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1.
Cells ; 13(19)2024 Oct 09.
Article in English | MEDLINE | ID: mdl-39404427

ABSTRACT

Human mesenchymal stem cells modulate the immune response and are good candidates for cell therapy in neuroinflammatory brain disorders affecting both adult and premature infants. Recent evidence indicates that through their secretome, mesenchymal stem cells direct microglia, brain-resident immune cells, toward pro-regenerative functions, but the mechanisms underlying microglial phenotypic transition are still under investigation. Using an in vitro coculture approach combined with transcriptomic analysis, we identified the extracellular matrix as the most relevant pathway altered by the human mesenchymal stem cell secretome in the response of microglia to inflammatory cytokines. We confirmed extracellular matrix remodeling in microglia exposed to the mesenchymal stem cell secretome via immunofluorescence analysis of the matrix component fibronectin and the extracellular crosslinking enzyme transglutaminase-2. Furthermore, an analysis of hallmark microglial functions revealed that changes in the extracellular matrix enhance ruffle formation by microglia and cell motility. These findings point to extracellular matrix changes, associated plasma membrane remodeling, and enhanced microglial migration as novel mechanisms by which mesenchymal stem cells contribute to the pro-regenerative microglial transition.


Subject(s)
Extracellular Matrix , Mesenchymal Stem Cells , Microglia , Umbilical Cord , Humans , Mesenchymal Stem Cells/metabolism , Mesenchymal Stem Cells/cytology , Extracellular Matrix/metabolism , Microglia/metabolism , Umbilical Cord/cytology , Cell Movement , Protein Glutamine gamma Glutamyltransferase 2/metabolism , Coculture Techniques , Cytokines/metabolism
2.
Blood ; 143(14): 1399-1413, 2024 Apr 04.
Article in English | MEDLINE | ID: mdl-38194688

ABSTRACT

ABSTRACT: SETBP1 mutations are found in various clonal myeloid disorders. However, it is unclear whether they can initiate leukemia, because SETBP1 mutations typically appear as later events during oncogenesis. To answer this question, we generated a mouse model expressing mutated SETBP1 in hematopoietic tissue: this model showed profound alterations in the differentiation program of hematopoietic progenitors and developed a myeloid neoplasm with megakaryocytic dysplasia, splenomegaly, and bone marrow fibrosis, prompting us to investigate SETBP1 mutations in a cohort of 36 triple-negative primary myelofibrosis (TN-PMF) cases. We identified 2 distinct subgroups, one carrying SETBP1 mutations and the other completely devoid of somatic variants. Clinically, a striking difference in disease aggressiveness was noted, with patients with SETBP1 mutation showing a much worse clinical course. In contrast to myelodysplastic/myeloproliferative neoplasms, in which SETBP1 mutations are mostly found as a late clonal event, single-cell clonal hierarchy reconstruction in 3 patients with TN-PMF from our cohort revealed SETBP1 to be a very early event, suggesting that the phenotype of the different SETBP1+ disorders may be shaped by the opposite hierarchy of the same clonal SETBP1 variants.


Subject(s)
Hematopoietic System , Myelodysplastic-Myeloproliferative Diseases , Myeloproliferative Disorders , Primary Myelofibrosis , Animals , Mice , Humans , Primary Myelofibrosis/genetics , Myeloproliferative Disorders/genetics , Mutation , Carrier Proteins/genetics , Nuclear Proteins/genetics
3.
Nat Commun ; 14(1): 3212, 2023 06 03.
Article in English | MEDLINE | ID: mdl-37270547

ABSTRACT

Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans.


Subject(s)
Enhancer Elements, Genetic , Histones , Humans , Histones/genetics , Histones/metabolism , Enhancer Elements, Genetic/genetics , Cell Differentiation/genetics , Chromatin/genetics , Promoter Regions, Genetic/genetics
4.
Blood ; 141(21): 2615-2628, 2023 05 25.
Article in English | MEDLINE | ID: mdl-36735903

