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1.
Annu Rev Genet ; 55: 377-400, 2021 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-34530639

RESUMO

Bacteria often encounter temperature fluctuations in their natural habitats and must adapt to survive. The molecular response of bacteria to sudden temperature upshift or downshift is termed the heat shock response (HSR) or the cold shock response (CSR), respectively. Unlike the HSR, which activates a dedicated transcription factor that predominantly copes with heat-induced protein folding stress, the CSR is mediated by a diverse set of inputs. This review provides a picture of our current understanding of the CSR across bacteria. The fundamental aspects of CSR involved in sensing and adapting to temperature drop, including regulation of membrane fluidity, protein folding, DNA topology, RNA metabolism, and protein translation, are discussed. Special emphasis is placed on recent findings of a CSR circuitry in Escherichia coli mediated by cold shock family proteins and RNase R that monitors and modulates messenger RNA structure to facilitate global translation recovery during acclimation.


Assuntos
Temperatura Baixa , Resposta ao Choque Frio , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Resposta ao Choque Frio/genética , Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica , RNA Mensageiro/genética
2.
EMBO J ; 42(14): e113168, 2023 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-37248947

RESUMO

Enhanced expression of the cold-shock protein RNA binding motif 3 (RBM3) is highly neuroprotective both in vitro and in vivo. Whilst upstream signalling pathways leading to RBM3 expression have been described, the precise molecular mechanism of RBM3 cold induction remains elusive. To identify temperature-dependent modulators of RBM3, we performed a genome-wide CRISPR-Cas9 knockout screen using RBM3-reporter human iPSC-derived neurons. We found that RBM3 mRNA and protein levels are robustly regulated by several splicing factors, with heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) being the strongest positive regulator. Splicing analysis revealed that moderate hypothermia significantly represses the inclusion of a poison exon, which, when retained, targets the mRNA for nonsense-mediated decay. Importantly, we show that HNRNPH1 mediates this cold-dependent exon skipping via its thermosensitive interaction with a G-rich motif within the poison exon. Our study provides novel mechanistic insights into the regulation of RBM3 and provides further targets for neuroprotective therapeutic strategies.


Assuntos
Venenos , Humanos , Proteínas e Peptídeos de Choque Frio/metabolismo , Temperatura Baixa , RNA Mensageiro/genética , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo
3.
Mol Cell ; 75(6): 1188-1202.e11, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31399345

RESUMO

The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment is converted to an environment of embryonic-driven development through dramatic reprogramming. However, how maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) modification in zebrafish early embryos, we found that m5C-modified maternal mRNAs display higher stability than non-m5C-modified mRNAs during MZT. We discovered that Y-box binding protein 1 (Ybx1) preferentially recognizes m5C-modified mRNAs through π-π interactions with a key residue, Trp45, in Ybx1's cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Together with the mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates an unexpected mechanism of RNA m5C-regulated maternal mRNA stabilization during zebrafish MZT, highlighting the critical role of m5C mRNA modification in early development.


Assuntos
5-Metilcitosina/metabolismo , Embrião não Mamífero/embriologia , Desenvolvimento Embrionário/fisiologia , Estabilidade de RNA/fisiologia , RNA Mensageiro Estocado/metabolismo , Peixe-Zebra/embriologia , Animais , Células HeLa , Humanos , Camundongos , RNA Mensageiro Estocado/genética , Peixe-Zebra/genética
4.
Mol Cell ; 70(2): 274-286.e7, 2018 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-29628307

RESUMO

Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. Whereas the circuitry controlling the heat shock response is well understood, that controlling the E. coli cold shock adaptation program is not. We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases, and open reading frame (ORF)-wide mRNA secondary structure decreases. To identify the regulatory system controlling this process, we screened for players required for increased translation. We identified a two-member mRNA surveillance system that enables recovery of translation during acclimation: RNase R assures appropriate mRNA degradation and the Csps dynamically adjust mRNA secondary structure to globally modulate protein expression level. An autoregulatory switch in which Csps tune their own expression to cellular demand enables dynamic control of global translation. The universality of Csps in bacteria suggests broad utilization of this control mechanism.


