amount of hydrophobic surface area buried upon folding was estimated by measuring both folded and extended structures. On the basis of Energy Landscape Theory, the local frustration and the simplified alpha-carbon structure-based model were modeled with a Debye-Hückel potential to take into account the electrostatics and the effects of an implicit solvent. Thermodynamic data for the structure-based model simulations were collected and analyzed using the Weighted Histogram Analysis and Stochastic Diffusion methods. Kinetic quantities including folding times, transition path times, folding routes, and Φ values were also obtained. As a result, we found that the methods are able to qualitatively infer that electrostatic interactions play an important role on the stabilization of the most stable thermophilic cold shock proteins, showing agreement with the experimental data.


Subject(s)
Cold Shock Proteins and Peptides/chemistry , Protein Folding , Sequence Homology, Amino Acid , Static Electricity , Temperature , Cold Shock Proteins and Peptides/metabolism , Kinetics , Models, Molecular , Protein Conformation , Protein Stability
8.
J Chem Theory Comput ; 16(1): 765-772, 2020 Jan 14.
Article in English | MEDLINE | ID: mdl-31756296

ABSTRACT

The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.


Subject(s)
Bacillus subtilis/chemistry , Bacterial Proteins/chemistry , Cold Shock Proteins and Peptides/chemistry , Amino Acid Sequence , Bacillus subtilis/genetics , Bacterial Proteins/genetics , Cold Shock Proteins and Peptides/genetics , Hydrogen-Ion Concentration , Models, Molecular , Monte Carlo Method , Mutation , Protein Folding , Protein Stability , Protein Unfolding , Static Electricity
9.
Phys Chem Chem Phys ; 21(22): 11924-11936, 2019 Jun 05.
Article in English | MEDLINE | ID: mdl-31134232

ABSTRACT

A comprehensive understanding of protein folding includes the knowledge of the formation of individual secondary structures, tertiary structure, and the effects of non-native contacts on these folding events. The measurement of these microscopic events has been posing challenges for experiment and molecular simulation. In this work, we performed enhanced sampling MD simulations for three proteins (NTL9, NuG2b, and CspA) and analyzed minimum free energy paths on multi-dimensional free energy landscapes to explore the underlying folding mechanisms. Consistencies can be seen between the present simulations and the existing experiments as well as other MD simulations. Quantitative analysis reveals the nucleation-condensation folding mechanism indicating the concurrent build-up of secondary and tertiary structures for the three proteins and gives the detailed formation sequence of individual native secondary structure elements. More importantly, nonnative contacts are generally observed among the proteins, creating a nonnative environment to affect the folding of individual secondary structure elements. A general tendency is that the secondary structure element(s) where the maximal nonnative contacts are observed have the largest formation free-energy barrier(s), corresponding to the rate-limiting step(s) of the folding for proteins that follow the nucleation-condensation mechanism. In summary, while native contacts determine the folding mechanism and pathway, non-native contacts play an important role in determining the protein folding thermodynamics by influencing the free energies of individual secondary structure element formation.


Subject(s)
Cold Shock Proteins and Peptides/chemistry , Escherichia coli Proteins/chemistry , GTP-Binding Proteins/chemistry , Protein Folding , Ribosomal Proteins/chemistry , Amino Acid Sequence , Escherichia coli/chemistry , Firmicutes/chemistry , GTP-Binding Proteins/genetics , Geobacillus stearothermophilus/chemistry , Molecular Dynamics Simulation , Mutation , Protein Structure, Secondary , Thermodynamics
10.
J Eukaryot Microbiol ; 66(3): 393-403, 2019 05.
Article in English | MEDLINE | ID: mdl-30099808