ABSTRACT

Recent investigations have improved our understanding of the molecular aberrations supporting Waldenström macroglobulinemia (WM) biology; however, whether the immune microenvironment contributes to WM pathogenesis remains unanswered. First, we showed how a transgenic murine model of human-like lymphoplasmacytic lymphoma/WM exhibits an increased number of regulatory T cells (Tregs) relative to control mice. These findings were translated into the WM clinical setting, in which the transcriptomic profiling of Tregs derived from patients with WM unveiled a peculiar WM-devoted messenger RNA signature, with significant enrichment for genes related to nuclear factor κB-mediated tumor necrosis factor α signaling, MAPK, and PI3K/AKT, which was paralleled by a different Treg functional phenotype. We demonstrated significantly higher Treg induction, expansion, and proliferation triggered by WM cells, compared with their normal cellular counterpart; with a more profound effect within the context of CXCR4C1013G-mutated WM cells. By investigating the B-cell-to-T-cell cross talk at single-cell level, we identified the CD40/CD40-ligand as a potentially relevant axis that supports WM cell-Tregs interaction. Our findings demonstrate the existence of a Treg-mediated immunosuppressive phenotype in WM, which can be therapeutically reversed by blocking the CD40L/CD40 axis to inhibit WM cell growth.


Subject(s)
Lymphoma, B-Cell , Waldenstrom Macroglobulinemia , Humans , Animals , Mice , Waldenstrom Macroglobulinemia/pathology , CD40 Ligand/genetics , Phosphatidylinositol 3-Kinases , Ligands , Signal Transduction , Lymphoma, B-Cell/complications , Tumor Microenvironment
5.
Rev. enferm. UFPE on line ; 17(1): [1-13], jan. 2023. graf, tab
Article in English, Portuguese | BDENF - Nursing | ID: biblio-1511741

ABSTRACT

Objetivo: analisar os traços latentes do conhecimento acerca da diabetes e do letramento em saúde de adultos com diabetes mellitus tipo 2. Método: pesquisa descritiva exploratória, de recorte transversal e abordagem quantitativa, com 33 participantes da Região Metropolitana de Curitiba, Paraná, Brasil. Os dados foram coletados no primeiro trimestre de 2020, por questionário sociodemográfico e clínico, Spoken Knowledge in Low Literacy Patients with Diabetes e Eight-Item Health Literacy Assessment Tool. Analisaram-se os dados descritivamente, pela Teoria de Resposta ao Item, alfa de Cronbach e Coeficiente de Correlação de Pearson. Resultados: predomínio do sexo feminino (n = 23), com média de idade de 57,0 ± 8,08 anos, escolaridade de 7,72 ± 3,69 anos e renda familiar de 3.118,18 ± 3.063,28. O traço latente com maior dificuldade do conhecimento da diabetes foi relativo aos sinais e sintomas da hiperglicemia e hipoglicemia. Constatou-se correlação positiva moderada (r = 0,4260) entre conhecimento da doença e renda familiar. Definir as fontes seguras da Internet foi o item com a menor dificuldade média do letramento em saúde. Conclusão: os traços latentes dos dois instrumentos, expressos pelos participantes, revelou as maiores dificuldades para manter o controle da doença, permitindo o desenvolvimento de ações para as lacunas.(AU)


Objective: to analyze the latent traits of knowledge about diabetes and health literacy of adults with type 2 diabetes mellitus. Method: an exploratory, descriptive, cross-sectional, and quantitative study was conducted with 33 participants from the Metropolitan Region of Curitiba, Paraná, Brazil. Data were collected in the first quarter of 2020 using a sociodemographic and clinical questionnaire, the Spoken Knowledge in Low Literacy Patients with Diabetes questionnaire, and the Eight-Item Health Literacy Assessment Tool. Data were analyzed descriptively, using Item Response Theory, Cronbach's alpha, and Pearson's Correlation Coefficient. Results: there was a female predominance (n = 23), with a mean age of 57.0 ± 8.08 years, education of 7.72± 3.69 years, and family income of 3,118.18 ± 3,063.28. The latent trait with the greatest difficulty in understanding diabetes was related to the signs and symptoms of hyperglycemia and hypoglycemia. A moderate positive correlation (r = 0.4260) was found between knowledge of the disease and family income. Defining high-quality internet sources was the item with the lowest average difficulty in health literacy. Conclusion: the latent traits of the two instruments, expressed by the participants, revealed the main difficulties in maintaining disease control, supporting the development of actions to address the gaps.(AU)


