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1.
Cell ; 174(2): 312-324.e16, 2018 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-29804838

RESUMO

The seven-transmembrane-spanning protein Smoothened is the central transducer in Hedgehog signaling, a pathway fundamental in development and in cancer. Smoothened is activated by cholesterol binding to its extracellular cysteine-rich domain (CRD). How this interaction leads to changes in the transmembrane domain and Smoothened activation is unknown. Here, we report crystal structures of sterol-activated Smoothened. The CRD undergoes a dramatic reorientation, allosterically causing the transmembrane domain to adopt a conformation similar to active G-protein-coupled receptors. We show that Smoothened contains a unique inhibitory π-cation lock, which is broken on activation and is disrupted in constitutively active oncogenic mutants. Smoothened activation opens a hydrophobic tunnel, suggesting a pathway for cholesterol movement from the inner membrane leaflet to the CRD. All Smoothened antagonists bind the transmembrane domain and block tunnel opening, but cyclopamine also binds the CRD, inducing the active transmembrane conformation. Together, these results define the mechanisms of Smoothened activation and inhibition.


Assuntos
Proteínas Hedgehog/metabolismo , Receptor Smoothened/química , Proteínas de Xenopus/química , Regulação Alostérica , Animais , Sítios de Ligação , Linhagem Celular , Colesterol/química , Colesterol/metabolismo , Cristalografia por Raios X , Citometria de Fluxo , Proteínas Hedgehog/genética , Humanos , Camundongos , Simulação de Dinâmica Molecular , Ligação Proteica , Domínios Proteicos , Estrutura Terciária de Proteína , Transdução de Sinais , Bibliotecas de Moléculas Pequenas/síntese química , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo , Receptor Smoothened/antagonistas & inibidores , Receptor Smoothened/metabolismo , Alcaloides de Veratrum/química , Alcaloides de Veratrum/metabolismo , Proteínas de Xenopus/antagonistas & inibidores , Proteínas de Xenopus/metabolismo , Xenopus laevis/metabolismo
2.
Cell ; 166(5): 1176-1187.e14, 2016 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-27545348

RESUMO

In vertebrates, sterols are necessary for Hedgehog signaling, a pathway critical in embryogenesis and cancer. Sterols activate the membrane protein Smoothened by binding its extracellular, cysteine-rich domain (CRD). Major unanswered questions concern the nature of the endogenous, activating sterol and the mechanism by which it regulates Smoothened. We report crystal structures of CRD complexed with sterols and alone, revealing that sterols induce a dramatic conformational change of the binding site, which is sufficient for Smoothened activation and is unique among CRD-containing receptors. We demonstrate that Hedgehog signaling requires sterol binding to Smoothened and define key residues for sterol recognition and activity. We also show that cholesterol itself binds and activates Smoothened. Furthermore, the effect of oxysterols is abolished in Smoothened mutants that retain activation by cholesterol and Hedgehog. We propose that the endogenous Smoothened activator is cholesterol, not oxysterols, and that vertebrate Hedgehog signaling controls Smoothened by regulating its access to cholesterol.


Assuntos
Colesterol/metabolismo , Proteínas Hedgehog/metabolismo , Receptor Smoothened/agonistas , Animais , Colesterol/química , Cristalografia por Raios X , Camundongos , Células NIH 3T3 , Oxisteróis/química , Oxisteróis/metabolismo , Ligação Proteica , Conformação Proteica , Transdução de Sinais , Receptor Smoothened/química , Receptor Smoothened/metabolismo , Xenopus laevis
4.
Proc Natl Acad Sci U S A ; 121(3): e2312455121, 2024 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-38194450

RESUMO

Type VII secretion systems are membrane-embedded nanomachines used by Gram-positive bacteria to export effector proteins from the cytoplasm to the extracellular environment. Many of these effectors are polymorphic toxins comprised of an N-terminal Leu-x-Gly (LXG) domain of unknown function and a C-terminal toxin domain that inhibits the growth of bacterial competitors. In recent work, it was shown that LXG effectors require two cognate Lap proteins for T7SS-dependent export. Here, we present the 2.6 Å structure of the LXG domain of the TelA toxin from the opportunistic pathogen Streptococcus intermedius in complex with both of its cognate Lap targeting factors. The structure reveals an elongated α-helical bundle within which each Lap protein makes extensive hydrophobic contacts with either end of the LXG domain. Remarkably, despite low overall sequence identity, we identify striking structural similarity between our LXG complex and PE-PPE heterodimers exported by the distantly related ESX type VII secretion systems of Mycobacteria implying a conserved mechanism of effector export among diverse Gram-positive bacteria. Overall, our findings demonstrate that LXG domains, in conjunction with their cognate Lap targeting factors, represent a tripartite secretion signal for a widespread family of T7SS toxins.