Assuntos
Temperatura Baixa , Resposta ao Choque Frio , Escherichia coli/genética , RNA Bacteriano/genética , RNA Mensageiro/genética , Regiões 5' não Traduzidas , Proteínas e Peptídeos de Choque Frio/genética , Proteínas e Peptídeos de Choque Frio/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Exorribonucleases/genética , Exorribonucleases/metabolismo , Regulação Bacteriana da Expressão Gênica , Conformação de Ácido Nucleico , Biossíntese de Proteínas , Estabilidade de RNA , RNA Bacteriano/química , RNA Bacteriano/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Relação Estrutura-Atividade
5.
Mol Cell ; 71(2): 271-283.e5, 2018 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-30029005

RESUMO

LIN28 is a bipartite RNA-binding protein that post-transcriptionally inhibits the biogenesis of let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remain poorly understood because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD), which binds a GGAG-like element in the precursor, and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U)GAU motif. This motif partitions the let-7 microRNAs into two subclasses, precursors with both CSD and ZKD binding sites (CSD+) and precursors with ZKD but no CSD binding sites (CSD-). LIN28 in vivo recognition-and subsequent 3' uridylation and degradation-of CSD+ precursors is more efficient, leading to their stronger suppression in LIN28-activated cells and cancers. Thus, CSD binding sites amplify the regulatory effects of LIN28.


Assuntos
MicroRNAs/metabolismo , Proteínas de Ligação a RNA/metabolismo , Animais , Sequência de Bases , Células-Tronco Embrionárias , Células Hep G2 , Humanos , Células K562 , Camundongos , MicroRNAs/genética , Modelos Moleculares , Conformação de Ácido Nucleico , Domínios Proteicos , Estrutura Terciária de Proteína , Precursores de RNA/metabolismo , Proteínas de Ligação a RNA/genética
6.
Mol Cell ; 68(4): 686-697.e3, 2017 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-29149596

RESUMO

The evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One useful but challenging situation is a switch between life and death depending on environment. Here are presented "essentializer" and "cryodeath" circuits, which act as kill switches in Escherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable. Both kill switches were shown to maintain functionality in vitro for at least 140 generations. Additionally, cryodeath was shown to control the growth environment of a population, with an escape frequency of less than 1 in 105 after 10 days of growth in the mammalian gut.


Assuntos
DNA Bacteriano , Evolução Molecular Direcionada , Escherichia coli K12 , Proteínas de Escherichia coli , Animais , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Escherichia coli K12/genética , Escherichia coli K12/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Camundongos , Camundongos Endogâmicos BALB C
7.
Infect Immun ; : e0001124, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38920386

RESUMO

Cold shock proteins (Csp) are pivotal nucleic acid binding proteins known for their crucial roles in the physiology and virulence of various bacterial pathogens affecting plant, insect, and mammalian hosts. However, their significance in bacterial pathogens of teleost fish remains unexplored. Aeromonas salmonicida subsp. salmonicida (hereafter A. salmonicida) is a psychrotrophic pathogen and the causative agent of furunculosis in marine and freshwater fish. Four csp genes (cspB, cspD, cspA, and cspC) have been identified in the genome of A. salmonicida J223 (wild type). Here, we evaluated the role of DNA binding proteins, CspB and CspD, in A. salmonicida physiology and virulence in lumpfish (Cyclopterus lumpus). A. salmonicida ΔcspB, ΔcspD, and the double ΔcspBΔcspD mutants were constructed and characterized. A. salmonicida ΔcspB and ΔcspBΔcspD mutants showed a faster growth at 28°C, and reduced virulence in lumpfish. A. salmonicida ΔcspD showed a slower growth at 28°C, biofilm formation, lower survival in low temperatures and freezing conditions (-20°C, 0°C, and 4°C), deficient in lipopolysaccharide synthesis, and low virulence in lumpfish. Additionally, ΔcspBΔcspD mutants showed less survival in the presence of bile compared to the wild type. Transcriptome analysis revealed that 200, 37, and 921 genes were differentially expressed in ΔcspB, ΔcspD, and ΔcspBΔcspD, respectively. In ΔcspB and ΔcspBΔcspD virulence genes in the chromosome and virulence plasmid were downregulated. Our analysis indicates that CspB and CspD mostly act as a transcriptional activator, influencing cell division (e.g., treB), virulence factors (e.g., aexT), and ultimately virulence.