Objetivo: analizar los rasgos latentes del conocimiento sobre diabetes y la alfabetización en salud de adultos con diabetes mellitus tipo 2. Método: investigación descriptiva exploratoria, transversal y cuantitativa, con 33 participantes de Región Metropolitana de Curitiba, Paraná, Brasil. Los datos se recopilaron en el primer trimestre de 2020, utilizando un cuestionario sociodemográfico y clínico y los cuestionarios Spoken Knowledge in Low Literacy Patients with Diabetes y Eight-Item Health Literacy Assessment Tool. Los datos fueron analizados descriptivamente utilizando la Teoría de Respuesta al Ítem, el Alfa de Cronbach y el Coeficiente de Correlación de Pearson. Resultados: predominio del sexo femenino (n = 23), con media de edad de 57,0 ± 8,08 años, escolaridad de 7,72 ± 3,69 años y renta de 3.118,18 ± 3.063,28. El rasgo latente con mayor dificultad fue relacionado con los signos y síntomas de hiperglucemia e hipoglucemia. Se encontró una correlación positiva moderada (r = 0,4260) entre el conocimiento de la enfermedad y la renta. Definir fuentes seguras de Internet fue el ítem con menor dificultad promedio en alfabetización en salud. Conclusión: los rasgos latentes de los dos instrumentos revelaron las mayores dificultades para mantener el control de la enfermedad, contribuyendo a el desarrollo de acciones.(AU)


Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Aged , Psychometrics , Health Knowledge, Attitudes, Practice , Adult Health , Diabetes Mellitus, Type 2 , Health Literacy , Cross-Sectional Studies , Surveys and Questionnaires
6.
Cancers (Basel) ; 14(21)2022 Oct 31.
Article in English | MEDLINE | ID: mdl-36358796

ABSTRACT

Within the context of precision medicine, the scientific community is giving particular attention to early diagnosis and intervention, guided by non-invasive methodologies. Liquid biopsy (LBx) is a recent laboratory approach consisting of a non-invasive blood draw, which allows the detection of information about potential prognostic factors, or markers to be used for diagnostic purposes; it might also allow the clinician to establish a treatment regimen and predict a patient's response. Since the discovery of circulating tumor cells (CTCs) in the nineteenth century, the possibility of integrating LBx into clinical practice has been explored, primarily because of its safeness and easy execution: indeed, compared to solid biopsy, sampling-related risks are less of a concern, and the quickness and repeatability of the process could help confirm a prompt diagnosis or to further corroborate the existence of a metastatic spreading of the disease. LBx's usefulness has been consolidated in a narrow range of oncological settings, first of all, non-small cell lung carcinoma (NSCLC), and it is now gradually being assessed also in lymphoproliferative diseases, such as acute lymphocytic leukemia (ALL), B-cell lymphomas, and multiple myeloma. The present review aims to summarize LBx's overall characteristics (such as its advantages and flaws, collection and analysis methodologies, indications, and targets of the test), and to highlight the applications of this technique within the specific field of B-cell malignancies. The perspectives on how such a simple and convenient technique could improve hemato-oncological clinical practice are broadly encouraging, yet far from a complete integration in routine clinical settings.

7.
iScience ; 25(6): 104487, 2022 Jun 17.
Article in English | MEDLINE | ID: mdl-35677393

ABSTRACT

A key task of genomic surveillance of infectious viral diseases lies in the early detection of dangerous variants. Unexpected help to this end is provided by the analysis of deep sequencing data of viral samples, which are typically discarded after creating consensus sequences. Such analysis allows one to detect intra-host low-frequency mutations, which are a footprint of mutational processes underlying the origination of new variants. Their timely identification may improve public-health decision-making with respect to traditional approaches exploiting consensus sequences. We present the analysis of 220,788 high-quality deep sequencing SARS-CoV-2 samples, showing that many spike and nucleocapsid mutations of interest associated to the most circulating variants, including Beta, Delta, and Omicron, might have been intercepted several months in advance. Furthermore, we show that a refined genomic surveillance system leveraging deep sequencing data might allow one to pinpoint emerging mutation patterns, providing an automated data-driven support to virologists and epidemiologists.