Assuntos
Gafanhotos , Toxinas Biológicas , Sistemas de Secreção Tipo VII , Animais , Sistemas de Secreção Tipo VII/genética , Citoplasma
5.
Proc Natl Acad Sci U S A ; 120(14): e2213771120, 2023 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-36989297

RESUMO

Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3'-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology.


Assuntos
Proteínas de Bactérias , Toxinas Biológicas , Proteínas de Bactérias/genética , Proteínas de Bactérias/química , Guanosina Pentafosfato , Bactérias/genética , Ligases/genética , Hidrolases/genética , Adenosina , Guanosina Tetrafosfato
6.
Proc Natl Acad Sci U S A ; 118(21)2021 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-33972410

RESUMO

The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog (m7GpppAm2'-O). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.


Assuntos
Capuzes de RNA/metabolismo , RNA Mensageiro/metabolismo , RNA Viral/metabolismo , SARS-CoV-2/química , Cristalografia , Metilação , Metiltransferases/química , Metiltransferases/metabolismo , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Análogos de Capuz de RNA/química , Análogos de Capuz de RNA/metabolismo , Capuzes de RNA/química , RNA Mensageiro/química , RNA Viral/química , S-Adenosil-Homocisteína/química , S-Adenosil-Homocisteína/metabolismo , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo , SARS-CoV-2/genética , SARS-CoV-2/metabolismo , Síncrotrons , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo , Proteínas Virais Reguladoras e Acessórias/química , Proteínas Virais Reguladoras e Acessórias/metabolismo
7.
Proteins ; 91(3): 293-299, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36201627

RESUMO

In Gram-negative bacteria, lipopolysaccharide (LPS) is an essential component of the asymmetric outer membrane (OM). LptE is an OM lipoprotein that forms a complex with the ß-barrel OM protein, LptD. Incorporation of LPS into the OM outer leaflet is essential for bacterial viability, and mediated by the LptD/E complex. The genome of Campylobacter jejuni, a major foodborne pathogen, contains over 20 putative lipoproteins including Cj1090c. Here, we report the crystal structure of Cj1090c at 2.4 Å resolution, revealing structural evidence for LptE in C. jejuni. The analysis of this crystal structure, along with the genomic context, allows us to propose the C. jejuni LPS transport system for the first time, and permits for discussion of the features of the LptD/E complex of C. jejuni.


Assuntos
Campylobacter jejuni , Lipopolissacarídeos , Membrana Celular/metabolismo , Lipopolissacarídeos/química , Lipopolissacarídeos/genética , Lipopolissacarídeos/metabolismo , Proteínas da Membrana Bacteriana Externa/química , Campylobacter jejuni/genética , Campylobacter jejuni/metabolismo , Transporte Biológico , Lipoproteínas/genética , Lipoproteínas/metabolismo
8.
Appl Microbiol Biotechnol ; 107(19): 5999-6011, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37548665

RESUMO

Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (ß/α)8-barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with kcat = 6.0 ± 0.6 s-1 and Km = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD. KEY POINTS: • Anaerobic fungi host a wealth of industrially useful enzymes but are understudied. • P. finnis CelD has endoglucanase activity and structure common to GH5_4 enzymes. • CelD's kinetics do not change with domain fusion, exhibiting high modularity.


Assuntos
Celulase , Piromyces , Celulase/metabolismo , Anaerobiose , Glucanos/metabolismo , Piromyces/metabolismo
9.
J Bacteriol ; 204(5): e0055521, 2022 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-35435721