8.
Kidney Int ; 106(2): 241-257, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38821446

RESUMO

DNA-binding protein-A (DbpA; gene: Ybx3) belongs to the cold shock protein family with known functions in cell cycling, transcription, translation, and tight junction communication. In chronic nephritis, DbpA is upregulated. However, its activities in acute injury models, such as kidney ischemia/reperfusion injury (IRI), are unclear. To study this, mice harboring Ybx3+/+, Ybx3+/- or the Ybx3-/- genotype were characterized over 24 months and following experimental kidney IRI. Mitochondrial function, number and integrity were analyzed by mitochondrial stress tests, MitoTracker staining and electron microscopy. Western Blot, immunohistochemistry and flow cytometry were performed to quantify tubular cell damage and immune cell infiltration. DbpA was found to be dispensable for kidney development and tissue homeostasis under healthy conditions. Furthermore, endogenous DbpA protein localizes within mitochondria in primary tubular epithelial cells. Genetic deletion of Ybx3 elevates the mitochondrial membrane potential, lipid uptake and metabolism, oxygen consumption rates and glycolytic activities of tubular epithelial cells. Ybx3-/- mice demonstrated protection from IRI with less immune cell infiltration, endoplasmic reticulum stress and tubular cell damage. A presumed protective mechanism was identified via upregulated antioxidant activities and reduced ferroptosis, when Ybx3 was deleted. Thus, our studies reveal DbpA acts as a mitochondrial protein with profound adverse effects on cell metabolism and highlights a protective effect against IRI when Ybx3 is genetically deleted. Hence, preemptive DbpA targeting in situations with expected IRI, such as kidney transplantation or cardiac surgery, may preserve post-procedure kidney function.


Assuntos
Camundongos Knockout , Mitocôndrias , Traumatismo por Reperfusão , Animais , Traumatismo por Reperfusão/metabolismo , Traumatismo por Reperfusão/genética , Traumatismo por Reperfusão/patologia , Mitocôndrias/metabolismo , Mitocôndrias/patologia , Camundongos , Masculino , Camundongos Endogâmicos C57BL , Modelos Animais de Doenças , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Ligação a DNA/deficiência , Potencial da Membrana Mitocondrial , Rim/patologia , Rim/metabolismo
9.
Protein Expr Purif ; 215: 106413, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38065246

RESUMO

Interferon (IFN)-λ1, a member of type III IFN, possesses unique antiviral, anti-tumor, and immune modulation properties. IFN-λ alone or combined with other drugs is considered an essential therapeutic regimen in the clinic. Obtaining high-quality, biologically-active recombinant human IFN-λ1 (rhIFN-λ1) is of great practical significance. In this study, pCold-II-IFN-λ1 expression plasmid was correctly constructed, the rhIFN-λ1 was expressed in BL21(DE3) E.coli and reached the highest level under the optimal condition of 15 °C culture temperature and at 1 µg/L IPTG induction for 12 h. The soluble rhIFN-λ1 was purified by Ni-NTA affinity chromatography. The purified rhIFN-λ1 can effectively activate the JAK1-STAT1 signaling pathway and induce the expression of a large number of interferon-stimulated genes (ISG) including ISG15, ISG54, ISG56, TRAIL, OAS1, MX1, IRF7 and IRF9. In addition, rhIFN-λ1 can effectively inhibit the growth/proliferation of cervical cancer HeLa cells in a dose-dependent pattern. Collectively, the soluble rhIFN-λ1 was successfully expressed in BL21(DE3) E.coli with the cold-shock system, and the purified rhIFN-λ1 demonstrated excellent biological activity. This study lays a solid basis for acquiring high-quality rhIFN-λ1 and its clinical application.