8.
Viruses ; 15(1)2022 12 20.
Article in English | MEDLINE | ID: mdl-36680048

ABSTRACT

We present a large-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) substitutions, considering 1,585,456 high-quality raw sequencing samples, aimed at investigating the existence and quantifying the effect of mutational processes causing mutations in SARS-CoV-2 genomes when interacting with the human host. As a result, we confirmed the presence of three well-differentiated mutational processes likely ruled by reactive oxygen species (ROS), apolipoprotein B editing complex (APOBEC), and adenosine deaminase acting on RNA (ADAR). We then evaluated the activity of these mutational processes in different continental groups, showing that some samples from Africa present a significantly higher number of substitutions, most likely due to higher APOBEC activity. We finally analyzed the activity of mutational processes across different SARS-CoV-2 variants, and we found a significantly lower number of mutations attributable to APOBEC activity in samples assigned to the Omicron variant.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Mutation , Africa
9.
PLoS One ; 16(7): e0254232, 2021.
Article in English | MEDLINE | ID: mdl-34214145

ABSTRACT

The type VI secretion system (T6SS) is a widespread mechanism of protein delivery into target cells, present in more than a quarter of all sequenced Gram-negative bacteria. The T6SS constitutes an important virulence factor, as it is responsible for targeting effectors in both prokaryotic and eukaryotic cells. The T6SS comprises a tail structure tethered to the cell envelope via a trans-envelope complex. In most T6SS, the membrane complex is anchored to the cell wall by the TagL accessory protein. In this study, we report the first crystal structure of a peptidoglycan-binding domain of TagL. The fold is conserved with members of the OmpA/Pal/MotB family, and more importantly, the peptidoglycan binding site is conserved. This structure further exemplifies how proteins involved in anchoring to the cell wall for different cellular functions rely on an interaction network with peptidoglycan strictly conserved.


Subject(s)
Bacterial Proteins/metabolism , Cell Wall/metabolism , Peptidoglycan/metabolism , Protein Domains/physiology , Type VI Secretion Systems/metabolism , Gram-Negative Bacteria/metabolism , Virulence Factors/metabolism
10.
Viruses ; 12(8)2020 08 11.
Article in English | MEDLINE | ID: mdl-32796652

ABSTRACT

Virulent phages infecting L. lactis, an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca2+. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected.


Subject(s)
Bacteriophages/chemistry , Lactococcus lactis/virology , Viral Tail Proteins/chemistry , Bacteriophages/genetics , Crystallography, X-Ray , Microscopy, Electron , Models, Molecular , Protein Binding , Protein Conformation , Single-Domain Antibodies/chemistry , Viral Tail Proteins/ultrastructure
11.
Methods Enzymol ; 642: 151-167, 2020.
Article in English | MEDLINE | ID: mdl-32828251

ABSTRACT

OBPs and CSPs are small soluble proteins used by organisms as shuttle to transport odorant molecules between air and the membrane-embedded receptors. Deciphering the interactions of these proteins with their ligands at a molecular level may give clue on the function and specificity of the olfactory chain. To reach this goal, protein crystallography is very helpful with more than hundred entries available in the protein data bank (PDB). In this chapter, we present the peculiarities of OBPs and CSPs concerning their crystallization and 3D structure determination by X-ray diffraction.


Subject(s)
Odorants , Receptors, Odorant , Carrier Proteins , Crystallography, X-Ray , Insect Proteins/metabolism , Phylogeny , Receptors, Odorant/genetics , Receptors, Odorant/metabolism
12.
Microb Biotechnol ; 13(6): 1765-1779, 2020 11.
Article in English | MEDLINE | ID: mdl-32525270

ABSTRACT

Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 Å resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP- or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.


Subject(s)
Lactococcus lactis , Viral Tail Proteins , Lactococcus lactis/genetics , Lactococcus lactis/metabolism , Protein Binding , Protein Conformation , Streptococcus thermophilus/genetics , Streptococcus thermophilus/metabolism , Viral Tail Proteins/genetics , Viral Tail Proteins/metabolism
13.
Viruses ; 12(5)2020 05 06.
Article in English | MEDLINE | ID: mdl-32384698