RESUMO

Alpha-pore-forming toxins (α-PFTs) are secreted by many species of bacteria, including Escherichia coli, Aeromonas hydrophila, and Bacillus thuringiensis, as part of their arsenal of virulence factors, and are often cytotoxic. In particular, for α-PFTs, the membrane-spanning channel they form is composed of hydrophobic α-helices. These toxins oligomerize at the surface of target cells and transition from a soluble to a protomer state in which they expose their hydrophobic regions and insert into the membrane to form a pore. The pores may be composed of homooligomers of one component or heterooligomers with two or three components, resulting in bi- or tripartite toxins. The multicomponent α-PFTs are often expressed from a single operon. Recently, motility-associated killing factor A (MakA), an α-PFT, was discovered in Vibrio cholerae. We report that makA is found on the V. cholerae GI-10 genomic island within an operon containing genes for two other potential α-PFTs, MakB and MakE. We determined the X-ray crystal structures for MakA, MakB, and MakE and demonstrated that all three are structurally related to the α-PFT family in the soluble state, and we modeled their protomer state based on the α-PFT AhlB from A. hydrophila. We found that MakA alone is cytotoxic at micromolar concentrations. However, combining MakA with MakB and MakE is cytotoxic at nanomolar concentrations, with specificity for J774 macrophage cells. Our data suggest that MakA, -B, and -E are α-PFTs that potentially act as a tripartite pore-forming toxin with specificity for phagocytic cells. IMPORTANCE The bacterium Vibrio cholerae causes gastrointestinal, wound, and skin infections. The motility-associated killing factor A (MakA) was recently shown to be cytotoxic against colon, prostate, and other cancer cells. However, at the outset of this study, the capacity of MakA to damage cells in combination with other Mak proteins encoded in the same operon had not been elucidated. We determined the structures of three Mak proteins and established that they are structurally related to the α-PFTs. Compared to MakA alone, the combination of all three toxins was more potent specifically in mouse macrophages. This study highlights the idea that the Mak toxins are selectively cytotoxic and thus may function as a tripartite toxin with cell type specificity.


Assuntos
Vibrio cholerae , Animais , Citotoxinas/genética , Citotoxinas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Ilhas Genômicas , Camundongos , Proteínas Citotóxicas Formadoras de Poros , Subunidades Proteicas/metabolismo , Vibrio cholerae/metabolismo , Fatores de Virulência/metabolismo
10.
J Synchrotron Radiat ; 29(Pt 5): 1141-1151, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36073872

RESUMO

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two ß-lactamases: a class D serine ß-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-ß-lactamase from Stenotrophomonas maltophilia K279a.


Assuntos
Stenotrophomonas maltophilia , Biologia , Cristalografia , Proteínas
11.
Genes Dev ; 28(20): 2276-90, 2014 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-25319828

RESUMO

Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI-FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.


Assuntos
Exodesoxirribonucleases/química , Modelos Moleculares , Pseudomonas aeruginosa/química , Pseudomonas aeruginosa/enzimologia , Domínio Catalítico , Cristalização , Exodesoxirribonucleases/metabolismo , Endonucleases Flap/química , Endonucleases Flap/metabolismo , Humanos , Ligação Proteica , Estrutura Terciária de Proteína
12.
Biophys J ; 120(15): 3152-3165, 2021 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-34197805

RESUMO

The replication transcription complex (RTC) from the virus SARS-CoV-2 is responsible for recognizing and processing RNA for two principal purposes. The RTC copies viral RNA for propagation into new virus and for ribosomal transcription of viral proteins. To accomplish these activities, the RTC mechanism must also conform to a large number of imperatives, including RNA over DNA base recognition, basepairing, distinguishing viral and host RNA, production of mRNA that conforms to host ribosome conventions, interfacing with error checking machinery, and evading host immune responses. In addition, the RTC will discontinuously transcribe specific sections of viral RNA to amplify certain proteins over others. Central to SARS-CoV-2 viability, the RTC is therefore dynamic and sophisticated. We have conducted a systematic structural investigation of three components that make up the RTC: Nsp7, Nsp8, and Nsp12 (also known as RNA-dependent RNA polymerase). We have solved high-resolution crystal structures of the Nsp7/8 complex, providing insight into the interaction between the proteins. We have used small-angle x-ray and neutron solution scattering (SAXS and SANS) on each component individually as pairs and higher-order complexes and with and without RNA. Using size exclusion chromatography and multiangle light scattering-coupled SAXS, we defined which combination of components forms transient or stable complexes. We used contrast-matching to mask specific complex-forming components to test whether components change conformation upon complexation. Altogether, we find that individual Nsp7, Nsp8, and Nsp12 structures vary based on whether other proteins in their complex are present. Combining our crystal structure, atomic coordinates reported elsewhere, SAXS, SANS, and other biophysical techniques, we provide greater insight into the RTC assembly, mechanism, and potential avenues for disruption of the complex and its functions.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Modelos Moleculares , RNA Viral/genética , Espalhamento a Baixo Ângulo , Proteínas não Estruturais Virais , Replicação Viral , Difração de Raios X
13.
Proteins ; 89(12): 1647-1672, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34561912

RESUMO

The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.