Assuntos
Escherichia coli , Interferons , Humanos , Células HeLa , Proteínas Recombinantes/genética , Proteínas Recombinantes/farmacologia , Interferons/genética , Plasmídeos/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Interleucinas/genética
10.
Mol Breed ; 44(3): 18, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38390031

RESUMO

Cold shock domain proteins (CSPs), initially identified in Escherichia coli, have been demonstrated to play a positive role in cold resistance. Previous studies in wheat, rice, and Arabidopsis have indicated the functional conservation of CSPs in cold resistance between bacteria and higher plants. However, the biological functions of PbrCSPs in pear pollen tubes, which represent the fragile reproductive organs highly sensitive to low temperature, remain largely unknown. In this study, a total of 22 CSPs were identified in the seven Rosaceae species, with a focus on characterizing four PbrCSPs in pear (Pyrus bretschneideri Rehder). All four PbrCSPs were structurally conserved and responsive to the abiotic stresses, such as cold, high osmotic, and abscisic acid (ABA) treatments. PbrCSP1, which is specifically expressed in pear pollen tubes, was selected for further research. PbrCSP1 was localized in both the cytoplasm and nucleus. Suppressing the expression of PbrCSP1 significantly inhibited the pollen tube growth in vitro. Conversely, overexpression of PbrCSP1 promoted the growth of pear pollen tubes under the normal condition and, notably, under the cold environment at 4 °C. These findings highlight an essential role of PbrCSP1 in facilitating the normal growth and enhancing cold resistance in pear pollen tubes. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01457-w.

11.
Environ Res ; 244: 117933, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38097061

RESUMO

Despite reliable nitrite supply through partial denitrification, the adaptation of denitrifying bacteria to low temperatures remains elusive in partial denitrification and anammox (PDA) systems. Here, temporal differentiations of the structure, activity, and relevant cold-adaptation mechanism of functional bacteria were investigated in a lab-scale PDA bioreactor at decreased temperature. Although distinct denitrifying bacteria dominated after low-temperature stress, both short- and long-term stresses exerted differential selectivity towards the species with close phylogenetic distance. Species Azonexus sp.149 showed high superiority over Azonexus sp.384 under short-term stress, and long-term stress improved the adaptation of Aquabacterium sp.93 instead of Aquabacterium sp.184. The elevated transcription of nitrite reductase genes suggested that several denitrifying bacteria (e.g., Azonexus sp.149) could compete with anammox bacteria for nitrite. Species Rivicola pingtungensis and Azonexus sp.149 could adapt through various adaptation pathways, such as the two-component system, cold shock protein (CSP), membrane alternation, and electron transport chain. By contrast, species Zoogloea sp.273 and Aquabacterium sp.93 mainly depended on the CSP and oxidative stress response. This study largely deepens our understanding of the performance deterioration in PDA systems during cold shock and provides several references for efficient adaptation to seasonal temperature fluctuation.


Assuntos
Desnitrificação , Nitritos , Nitritos/metabolismo , Temperatura , Oxidação Anaeróbia da Amônia , Filogenia , Bactérias/genética , Bactérias/metabolismo , Oxirredução , Reatores Biológicos/microbiologia , Nitrogênio/metabolismo , Esgotos
12.
Mar Drugs ; 22(6)2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38921549

RESUMO

Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.


Assuntos
Gammaproteobacteria , Genoma Bacteriano , Genômica , Filogenia , Regiões Antárticas , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Genômica/métodos , Psychrobacter/genética , Psychrobacter/isolamento & purificação , Pseudoalteromonas/genética , Família Multigênica
13.
J Therm Biol ; 119: 103775, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38211547

RESUMO

Cold water immersion (CWI) evokes the life-threatening reflex cold shock response (CSR), inducing hyperventilation, increasing cardiac arrhythmias, and increasing drowning risk by impairing safety behaviour. Repeated CWI induces CSR habituation (i.e., diminishing response with same stimulus magnitude) after ∼4 immersions, with variation between studies. We quantified the magnitude and coefficient of variation (CoV) in the CSR in a systematic review and meta-analysis with search terms entered to Medline, SportDiscus, PsychINFO, Pubmed, and Cochrane Central Register. Random effects meta-analyses, including effect sizes (Cohen's d) from 17 eligible groups (k), were conducted for heart rate (HR, n = 145, k = 17), respiratory frequency (fR, n = 73, k = 12), minute ventilation (Ve, n = 106, k = 10) and tidal volume (Vt, n = 46, k=6). All CSR variables habituated (p < 0.001) with large or moderate pooled effect sizes: ΔHR -14 (10) bt. min-1 (d: -1.19); ΔfR -8 (7) br. min-1 (d: -0.78); ΔVe, -21.3 (9.8) L. min-1 (d: -1.64); ΔVt -0.4 (0.3) L -1. Variation was greatest in Ve (control vs comparator immersion: 32.5&24.7%) compared to Vt (11.8&12.1%). Repeated CWI induces CSR habituation potentially reducing drowning risk. We consider the neurophysiological and behavioural consequences.