ABSTRACT

Bacteriophages can play beneficial roles in phage therapy and destruction of food pathogens. Conversely, they play negative roles as they infect bacteria involved in fermentation, resulting in serious industrial losses. Siphoviridae phages possess a long non-contractile tail and use a mechanism of infection whose first step is host recognition and binding. They have evolved adhesion devices at their tails' distal end, tuned to recognize specific proteinaceous or saccharidic receptors on the host's surface that span a large spectrum of shapes. In this review, we aimed to identify common patterns beyond this apparent diversity. To this end, we analyzed siphophage tail tips or baseplates, evaluating their known structures, where available, and uncovering patterns with bioinformatics tools when they were not. It was thereby identified that a triad formed by three proteins in complex, i.e., the tape measure protein (TMP), the distal tail protein (Dit), and the tail-associated lysozyme (Tal), is conserved in all phages. This common scaffold may harbor various functional extensions internally while it also serves as a platform for plug-in ancillary or receptor-binding proteins (RBPs). Finally, a group of siphophage baseplates involved in saccharidic receptor recognition exhibits an activation mechanism reminiscent of that observed in Myoviridae.


Subject(s)
Bacterial Proteins/metabolism , Bacteriophages/metabolism , Lactococcus lactis/metabolism , Siphoviridae/metabolism , Viral Tail Proteins/chemistry , Viral Tail Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacteriophages/chemistry , Bacteriophages/genetics , Crystallography, X-Ray , Lactococcus lactis/chemistry , Lactococcus lactis/genetics , Lactococcus lactis/virology , Receptors, Virus/genetics , Siphoviridae/chemistry , Siphoviridae/genetics , Viral Tail Proteins/genetics
14.
Mol Cell ; 76(6): 922-937.e7, 2019 12 19.
Article in English | MEDLINE | ID: mdl-31604602

ABSTRACT

In the arms race against bacteria, bacteriophages have evolved diverse anti-CRISPR proteins (Acrs) that block CRISPR-Cas immunity. Acrs play key roles in the molecular coevolution of bacteria with their predators, use a variety of mechanisms of action, and provide tools to regulate Cas-based genome manipulation. Here, we present structural and functional analyses of AcrIIA6, an Acr from virulent phages, exploring its unique anti-CRISPR action. Our cryo-EM structures and functional data of AcrIIA6 binding to Streptococcus thermophilus Cas9 (St1Cas9) show that AcrIIA6 acts as an allosteric inhibitor and induces St1Cas9 dimerization. AcrIIA6 reduces St1Cas9 binding affinity for DNA and prevents DNA binding within cells. The PAM and AcrIIA6 recognition sites are structurally close and allosterically linked. Mechanistically, AcrIIA6 affects the St1Cas9 conformational dynamics associated with PAM binding. Finally, we identify a natural St1Cas9 variant resistant to AcrIIA6 illustrating Acr-driven mutational escape and molecular diversification of Cas9 proteins.


Subject(s)
Bacteriophages/metabolism , CRISPR-Associated Protein 9/metabolism , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , DNA/metabolism , Streptococcus thermophilus/enzymology , Viral Proteins/metabolism , Allosteric Regulation , Bacteriophages/genetics , Binding Sites , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/ultrastructure , DNA/genetics , DNA/ultrastructure , Escherichia coli/enzymology , Escherichia coli/genetics , Humans , K562 Cells , Kinetics , Mutation , Protein Binding , Protein Conformation , Streptococcus thermophilus/genetics , Structure-Activity Relationship , Viral Proteins/genetics , Viral Proteins/ultrastructure
15.
Res Microbiol ; 169(10): 628-637, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30138723

ABSTRACT

General knowledge on the diversity and biology of microbial viruses infecting bacterial hosts from extreme acidic environments lags behind most other econiches. In this study, we analyse the AcaML1 virus occurrence in the taxon, its genetic composition and infective behaviour under standard acidic and SOS-inducing conditions to assess its integrity and functionality. Occurrence analysis in sequenced acidithiobacilli showed that AcaML1-like proviruses are confined to the mesothermophiles Acidithiobacillus caldus and Thermithiobacillus tepidarius. Among A. caldus strains and isolates this provirus had a modest prevalence (30%). Comparative genomic analysis revealed a significant conservation with the T. tepidarius AcaML1-like provirus, excepting the tail genes, and a high conservation of the virus across strains of the A. caldus species. Such conservation extends from the modules architecture to the gene level, suggesting that organization and composition of these viruses are preserved for functional reasons. Accordingly, the AcaML1 proviruses were demonstrated to excise from their host genomes under DNA-damaging conditions triggering the SOS-response and to produce DNA-containing VLPs. Despite this fact, under the conditions evaluated (acidic) the VLPs obtained from A. caldus ATCC 51756 could not produce productive infections of a candidate sensitive strain (#6) nor trigger it lysis.