Assuntos
Modelos Moleculares , Conformação Proteica , Proteínas/química , Software , Sequência de Aminoácidos , Biologia Computacional , Microscopia Crioeletrônica , Cristalografia por Raios X , Análise de Sequência de Proteína
14.
Nat Chem Biol ; 15(4): 367-376, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30804532

RESUMO

Hypoxia-inducible factor-2 (HIF-2) is a heterodimeric transcription factor formed through dimerization between an oxygen-sensitive HIF-2α subunit and its obligate partner subunit ARNT. Enhanced HIF-2 activity drives some cancers, whereas reduced activity causes anemia in chronic kidney disease. Therefore, modulation of HIF-2 activity via direct-binding ligands could provide many new therapeutic benefits. Here, we explored HIF-2α chemical ligands using combined crystallographic, biophysical, and cell-based functional studies. We found chemically unrelated antagonists to employ the same mechanism of action. Their binding displaced residue M252 from inside the HIF-2α PAS-B pocket toward the ARNT subunit to weaken heterodimerization. We also identified first-in-class HIF-2α agonists and found that they significantly displaced pocket residue Y281. Its dramatic side chain movement increases heterodimerization stability and transcriptional activity. Our findings show that despite binding to the same HIF-2α PAS-B pocket, ligands can manifest as inhibitors versus activators by mobilizing different pocket residues to allosterically alter HIF-2α-ARNT heterodimerization.


Assuntos
Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Animais , Translocador Nuclear Receptor Aril Hidrocarboneto/metabolismo , Translocador Nuclear Receptor Aril Hidrocarboneto/fisiologia , Fatores de Transcrição Hélice-Alça-Hélice Básicos , Cristalografia por Raios X , Dimerização , Ligantes , Camundongos , Modelos Moleculares , Ligação Proteica , Multimerização Proteica , Fatores de Transcrição/fisiologia
15.
Nature ; 524(7565): 303-8, 2015 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-26245371

RESUMO

The hypoxia-inducible factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating transcriptional programs in erythropoiesis, angiogenesis and metabolism. These programs promote the growth and progression of many tumours, making HIFs attractive anticancer targets. Transcriptionally active HIFs consist of HIF-α and ARNT (also called HIF-1ß) subunits. Here we describe crystal structures for each of mouse HIF-2α-ARNT and HIF-1α-ARNT heterodimers in states that include bound small molecules and their hypoxia response element. A highly integrated quaternary architecture is shared by HIF-2α-ARNT and HIF-1α-ARNT, wherein ARNT spirals around the outside of each HIF-α subunit. Five distinct pockets are observed that permit small-molecule binding, including PAS domain encapsulated sites and an interfacial cavity formed through subunit heterodimerization. The DNA-reading head rotates, extends and cooperates with a distal PAS domain to bind hypoxia response elements. HIF-α mutations linked to human cancers map to sensitive sites that establish DNA binding and the stability of PAS domains and pockets.


Assuntos
Translocador Nuclear Receptor Aril Hidrocarboneto/química , Fatores de Transcrição Hélice-Alça-Hélice Básicos/química , Subunidade alfa do Fator 1 Induzível por Hipóxia/química , Fatores de Transcrição ARNTL/química , Fatores de Transcrição ARNTL/metabolismo , Animais , Translocador Nuclear Receptor Aril Hidrocarboneto/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Sítios de Ligação , Proteínas CLOCK/química , Proteínas CLOCK/metabolismo , Hipóxia Celular/genética , Cristalografia por Raios X , DNA/química , DNA/metabolismo , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Camundongos , Modelos Moleculares , Mutação/genética , Neoplasias/genética , Fosforilação , Multimerização Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Elementos de Resposta/genética
16.
BMC Bioinformatics ; 21(1): 160, 2020 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-32349673

RESUMO

BACKGROUND: Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner. RESULTS: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences. CONCLUSIONS: CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.