14.
Int J Mol Sci ; 25(6)2024 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-38542352

RESUMO

Previously, we found for the first time the participation of osmolytes in adaptation to acidic conditions in three acidophilic fungi. Because trehalose can protect membranes, we hypothesized a relationship between osmolyte and membrane systems in adaptation to stressors. In the mycelium of Phlebiopsis gigantea, the level of osmolytes reaches 8% of the dry mass, while trehalose and arabitol make up 60% and 33% of the sum, respectively. Cold shock does not change the composition of osmolytes, heat shock causes a twofold increase in the trehalose level, and osmotic shock leads to a marked increase in the amount of trehalose and arabitol. Predominance of phospholipids (89% of the sum) and low proportions of sterols and sphingolipids are characteristic features of the membrane lipids' composition. Phosphatidic acids, along with phosphatidylethanolamines and phosphatidylcholines, are the main membrane lipids. The composition of the membrane lipids remains constant under all shocks. The predominance of linoleic (75% of the sum) and palmitic (20%) acids in phospholipids results in a high degree of unsaturation (1.5). Minor fluctuations in the fatty acid composition are observed under all shocks. The results demonstrate that maintaining or increasing the trehalose level provides stability in the membrane lipid composition during adaptation.


Assuntos
Basidiomycota , Lipídeos de Membrana , Polyporales , Álcoois Açúcares , Trealose , Pressão Osmótica , Fosfolipídeos
15.
J Bacteriol ; 205(1): e0038222, 2023 01 26.
Artigo em Inglês | MEDLINE | ID: mdl-36507682

RESUMO

Peptidoglycan (PG) is a unique and essential component of the bacterial cell envelope. It is made up of several linear glycan polymers cross-linked through covalently attached stem peptides making it a fortified mesh-like sacculus around the bacterial cytosolic membrane. In most bacteria, including Escherichia coli, the stem peptide is made up of l-alanine (l-Ala1), d-glutamate (d-Glu2), meso-diaminopimelic acid (mDAP3), d-alanine (d-Ala4), and d-Ala5 with cross-links occurring either between d-ala4 and mDAP3 or between two mDAP3 residues. Of these, the cross-links of the 4-3 (d-Ala4-mDAP3) type are the most predominant and are formed by penicillin-binding D,D-transpeptidases, whereas the formation of less frequent 3-3 linkages (mDAP3-mDAP3) is catalyzed by L,D-transpeptidases. In this study, we found that the frequency of the 3-3 cross-linkages increased upon cold shock in exponentially growing E. coli and that the increase was mediated by an L,D-transpeptidase, LdtD. We found that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation resulting in an increased abundance of 3-3 cross-linkages during cold shock. However, DeaD was also required for optimal expression of LdtD during growth at ambient temperature. Overall, our study finds that E. coli undergoes PG remodeling during cold shock by altering the frequency of 3-3 cross-linkages, implying a role for these modifications in conferring fitness and survival advantage to bacteria growing in diverse environmental conditions. IMPORTANCE Most bacteria are surrounded by a protective exoskeleton called peptidoglycan (PG), an extensively cross-linked mesh-like macromolecule. In bacteria, such as Escherichia coli, the cross-links in the PG are of two types: a major fraction is of 4-3 type whereas a minor fraction is of 3-3 type. Here, we showed that E. coli exposed to cold shock had elevated levels of 3-3 cross-links due to the upregulation of an enzyme, LdtD, that catalyzed their formation. We showed that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation, resulting in increased 3-3 cross-links during cold shock. Our results suggest that PG remodeling contributes to the survival and fitness of bacteria growing in conditions of cold stress.