Subject(s)
Acidithiobacillus/virology , Bacteriophages/physiology , Proviruses/physiology , Acidithiobacillus/genetics , Acidithiobacillus/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacteriophages/genetics , Bacteriophages/isolation & purification , Proviruses/genetics , Proviruses/isolation & purification , Viral Proteins/genetics , Viral Proteins/metabolism , Virus Integration
16.
J Mol Biol ; 430(3): 297-309, 2018 02 02.
Article in English | MEDLINE | ID: mdl-29223729

ABSTRACT

The type VI secretion system (T6SS) is a specialized macromolecular complex dedicated to the delivery of protein effectors into both eukaryotic and bacterial cells. The general mechanism of action of the T6SS is similar to the injection of DNA by contractile bacteriophages. The cytoplasmic portion of the T6SS is evolutionarily, structurally and functionally related to the phage tail complex. It is composed of an inner tube made of stacked Hcp hexameric rings, engulfed within a sheath and built on a baseplate. This sheath undergoes cycles of extension and contraction, and the current model proposes that the sheath contraction propels the inner tube toward the target cell for effector delivery. The sheath comprises two subunits: TssB and TssC that polymerize under an extended conformation. Here, we show that isolated TssB forms trimers, and we report the crystal structure of a C-terminal fragment of TssB. This fragment comprises a long helix followed by a helical hairpin that presents surface-exposed charged residues. Site-directed mutagenesis coupled to functional assay further showed that these charges are required for proper assembly of the sheath. Positioning of these residues in the extended T6SS sheath structure suggests that they may mediate contacts with the baseplate.


Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli/chemistry , Type VI Secretion Systems/chemistry , Crystallography, X-Ray , Models, Molecular , Protein Conformation , Protein Domains , Protein Multimerization
17.
Proc Natl Acad Sci U S A ; 114(46): E9802-E9810, 2017 11 14.
Article in English | MEDLINE | ID: mdl-29078359

ABSTRACT

The giant panda Ailuropoda melanoleuca belongs to the family of Ursidae; however, it is not carnivorous, feeding almost exclusively on bamboo. Being equipped with a typical carnivorous digestive apparatus, the giant panda cannot get enough energy for an active life and spends most of its time digesting food or sleeping. Feeding and mating are both regulated by odors and pheromones; therefore, a better knowledge of olfaction at the molecular level can help in designing strategies for the conservation of this species. In this context, we have identified the odorant-binding protein (OBP) repertoire of the giant panda and mapped the protein expression in nasal mucus and saliva through proteomics. Four OBPs have been identified in nasal mucus, while the other two were not detected in the samples examined. In particular, AimelOBP3 is similar to a subset of OBPs reported as pheromone carriers in the urine of rodents, saliva of the boar, and seminal fluid of the rabbit. We expressed this protein, mapped its binding specificity, and determined its crystal structure. Structural data guided the design and preparation of three protein mutants bearing single-amino acid replacements in the ligand-binding pocket, for which the corresponding binding affinity spectra were measured. We also expressed AimelOBP5, which is markedly different from AimelOBP3 and complementary in its binding spectrum. By comparing our binding data with the structures of bamboo volatiles and those of typical mammalian pheromones, we formulate hypotheses on which may be the most relevant semiochemicals for the giant panda.


Subject(s)
Bambusa/chemistry , Ecology , Pheromones/metabolism , Receptors, Odorant/chemistry , Receptors, Odorant/metabolism , Smell/physiology , Ursidae/metabolism , Animal Feed , Animals , Behavior, Animal , Crystallography, X-Ray , Models, Molecular , Molecular Docking Simulation , Nasal Mucosa/chemistry , Protein Conformation , Protein Interaction Domains and Motifs , Proteomics , Rabbits , Receptors, Odorant/genetics , Receptors, Odorant/isolation & purification , Saliva/chemistry , Sequence Alignment , Sequence Analysis, Protein , Swine
18.
Front Immunol ; 8: 884, 2017.
Article in English | MEDLINE | ID: mdl-28871249