ABSTRACT

CSPs, cold shock domain (CSD) containing proteins, are demonstrated to be involved in low temperature responses and various cellular processes under normal growth conditions. Here, we used the cosmopolitan, toxic, and resting cyst-producing dinoflagellate Scrippsiella trochoidea as a representative harmful algal bloom-forming dinoflagellate to investigate the expression patterns of CSP in vegetative cells in response to temperature shocks and in resting cysts, with an objective to probe the possible function of CSP in dinoflagellates. The full-length cDNA of a CSP gene from S. trochoidea (StCSP) was obtained which has a solely N-terminal CSD with conserved nucleic acids binding motifs. The qPCR results together indicated StCSP expression was not modulated by temperature at the transcriptional level and implied this gene may not be associated with temperature stress responses in S. trochoidea as the gene's name implies. However, we observed significantly higher StCSP transcripts in resting cysts (newly formed and maintained in dormancy for different periods of time) than that observed in vegetative cells (at exponential and stationary stages), indicating StCSP is actively expressed during dormancy of S. trochoidea. Taking together our recent transcriptomic work on S. trochoidea into consideration, we postulate that StCSP may play roles during encystment and cyst dormancy of the species.


Subject(s)
Cold Shock Proteins and Peptides/genetics , Dinoflagellida/genetics , Protozoan Proteins/genetics , Algal Proteins/chemistry , Algal Proteins/genetics , Algal Proteins/metabolism , Amino Acid Sequence , Base Sequence , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/metabolism , Dinoflagellida/metabolism , Phylogeny , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism
11.
Biochemistry (Mosc) ; 83(11): 1369-1379, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30482148

ABSTRACT

Plant cold shock domain proteins (CSDPs) are DNA/RNA-binding proteins. CSDPs contain the conserved cold shock domain (CSD) in the N-terminal part and a varying number of the CCHC-type zinc finger (ZnF) motifs alternating with glycine-rich regions in the C-terminus. CSDPs exhibit RNA chaperone and RNA-melting activities due to their nonspecific interaction with RNA. At the same time, there are reasons to believe that CSDPs also interact with specific RNA targets. In the present study, we used three recombinant CSDPs from the saltwater cress plant (Eutrema salsugineum) - EsCSDP1, EsCSDP2, EsCSDP3 with 6, 2, and 7 ZnF motifs, respectively, and showed that their nonspecific interaction with RNA is determined by their C-terminal fragments. All three proteins exhibited high affinity to the single-stranded regions over four nucleotides long within RNA oligonucleotides. The presence of guanine in the single- or double-stranded regions was crucial for the interaction with CSDPs. Complementation test using E. coli BX04 cells lacking four cold shock protein genes (ΔcspA, ΔcspB, ΔcspE, ΔcspG) revealed that the specific binding of plant CSDPs with RNA is determined by CSD.


Subject(s)
Brassicaceae , Cold Shock Proteins and Peptides , Plant Proteins , RNA, Plant , Amino Acid Motifs , Brassicaceae/chemistry , Brassicaceae/genetics , Brassicaceae/metabolism , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/genetics , Cold Shock Proteins and Peptides/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Genetic Complementation Test , Plant Proteins/chemistry , Plant Proteins/genetics , Plant Proteins/metabolism , Protein Domains , RNA, Plant/chemistry , RNA, Plant/genetics
12.
Biochemistry ; 57(26): 3625-3640, 2018 07 03.
Article in English | MEDLINE | ID: mdl-29737840

ABSTRACT

Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Although Cp-Csp shares sequence homology, common folding patterns, and motifs, including a five ß-stranded barrel, with its thermophilic counterparts, its thermostability (37 °C) was markedly lower than those of other Csps. Cp-Csp binds heptathymidine with an affinity of 10-7 M, thereby increasing its thermostability to 50 °C. Nuclear magnetic resonance spectroscopic analysis of the Cp-Csp structure and backbone dynamics revealed a flexible structure with only one salt bridge and 10 residues in the hydrophobic cavity. Notably, Cp-Csp contains Tyr51 instead of the conserved Phe in the hydrophobic core, and its phenolic hydroxyl group projects toward the surface. The Y51F mutation increased the stability of hydrophobic packing and may have allowed for the formation of a K3-E21 salt bridge, thereby increasing its thermostability to 43 °C. Cp-Csp exhibited conformational exchanges in its ribonucleoprotein motifs 1 and 2 (754 and 642 s-1), and heptathymidine binding markedly decreased these motions. Cp-Csp lacks salt bridges and has longer flexible loops and a less compact hydrophobic cavity resulting from Tyr51 compared to mesophilic and thermophilic Csps. These might explain the low thermostability of Cp-Csp. The conformational flexibility of Cp-Csp facilitates its accommodation of nucleic acids at low temperatures in polar oceans and its function as an RNA chaperone for cold adaptation.


