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1.
Protein Sci ; 32(9): e4737, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37497650

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas , Proteínas y Péptidos de Choque por Frío , Endopeptidasas , Proteínas de Choque Térmico , Staphylococcus aureus Resistente a Meticilina , Fagos de Staphylococcus , Humanos , Proteínas y Péptidos de Choque por Frío/química , Endopeptidasas/química , Endopeptidasas/genética , Endopeptidasas/metabolismo , Staphylococcus aureus Resistente a Meticilina/virología , Proteínas Bacterianas/química , Proteínas de Choque Térmico/química , Fagos de Staphylococcus/enzimología
2.
Int J Biol Macromol ; 220: 743-753, 2022 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-35987358

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío , Respuesta al Choque por Frío , Proteínas Intrínsecamente Desordenadas , Proteínas Bacterianas/química , Proteínas y Péptidos de Choque por Frío/química , Frío , Humanos , Proteínas Intrínsecamente Desordenadas/química , Estructura Secundaria de Proteína , ARN Mensajero/genética
3.
EMBO J ; 41(4): e109175, 2022 02 15.
Artículo en Inglés | MEDLINE | ID: mdl-34994471

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Dicroismo Circular , Proteínas y Péptidos de Choque por Frío/genética , Microscopía por Crioelectrón , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Modelos Moleculares , Biosíntesis de Proteínas , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Pliegue de Proteína , Procesamiento Proteico-Postraduccional , Ribosomas/genética , Ribosomas/metabolismo
4.
Malar J ; 19(1): 382, 2020 Oct 27.
Artículo en Inglés | MEDLINE | ID: mdl-33109193

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/genética , Regulación de la Expresión Génica , Pleiotropía Genética , Plasmodium falciparum/genética , Proteínas Protozoarias/genética , Secuencia de Aminoácidos , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/metabolismo , Perfilación de la Expresión Génica , Plasmodium falciparum/metabolismo , Proteínas Protozoarias/química , Proteínas Protozoarias/metabolismo , Alineación de Secuencia
5.
Protein J ; 39(5): 487-500, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-33094361

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas/química , Proteínas y Péptidos de Choque por Frío/química , Proteínas de Unión al ADN/química , Epítopos/química , Proteínas de Unión al ARN/química , Thermotoga maritima/química , Secuencias de Aminoácidos , Proteínas Bacterianas/genética , Proteínas y Péptidos de Choque por Frío/genética , Proteínas de Unión al ADN/genética , Epítopos/genética , Proteínas de Unión al ARN/genética , Thermotoga maritima/genética
6.
Biochemistry (Mosc) ; 85(Suppl 1): S1-S19, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32087051

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/metabolismo , Ácidos Nucleicos/metabolismo , Dominios Proteicos , Procesamiento Proteico-Postraduccional , Proteína 1 de Unión a la Caja Y/metabolismo , Secuencia de Aminoácidos , Animales , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas y Péptidos de Choque por Frío/genética , Frío , Regulación de la Expresión Génica , Humanos , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Proteína 1 de Unión a la Caja Y/química
7.
J Chem Inf Model ; 60(2): 546-561, 2020 02 24.
Artículo en Inglés | MEDLINE | ID: mdl-31910002

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/química , Pliegue de Proteína , Homología de Secuencia de Aminoácido , Electricidad Estática , Temperatura , Proteínas y Péptidos de Choque por Frío/metabolismo , Cinética , Modelos Moleculares , Conformación Proteica , Estabilidad Proteica
8.
J Chem Theory Comput ; 16(1): 765-772, 2020 Jan 14.
Artículo en Inglés | MEDLINE | ID: mdl-31756296

RESUMEN

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.


Asunto(s)
Bacillus subtilis/química , Proteínas Bacterianas/química , Proteínas y Péptidos de Choque por Frío/química , Secuencia de Aminoácidos , Bacillus subtilis/genética , Proteínas Bacterianas/genética , Proteínas y Péptidos de Choque por Frío/genética , Concentración de Iones de Hidrógeno , Modelos Moleculares , Método de Montecarlo , Mutación , Pliegue de Proteína , Estabilidad Proteica , Desplegamiento Proteico , Electricidad Estática
9.
Phys Chem Chem Phys ; 21(22): 11924-11936, 2019 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-31134232

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/química , Proteínas de Escherichia coli/química , Proteínas de Unión al GTP/química , Pliegue de Proteína , Proteínas Ribosómicas/química , Secuencia de Aminoácidos , Escherichia coli/química , Firmicutes/química , Proteínas de Unión al GTP/genética , Geobacillus stearothermophilus/química , Simulación de Dinámica Molecular , Mutación , Estructura Secundaria de Proteína , Termodinámica
10.
J Eukaryot Microbiol ; 66(3): 393-403, 2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-30099808

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/genética , Dinoflagelados/genética , Proteínas Protozoarias/genética , Proteínas Algáceas/química , Proteínas Algáceas/genética , Proteínas Algáceas/metabolismo , Secuencia de Aminoácidos , Secuencia de Bases , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/metabolismo , Dinoflagelados/metabolismo , Filogenia , Proteínas Protozoarias/química , Proteínas Protozoarias/metabolismo
11.
Biochemistry (Mosc) ; 83(11): 1369-1379, 2018 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-30482148

RESUMEN

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.