ABSTRACT

The heterodimeric cytokine interleukin (IL) 23 comprises the IL12-shared p40 subunit and an IL23-specific subunit, p19. Together with IL12 and IL27, IL23 sits at the apex of the regulatory mechanisms shaping adaptive immune responses. IL23, together with IL17, plays an important role in the development of chronic inflammation and autoimmune inflammatory diseases. In this context, we generated monovalent antihuman IL23 variable heavy chain domain of llama heavy chain antibody (VHH) domains (Nanobodies®) with low nanomolar affinity for human interleukin (hIL) 23. The crystal structure of a quaternary complex assembling hIL23 and several nanobodies against p19 and p40 subunits allowed identification of distinct epitopes and enabled rational design of a multivalent IL23-specific blocking nanobody. Taking advantage of the ease of nanobody formatting, multivalent IL23 nanobodies were assembled with properly designed linkers flanking an antihuman serum albumin nanobody, with improved hIL23 neutralization capacity in vitro and in vivo, as compared to the monovalent nanobodies. These constructs with long exposure time are excellent candidates for further developments targeting Crohn's disease, rheumatoid arthritis, and psoriasis.

19.
Front Immunol ; 8: 867, 2017.
Article in English | MEDLINE | ID: mdl-28824615

ABSTRACT

The activity of tumor necrosis factor (TNF), a cytokine involved in inflammatory pathologies, can be inhibited by antibodies or trap molecules. Herein, llama-derived variable heavy-chain domains of heavy-chain antibody (VHH, also called Nanobodies™) were generated for the engineering of bivalent constructs, which antagonize the binding of TNF to its receptors with picomolar potencies. Three monomeric VHHs (VHH#1, VHH#2, and VHH#3) were characterized in detail and found to bind TNF with sub-nanomolar affinities. The crystal structures of the TNF-VHH complexes demonstrate that VHH#1 and VHH#2 share the same epitope, at the center of the interaction area of TNF with its TNFRs, while VHH#3 binds to a different, but partially overlapping epitope. These structures rationalize our results obtained with bivalent constructs in which two VHHs were coupled via linkers of different lengths. Contrary to conventional antibodies, these bivalent Nanobody™ constructs can bind to a single trimeric TNF, thus binding with avidity and blocking two of the three receptor binding sites in the cytokine. The different mode of binding to antigen and the engineering into bivalent constructs supports the design of highly potent VHH-based therapeutic entities.

20.
Nat Microbiol ; 2: 17103, 2017 Jun 26.
Article in English | MEDLINE | ID: mdl-28650463

ABSTRACT

The type VI secretion system (T6SS) is a multiprotein machine widespread in Gram-negative bacteria that delivers toxins into both eukaryotic and prokaryotic cells. The mechanism of action of the T6SS is comparable to that of contractile myophages. The T6SS builds a tail-like structure made of an inner tube wrapped by a sheath, assembled under an extended conformation. Contraction of the sheath propels the inner tube towards the target cell. The T6SS tail is assembled on a platform-the baseplate-which is functionally similar to bacteriophage baseplates. In addition, the baseplate docks the tail to a trans-envelope membrane complex that orients the tail towards the target. Here, we report the crystal structure of TssK, a central component of the T6SS baseplate. We show that TssK is composed of three domains, and establish the contribution of each domain to the interaction with TssK partners. Importantly, this study reveals that the N-terminal domain of TssK is structurally homologous to the shoulder domain of phage receptor-binding proteins, and the C-terminal domain binds the membrane complex. We propose that TssK has conserved the domain of attachment to the virion particle but has evolved the reception domain to use the T6SS membrane complex as receptor.


Subject(s)
Bacteriophages/chemistry , Escherichia coli/chemistry , Type VI Secretion Systems/chemistry , Viral Proteins/chemistry , Bacteriophages/genetics , Bacteriophages/metabolism , Crystallization , Crystallography, X-Ray , Escherichia coli/metabolism , Membrane Proteins/metabolism , Models, Molecular , Protein Binding , Protein Domains , Protein Multimerization , Protein Transport , Receptors, Virus/metabolism , Type VI Secretion Systems/genetics , Type VI Secretion Systems/metabolism , Viral Proteins/genetics , Viral Proteins/metabolism
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