Subject(s)
Alteromonadaceae/chemistry , Bacterial Proteins/chemistry , Cold Shock Proteins and Peptides/chemistry , Alteromonadaceae/metabolism , Amino Acid Sequence , Bacterial Proteins/metabolism , Cold Shock Proteins and Peptides/metabolism , Hot Temperature , Hydrophobic and Hydrophilic Interactions , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation , Protein Folding , Protein Stability , Sequence Alignment , Thymidine/analogs & derivatives , Thymidine/metabolism , Tyrosine/chemistry , Tyrosine/metabolism
13.
J Chem Phys ; 148(12): 123336, 2018 Mar 28.
Article in English | MEDLINE | ID: mdl-29604829

ABSTRACT

We demonstrate that fused silica capillaries are suitable for single molecule fluorescence resonance energy transfer (smFRET) measurements at high pressure with an optical quality comparable to the measurement on microscope coverslips. Therefore, we optimized the imaging conditions in a standard square fused silica capillary with an adapted arrangement and evaluated the performance by imaging the focal volume, fluorescence correlation spectroscopy benchmarks, and FRET measurements. We demonstrate single molecule FRET measurements of cold shock protein A unfolding at a pressure up to 2000 bars and show that the unfolded state exhibits an expansion almost independent of pressure.


Subject(s)
Cold Shock Proteins and Peptides/chemistry , Fluorescence Resonance Energy Transfer , Pressure , Protein Unfolding
14.
FEBS J ; 285(2): 372-390, 2018 01.
Article in English | MEDLINE | ID: mdl-29197185

ABSTRACT

Cold shock proteins (Csps) function to preserve cell viability at low temperatures by binding to nucleic acids and consequently control gene expression. The mesophilic bacterium Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis in animals, and infection in livestock is a considerable economic burden worldwide. In this report, the structure of cold shock protein A from Cp (Cp-CspA) and biochemical analysis of its temperature-dependent interaction with a Y-box ssDNA motif is presented. The Cp-CspA structure contains five ß-strands making up a ß-barrel fold with 11 hydrophobic core residues and two salt bridges that confers it with a melting temperature of ~ 54 °C that is similar to mesophilic Bs-CspB. Chemical shift perturbations analysis revealed that residues in the nucleic acid-binding motifs (RNP 1 and 2) and loop 3 are involved in binding to the Y-box fragment either by direct interaction or by conformational rearrangements remote from the binding region. Fluorescence quenching experiments of Cp-CspA showed that the dissociation constants for Y-box ssDNA binding is nanomolar and the binding affinity decreased as the temperature increased, indicating that the interaction is enthalpically driven and the hydrogen bonds and van der Waals forces are important contributions for complex stabilization. The Y31 of Cp-CspA is a particular occurrence among Csps from mesophilic bacteria that provide a possible explanation for the higher binding affinity to ssDNA than that observed for Bs-CspB. Anisotropy measurements indicated that the reduction in molecular mobility of Cp-CspA upon Y-box binding is characterized by a cooperative process. DATABASE: Resonance assignment and structural data are available in the Biological Magnetic Resonance Data Bank and Protein Data Bank under accession number 26802 and 5O6F, respectively.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/metabolism , Corynebacterium pseudotuberculosis/metabolism , DNA, Single-Stranded/metabolism , Amino Acid Sequence , Calorimetry, Differential Scanning , Computational Biology , Fluorescence Polarization , Protein Binding , Protein Conformation , Protein Stability , Sequence Homology, Amino Acid
15.
Biochim Biophys Acta Mol Cell Res ; 1865(2): 231-246, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29100789