Asunto(s)
Brassicaceae , Proteínas y Péptidos de Choque por Frío , Proteínas de Plantas , ARN de Planta , Secuencias de Aminoácidos , Brassicaceae/química , Brassicaceae/genética , Brassicaceae/metabolismo , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/genética , Proteínas y Péptidos de Choque por Frío/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Prueba de Complementación Genética , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Dominios Proteicos , ARN de Planta/química , ARN de Planta/genética
12.
Biochemistry ; 57(26): 3625-3640, 2018 07 03.
Artículo en Inglés | MEDLINE | ID: mdl-29737840

RESUMEN

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.


Asunto(s)
Alteromonadaceae/química , Proteínas Bacterianas/química , Proteínas y Péptidos de Choque por Frío/química , Alteromonadaceae/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/metabolismo , Proteínas y Péptidos de Choque por Frío/metabolismo , Calor , Interacciones Hidrofóbicas e Hidrofílicas , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica , Pliegue de Proteína , Estabilidad Proteica , Alineación de Secuencia , Timidina/análogos & derivados , Timidina/metabolismo , Tirosina/química , Tirosina/metabolismo
13.
J Chem Phys ; 148(12): 123336, 2018 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-29604829

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/química , Transferencia Resonante de Energía de Fluorescencia , Presión , Desplegamiento Proteico
14.
Biochim Biophys Acta Mol Cell Res ; 1865(2): 231-246, 2018 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-29100789

RESUMEN

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.


Asunto(s)
Empalme Alternativo/fisiología , Proteínas y Péptidos de Choque por Frío , Oryza , Proteínas de Plantas , Proteínas Quinasas , Calcio/metabolismo , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/genética , Proteínas y Péptidos de Choque por Frío/metabolismo , Oryza/enzimología , Oryza/genética , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Dominios Proteicos , Proteínas Quinasas/química , Proteínas Quinasas/genética , Proteínas Quinasas/metabolismo
15.
FEBS J ; 285(2): 372-390, 2018 01.
Artículo en Inglés | MEDLINE | ID: mdl-29197185

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/metabolismo , Corynebacterium pseudotuberculosis/metabolismo , ADN de Cadena Simple/metabolismo , Secuencia de Aminoácidos , Rastreo Diferencial de Calorimetría , Biología Computacional , Polarización de Fluorescencia , Unión Proteica , Conformación Proteica , Estabilidad Proteica , Homología de Secuencia de Aminoácido
16.
Proc Natl Acad Sci U S A ; 114(28): 7385-7390, 2017 07 11.
Artículo en Inglés | MEDLINE | ID: mdl-28642345

RESUMEN

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.


Asunto(s)
Altitud , Rodopsina/química , Animales , Teorema de Bayes , Evolución Biológica , Bolivia , Bagres , Proteínas y Péptidos de Choque por Frío/química , Frío , Cristalografía por Rayos X , Ecuador , Evolución Molecular , Geografía , Células HEK293 , Humanos , Cinética , Mutación , Perú , Filogenia
17.
Proc Natl Acad Sci U S A ; 114(26): 6824-6829, 2017 06 27.
Artículo en Inglés | MEDLINE | ID: mdl-28611217

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas , Proteínas y Péptidos de Choque por Frío , Proteínas de Choque Térmico , Proteínas de Unión al ARN , Infecciones por Salmonella , Salmonella typhimurium , Factores de Virulencia , Animales , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/genética , Proteínas y Péptidos de Choque por Frío/metabolismo , Escherichia coli , Femenino , Proteínas de Choque Térmico/química , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/metabolismo , Ratones Endogámicos BALB C , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Infecciones por Salmonella/genética , Infecciones por Salmonella/metabolismo , Salmonella typhimurium/química , Salmonella typhimurium/genética , Salmonella typhimurium/metabolismo , Salmonella typhimurium/patogenicidad , Factores de Virulencia/química , Factores de Virulencia/genética , Factores de Virulencia/metabolismo
18.
Nucleic Acids Res ; 45(7): 4255-4268, 2017 04 20.
Artículo en Inglés | MEDLINE | ID: mdl-28126922

RESUMEN

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.


Asunto(s)
Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Pliegue del ARN , ARN/química , Aminoácidos Aromáticos/química , Resonancia Magnética Nuclear Biomolecular , Conformación de Ácido Nucleico , Unión Proteica , Conformación Proteica , ARN/metabolismo
19.
Nat Commun ; 8: 14242, 2017 01 27.
Artículo en Inglés | MEDLINE | ID: mdl-28128346

RESUMEN

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.


Asunto(s)
Bryopsida/fisiología , Reprogramación Celular/fisiología , Proteínas y Péptidos de Choque por Frío/fisiología , Proteínas de Plantas/fisiología , Células Madre/fisiología , Regiones no Traducidas 3'/fisiología , Diferenciación Celular/fisiología , Proteínas y Péptidos de Choque por Frío/química , Regulación de la Expresión Génica de las Plantas/fisiología , Hojas de la Planta/citología , Hojas de la Planta/fisiología , Proteínas de Plantas/química , Plantas Modificadas Genéticamente , Dominios Proteicos/fisiología
20.
Sci Rep ; 6: 35560, 2016 10 20.
Artículo en Inglés | MEDLINE | ID: mdl-27762322

RESUMEN

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.


Asunto(s)
Bacillus thuringiensis/química , Proteínas Bacterianas , Bacteriocinas , Proteínas y Péptidos de Choque por Frío , Proteínas Bacterianas/química , Proteínas Bacterianas/aislamiento & purificación , Bacteriocinas/química , Bacteriocinas/aislamiento & purificación , Proteínas y Péptidos de Choque por Frío/química , Proteínas y Péptidos de Choque por Frío/aislamiento & purificación , Concentración de Iones de Hidrógeno , Dominios Proteicos , Estabilidad Proteica
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