Assuntos
Sistema Enzimático do Citocromo P-450/análise , Sistema Enzimático do Citocromo P-450/metabolismo , Análise de Dados , Bases de Dados Genéticas , Genoma , Filogenia , Automação , Análise por Conglomerados , Fungos/genética , Redes Reguladoras de Genes , Software , Interface Usuário-Computador
17.
Mol Microbiol ; 111(3): 637-661, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30536925

RESUMO

Molecular components of the Brucella abortus cell envelope play a major role in its ability to infect, colonize and survive inside mammalian host cells. In this study, we have defined a role for a conserved gene of unknown function in B. abortus envelope stress resistance and infection. Expression of this gene, which we name eipA, is directly activated by the essential cell cycle regulator, CtrA. eipA encodes a soluble periplasmic protein that adopts an unusual eight-stranded ß-barrel fold. Deletion of eipA attenuates replication and survival in macrophage and mouse infection models, and results in sensitivity to treatments that compromise the cell envelope integrity. Transposon disruption of genes required for LPS O-polysaccharide biosynthesis is synthetically lethal with eipA deletion. This genetic connection between O-polysaccharide and eipA is corroborated by our discovery that eipA is essential in Brucella ovis, a naturally rough species that harbors mutations in several genes required for O-polysaccharide production. Conditional depletion of eipA expression in B. ovis results in a cell chaining phenotype, providing evidence that eipA directly or indirectly influences cell division in Brucella. We conclude that EipA is a molecular determinant of Brucella virulence that functions to maintain cell envelope integrity and influences cell division.


Assuntos
Brucella abortus/crescimento & desenvolvimento , Brucella abortus/patogenicidade , Ciclo Celular , Parede Celular/metabolismo , Antígenos O/metabolismo , Proteínas Periplásmicas/metabolismo , Fatores de Virulência/metabolismo , Animais , Brucella abortus/enzimologia , Brucella abortus/genética , Brucella ovis/genética , Brucella ovis/crescimento & desenvolvimento , Brucelose/microbiologia , Brucelose/patologia , Modelos Animais de Doenças , Deleção de Genes , Técnicas de Silenciamento de Genes , Genes Bacterianos , Genes Essenciais , Histocitoquímica , Macrófagos/microbiologia , Camundongos Endogâmicos BALB C , Viabilidade Microbiana , Proteínas Periplásmicas/química , Proteínas Periplásmicas/genética , Conformação Proteica , Dobramento de Proteína , Baço/patologia , Fatores de Virulência/química , Fatores de Virulência/genética
18.
J Bacteriol ; 201(12)2019 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-30936371

RESUMO

The Gram-negative cell envelope is a remarkable structure with core components that include an inner membrane, an outer membrane, and a peptidoglycan layer in the periplasmic space between. Multiple molecular systems function to maintain integrity of this essential barrier between the interior of the cell and its surrounding environment. We show that a conserved DUF1849 family protein, EipB, is secreted to the periplasmic space of Brucella species, a monophyletic group of intracellular pathogens. In the periplasm, EipB folds into an unusual 14-stranded ß-spiral structure that resembles the LolA and LolB lipoprotein delivery system, though the overall fold of EipB is distinct from LolA/LolB. Deletion of eipB results in defects in Brucella cell envelope integrity in vitro and in maintenance of spleen colonization in a mouse model of Brucella abortus infection. Transposon disruption of ttpA, which encodes a periplasmic protein containing tetratricopeptide repeats, is synthetically lethal with eipB deletion. ttpA is a reported virulence determinant in Brucella, and our studies of ttpA deletion and overexpression strains provide evidence that this gene also contributes to cell envelope function. We conclude that eipB and ttpA function in the Brucella periplasmic space to maintain cell envelope integrity, which facilitates survival in a mammalian host.IMPORTANCEBrucella species cause brucellosis, a global zoonosis. A gene encoding a conserved DUF1849-family protein, which we have named EipB, is present in all sequenced Brucella and several other genera in the class Alphaproteobacteria The manuscript provides the first functional and structural characterization of a DUF1849 protein. We show that EipB is secreted to the periplasm where it forms a spiral-shaped antiparallel ß protein that is a determinant of cell envelope integrity in vitro and virulence in an animal model of disease. eipB genetically interacts with ttpA, which also encodes a periplasmic protein. We propose that EipB and TtpA function as part of a system required for cell envelope homeostasis in select Alphaproteobacteria.