Assuntos
Escherichia coli , Peptidil Transferases , Peptidil Transferases/análise , Peptidil Transferases/metabolismo , Resposta ao Choque Frio , Peptidoglicano/metabolismo , Parede Celular/metabolismo , Bactérias/metabolismo
16.
Am J Physiol Cell Physiol ; 325(2): C456-C470, 2023 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-37399499

RESUMO

In aging kidneys, a decline of function resulting from extracellular matrix (ECM) deposition and organ fibrosis is regarded as "physiological." Whether a direct link between high salt intake and fibrosis in aging kidney exists autonomously from arterial hypertension is unclear. This study explores kidney intrinsic changes (inflammation, ECM derangement) induced by a high-salt diet (HSD) in a murine model lacking arterial hypertension. The contribution of cold shock Y-box binding protein (YB-1) as a key orchestrator of organ fibrosis to the observed differences is determined by comparison with a knockout strain (Ybx1ΔRosaERT+TX). Comparisons of tissue from mice fed with normal-salt diet (NSD, standard chow) or high-salt diet (HSD, 4% NaCl in chow; 1% NaCl in water) for up to 16 mo revealed that with HSD tubular cell numbers decrease and tubulointerstitial scarring [periodic acid-Schiff (PAS), Masson's trichrome, Sirius red staining] prevails. In Ybx1ΔRosaERT+TX animals tubular cell damage, a loss of cell contacts with profound tubulointerstitial alterations, and tubular cell senescence was seen. A distinct tubulointerstitial distribution of fibrinogen, collagen type VI, and tenascin-C was detected under HSD, transcriptome analyses determined patterns of matrisome regulation. Temporal increase of immune cell infiltration was seen under HSD of wild type, but not Ybx1ΔRosaERT+TX animals. In vitro Ybx1ΔRosaERT+TX bone marrow-derived macrophages exhibited a defect in polarization (IL-4/IL-13) and abrogated response to sodium chloride. Taken together, HSD promotes progressive kidney fibrosis with premature cell aging, ECM deposition, and immune cell recruitment that is exacerbated in Ybx1ΔRosaERT+TX animals.NEW & NOTEWORTHY Short-term experimental studies link excessive sodium ingestion with extracellular matrix accumulation and inflammatory cell recruitment, yet long-term data are scarce. Our findings with a high-salt diet over 16 mo in aging mice pinpoints to a decisive tipping point after 12 mo with tubular stress response, skewed matrisome transcriptome, and immune cell infiltration. Cell senescence was aggravated in knockout animals for cold shock Y-box binding protein (YB-1), suggesting a novel protective protein function.


Assuntos
Hipertensão , Nefropatias , Camundongos , Animais , Cloreto de Sódio , Rim/metabolismo , Nefropatias/induzido quimicamente , Nefropatias/genética , Nefropatias/patologia , Inflamação/metabolismo , Envelhecimento , Hipertensão/metabolismo , Cloreto de Sódio na Dieta/efeitos adversos , Fibrose , Ingestão de Alimentos
17.
Mol Microbiol ; 117(1): 67-85, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34379855

RESUMO

Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homolog to have an RNA-related function. We apply an in silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic coconservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.


Assuntos
Bacteroides thetaiotaomicron/genética , Bacteroides/genética , Microbioma Gastrointestinal , Regulação Bacteriana da Expressão Gênica , Genômica , Pequeno RNA não Traduzido/metabolismo , Proteínas de Bactérias , Bacteroides/metabolismo , Bacteroides thetaiotaomicron/metabolismo , Biologia Computacional , RNA Bacteriano/genética , RNA Bacteriano/metabolismo , Pequeno RNA não Traduzido/genética , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Sintenia
18.
Plant Biotechnol J ; 21(6): 1103-1105, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36917445

RESUMO

Nicotiana benthamiana is increasingly used for transient gene expression to produce antibodies, vaccines, and other pharmaceutical proteins but transient gene expression is low in fully developed, 6-8-week old plants. This low gene expression is thought to be caused by the perception of the cold shock protein (CSP) of Agrobacterium tumefaciens. The CSP receptor is contested because both NbCSPR and NbCORE have been claimed to perceive CSP. Here, we demonstrate that CSP perception is abolished in 6-week-old plants silenced for NbCORE but not NbCSPR. Importantly, older NbCORE-silenced plants support a highly increased level of GFP fluorescence and protein upon agroinfiltration. The drastic increase in transient protein production in NbCORE-depleted plants offers new opportunities for molecular farming, where older plants with larger biomass can now be used for efficient protein expression.