ABSTRACT

Plant calcium-dependent protein kinases (CDPKs) are key proteins implicated in calcium-mediated signaling pathways of a wide range of biological events in the organism. The action of each particular CDPK is strictly regulated by many mechanisms in order to ensure an accurate signal translation and the activation of the adequate response processes. In this work, we investigated the regulation of a CDPK involved in rice cold stress response, OsCPK17, to better understand its mode of action. We identified two new alternative splicing (AS) mRNA forms of OsCPK17 encoding truncated versions of the protein, missing the CDPK activation domain. We analyzed the expression patterns of all AS variants in rice tissues and examined their subcellular localization in onion epidermal cells. The results indicate that the AS of OsCPK17 putatively originates truncated forms of the protein with distinct functions, and different subcellular and tissue distributions. Additionally, we addressed the regulation of OsCPK17 by post-translational modifications in several in vitro experiments. Our analysis indicated that OsCPK17 activity depends on its structural rearrangement induced by calcium binding, and that the protein can be autophosphorylated. The identified phosphorylation sites mostly populate the OsCPK17 N-terminal domain. Exceptions are phosphosites T107 and S136 in the kinase domain and S558 in the C-terminal domain. These phosphosites seem conserved in CDPKs and may reflect a common regulatory mechanism for this protein family.


Subject(s)
Alternative Splicing/physiology , Cold Shock Proteins and Peptides , Oryza , Plant Proteins , Protein Kinases , Calcium/metabolism , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/genetics , Cold Shock Proteins and Peptides/metabolism , Oryza/enzymology , Oryza/genetics , Plant Proteins/chemistry , Plant Proteins/genetics , Plant Proteins/metabolism , Protein Domains , Protein Kinases/chemistry , Protein Kinases/genetics , Protein Kinases/metabolism
16.
Proc Natl Acad Sci U S A ; 114(28): 7385-7390, 2017 07 11.
Article in English | MEDLINE | ID: mdl-28642345

ABSTRACT

High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.


Subject(s)
Altitude , Rhodopsin/chemistry , Animals , Bayes Theorem , Biological Evolution , Bolivia , Catfishes , Cold Shock Proteins and Peptides/chemistry , Cold Temperature , Crystallography, X-Ray , Ecuador , Evolution, Molecular , Geography , HEK293 Cells , Humans , Kinetics , Mutation , Peru , Phylogeny
17.
Proc Natl Acad Sci U S A ; 114(26): 6824-6829, 2017 06 27.
Article in English | MEDLINE | ID: mdl-28611217

ABSTRACT

The functions of many bacterial RNA-binding proteins remain obscure because of a lack of knowledge of their cellular ligands. Although well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, others are highly expressed in infection-relevant conditions. Here, we have profiled transcripts bound in vivo by the CspA family members of Salmonella enterica serovar Typhimurium to link the constitutively expressed CspC and CspE proteins with virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, double deletion of cspC and cspE fully attenuates Salmonella in systemic mouse infection. In other words, the RNA ligand-centric approach taken here overcomes a problematic molecular redundancy of CspC and CspE that likely explains why these proteins have evaded selection in previous virulence factor screens in animals. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy. They also suggest that globally acting RNA-binding proteins are more common in bacteria than currently appreciated.


Subject(s)
Bacterial Proteins , Cold Shock Proteins and Peptides , Heat-Shock Proteins , RNA-Binding Proteins , Salmonella Infections , Salmonella typhimurium , Virulence Factors , Animals , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/genetics , Cold Shock Proteins and Peptides/metabolism , Escherichia coli , Female , Heat-Shock Proteins/chemistry , Heat-Shock Proteins/genetics , Heat-Shock Proteins/metabolism , Mice, Inbred BALB C , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Salmonella Infections/genetics , Salmonella Infections/metabolism , Salmonella typhimurium/chemistry , Salmonella typhimurium/genetics , Salmonella typhimurium/metabolism , Salmonella typhimurium/pathogenicity , Virulence Factors/chemistry , Virulence Factors/genetics , Virulence Factors/metabolism
18.
Nat Commun ; 8: 14242, 2017 01 27.
Article in English | MEDLINE | ID: mdl-28128346