Assuntos
Membrana Externa Bacteriana/química , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Brucella abortus/genética , Brucella abortus/patogenicidade , Periplasma/química , Animais , Brucella abortus/química , Brucelose/microbiologia , Feminino , Regulação Bacteriana da Expressão Gênica , Camundongos , Camundongos Endogâmicos BALB C , Virulência , Fatores de Virulência/genética
19.
J Biol Chem ; 293(19): 7437-7456, 2018 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-29567835

RESUMO

The general stress response sigma factor σE1 directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection in the zoonotic pathogen Brucella abortus Characterizing the functions of σE1-regulated genes therefore would contribute to our understanding of B. abortus physiology and infection biology. σE1 indirectly activates transcription of the IclR family regulator Bab2_0215, but the function of this regulator remains undefined. Here, we present a structural and functional characterization of Bab2_0215, which we have named B rucella adipic acid-activated regulator (BaaR). We found that BaaR adopts a classic IclR-family fold and directly represses the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase (acaD2), and it represses transcription of both genes. We identified three carboxylic acids (adipic acid, tetradecanedioic acid, and ϵ-aminocaproic acid) and a lactone (ϵ-caprolactone) that enhance transcription from the baaR and acaD2 promoters. However, neither the activating acids nor caprolactone enhanced transcription by binding directly to BaaR. Induction of baaR transcription by adipic acid required the gene bab2_0213, which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a suite of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program in B. abortus that is downstream of σE1.


Assuntos
Proteínas de Bactérias/fisiologia , Brucella abortus/fisiologia , Regulação Bacteriana da Expressão Gênica/genética , Proteínas Repressoras/fisiologia , Transcrição Gênica/genética , Adipatos/farmacologia , Ácido Aminocaproico/farmacologia , Aderência Bacteriana , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Brucella abortus/genética , Brucella abortus/crescimento & desenvolvimento , Caproatos/farmacologia , Cromossomos Bacterianos , Cristalografia por Raios X , Regulação Bacteriana da Expressão Gênica/efeitos dos fármacos , Regulação Bacteriana da Expressão Gênica/fisiologia , Peróxido de Hidrogênio/metabolismo , Lactonas/farmacologia , Ácido Mirístico/farmacologia , Óperon , Regiões Promotoras Genéticas , Ligação Proteica , Dobramento de Proteína , Fator sigma/fisiologia , Transcrição Gênica/efeitos dos fármacos , Transcrição Gênica/fisiologia
20.
Mol Microbiol ; 110(4): 550-561, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30168204

RESUMO

LysR-type transcriptional regulators (LTTRs) generally bind to target promoters in two conformations, depending on the availability of inducing ligands. OccR is an LTTR that regulates the octopine catabolism operon of Agrobacterium tumefaciens. OccR binds to a site located between the divergent occQ and occR promoters. Octopine triggers a conformational change that activates the occQ promoter, and does not affect autorepression. This change shortens the length of bound DNA and relaxes a high-angle DNA bend. Here, we describe the crystal structure of the ligand-binding domain (LBD) of OccR apoprotein and holoprotein. Pairs of LBDs form dimers with extensive hydrogen bonding, while pairs of dimers interact via a single helix, creating a tetramer interface. Octopine causes a 70° rotation of each dimer with respect to the opposite dimer, precisely at the tetramer interface. We modeled the DNA binding domain (DBD), linker helix and bound DNA onto the apoprotein and holoprotein. The two DBDs of the modeled apoprotein lie far apart and the bound DNA between them has a high-angle DNA bend. In contrast, the two DBDs of the holoprotein lie closer to each other, with a low DNA bend angle. This inter-dimer pivot fully explains earlier studies of this LTTR.


Assuntos
Agrobacterium tumefaciens/genética , Arginina/análogos & derivados , Proteínas de Bactérias/metabolismo , Proteínas de Ligação a DNA/metabolismo , Estrutura Quaternária de Proteína/efeitos dos fármacos , Fatores de Transcrição/metabolismo , Ativação Transcricional/genética , Arginina/farmacologia , Proteínas de Bactérias/genética , Sítios de Ligação/fisiologia , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Cristalografia por Raios X , DNA Bacteriano/genética , Proteínas de Ligação a DNA/genética , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Regiões Promotoras Genéticas/efeitos dos fármacos , Regiões Promotoras Genéticas/genética , Ligação Proteica/fisiologia , Fatores de Transcrição/genética
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