Assuntos
Agrobacterium tumefaciens , Nicotiana , Nicotiana/metabolismo , Plantas Geneticamente Modificadas/genética , Agrobacterium tumefaciens/genética , Anticorpos/metabolismo
19.
Appl Microbiol Biotechnol ; 107(24): 7475-7488, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37755510

RESUMO

Geobacillus spp. are moderate thermophiles that can efficiently produce recombinant proteins. Considering the protein production exhibited by these species, we searched for robust promoters in Geobacillus kaustophilus HTA426. Transcriptome data revealed that several genes were highly expressed during the proliferative phase; their promoters were characterized using reporter assays with Venus fluorescent protein (VFP). The results suggested that the cspD promoter (PcspD) directed robust vfp expression at 60°C in G. kaustophilus. Although cspD potentially encodes a cold-shock protein, PcspD functioned at elevated temperatures. The promoter strongly functioned even in Escherichia coli; this prevented the cloning of some genes (e.g., vfp) downstream of it on a plasmid vector via E. coli-based genetic manipulation. Consequently, we generated a mutated PcspD that functioned inefficiently in E. coli and constructed the pGKE124 plasmid using the mutant promoter. The plasmid could carry vfp in E. coli and afford the production of VFP in G. kaustophilus at a yield of 390 mg/L. pGKE124 directed a similar production in other thermophilic species; the highest yield was observed in Geobacillus thermodenitrificans K1041. Several proteins could be produced using a system involving G. thermodenitrificans K1041 and pGKE124. Notably, the extracellular production of xylanase at a yield of 1 g/L was achieved using this system. Although the leaky production of nonsecretory proteins was observed, we developed a simple process to collectively purify recombinant proteins from the intracellular and extracellular fractions. The findings presented there propose an effective host-vector system for the production of recombinant proteins at elevated temperatures. KEY POINTS: • A thermophilic system to produce recombinant proteins was constructed. • The system produced diverse proteins using inexpensive media at elevated temperatures. • The system produced an extracellular protein at a yield of 1 g/L of culture.


Assuntos
Escherichia coli , Temperatura , Escherichia coli/genética , Plasmídeos/genética , Proteínas Recombinantes/genética
20.
J Therm Biol ; 118: 103727, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37866096

RESUMO

Cold water immersion (CWI) may provide benefits for physical and mental health. Our purpose was to investigate the effects of an acute bout of CWI on vascular shear stress and affect (positive and negative). Sixteen healthy adults (age: 23 ± 4 y; (9 self-reported men and 7 self-reported women) completed one 15-min bout of CWI (10 °C). Self-reported affect (positive and negative) was assessed at pre-CWI (Pre), 30-min post-immersion, and 180-min post-immersion in all participants. Brachial artery diameter and blood velocity were measured (Doppler ultrasound) at Pre, after 1-min and 15-min of CWI, and 30-min post-immersion (n = 8). Total, antegrade, and retrograde shear stress, oscillatory shear index (OSI), and forearm vascular conductance (FVC) were calculated. Venous blood samples were collected at Pre, after 1-min and 15-min of CWI, 30-min post-immersion, and 180-min post-immersion (n = 8) to quantify serum ß-endorphins and cortisol. Data were analyzed using a one-way ANOVA with Fisher's least significance difference and compared to Pre. Positive affect did not change (ANOVA p = 0.450) but negative affect was lower at 180-min post-immersion (p < 0.001). FVC was reduced at 15-min of CWI and 30-min post-immersion (p < 0.020). Total and antegrade shear and OSI were reduced at 30-min post-immersion (p < 0.040) but there were no differences in retrograde shear (ANOVA p = 0.134). ß-endorphins did not change throughout the trial (ANOVA p = 0.321). Cortisol was lower at 180-min post-immersion (p = 0.014). An acute bout of CWI minimally affects shear stress patterns but may benefit mental health by reducing negative feelings and cortisol levels.


Assuntos
Temperatura Baixa , Endorfinas , Adulto , Feminino , Humanos , Masculino , Adulto Jovem , Afeto , Hidrocortisona , Imersão , Água
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