ABSTRACT

Both land plants and metazoa have the capacity to reprogram differentiated cells to stem cells. Here we show that the moss Physcomitrella patens Cold-Shock Domain Protein 1 (PpCSP1) regulates reprogramming of differentiated leaf cells to chloronema apical stem cells and shares conserved domains with the induced pluripotent stem cell factor Lin28 in mammals. PpCSP1 accumulates in the reprogramming cells and is maintained throughout the reprogramming process and in the resultant stem cells. Expression of PpCSP1 is negatively regulated by its 3'-untranslated region (3'-UTR). Removal of the 3'-UTR stabilizes PpCSP1 transcripts, results in accumulation of PpCSP1 protein and enhances reprogramming. A quadruple deletion mutant of PpCSP1 and three closely related PpCSP genes exhibits attenuated reprogramming indicating that the PpCSP genes function redundantly in cellular reprogramming. Taken together, these data demonstrate a positive role of PpCSP1 in reprogramming, which is similar to the function of mammalian Lin28.


Subject(s)
Bryopsida/physiology , Cellular Reprogramming/physiology , Cold Shock Proteins and Peptides/physiology , Plant Proteins/physiology , Stem Cells/physiology , 3' Untranslated Regions/physiology , Cell Differentiation/physiology , Cold Shock Proteins and Peptides/chemistry , Gene Expression Regulation, Plant/physiology , Plant Leaves/cytology , Plant Leaves/physiology , Plant Proteins/chemistry , Plants, Genetically Modified , Protein Domains/physiology
19.
Nucleic Acids Res ; 45(7): 4255-4268, 2017 04 20.
Article in English | MEDLINE | ID: mdl-28126922

ABSTRACT

Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein.


Subject(s)
Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , RNA Folding , RNA/chemistry , Amino Acids, Aromatic/chemistry , Nuclear Magnetic Resonance, Biomolecular , Nucleic Acid Conformation , Protein Binding , Protein Conformation , RNA/metabolism
20.
Sci Rep ; 6: 35560, 2016 10 20.
Article in English | MEDLINE | ID: mdl-27762322

ABSTRACT

Bacillus thuringiensis (Bt), one of the most successful biopesticides, may expand its potential by producing bacteriocins (thuricins). The aim of this study was to investigate the antimicrobial potential of a novel Bt bacteriocin, thuricin BtCspB, produced by Bt BRC-ZYR2. The results showed that this bacteriocin has a high similarity with cold-shock protein B (CspB). BtCspB lost its activity after proteinase K treatment; however it was active at 60 °C for 30 min and was stable in the pH range 5-7. The partial loss of activity after the treatments of lipase II and catalase were likely due to the change in BtCspB structure and the partial degradation of BtCspB, respectively. The loss of activity at high temperatures and the activity variation at different pHs were not due to degradation or large conformational change. BtCspB did not inhibit four probiotics. It was only active against B. cereus strains 0938 and ATCC 10987 with MIC values of 3.125 µg/mL and 0.781 µg/mL, and MBC values of 12.5 µg/mL and 6.25 µg/mL, respectively. Taken together, these results provide new insights into a novel cold shock protein-like bacteriocin, BtCspB, which displayed promise for its use in food preservation and treatment of B. cereus-associated diseases.


Subject(s)
Bacillus thuringiensis/chemistry , Bacterial Proteins , Bacteriocins , Cold Shock Proteins and Peptides , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacteriocins/chemistry , Bacteriocins/isolation & purification , Cold Shock Proteins and Peptides/chemistry , Cold Shock Proteins and Peptides/isolation & purification , Hydrogen-Ion Concentration , Protein Domains , Protein Stability
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