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1.
Nature ; 534(7607): 417-20, 2016 06 16.
Artículo en Inglés | MEDLINE | ID: mdl-27281193

RESUMEN

The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites. YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis. Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.


Asunto(s)
Sistemas de Transporte de Aminoácidos Neutros/química , Sistemas de Transporte de Aminoácidos Neutros/metabolismo , Aminoácidos/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/metabolismo , Transporte Biológico , Cristalografía por Rayos X , Escherichia coli/química , Escherichia coli/metabolismo , Liposomas/química , Liposomas/metabolismo , Modelos Moleculares , Conformación Proteica , Relación Estructura-Actividad
2.
Proc Natl Acad Sci U S A ; 115(39): E9051-E9057, 2018 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-30194231

RESUMEN

Natural light-harvesting is performed by pigment-protein complexes, which collect and funnel the solar energy at the start of photosynthesis. The identity and arrangement of pigments largely define the absorption spectrum of the antenna complex, which is further regulated by a palette of structural factors. Small alterations are induced by pigment-protein interactions. In light-harvesting systems 2 and 3 from Rhodoblastus acidophilus, the pigments are arranged identically, yet the former has an absorption peak at 850 nm that is blue-shifted to 820 nm in the latter. While the shift has previously been attributed to the removal of hydrogen bonds, which brings changes in the acetyl moiety of the bacteriochlorophyll, recent work has shown that other mechanisms are also present. Using computational and modeling tools on the corresponding crystal structures, we reach a different conclusion: The most critical factor for the shift is the curvature of the macrocycle ring. The bending of the planar part of the pigment is identified as the second-most important design principle for the function of pigment-protein complexes-a finding that can inspire the design of novel artificial systems.


Asunto(s)
Alphaproteobacteria/química , Proteínas Bacterianas/química , Bacterioclorofilas/química , Complejos de Proteína Captadores de Luz/química , Alphaproteobacteria/metabolismo , Proteínas Bacterianas/metabolismo , Bacterioclorofilas/metabolismo , Complejos de Proteína Captadores de Luz/metabolismo , Fotosíntesis/fisiología
3.
Proteins ; 88(3): 527-539, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31589792

RESUMEN

The selectivity filter (SF) of bacterial voltage-gated sodium channels consists of four glutamate residues arranged in a C4 symmetry. The protonation state population of this tetrad is unclear. To address this question, we simulate the pore domain of bacterial voltage-gated sodium channel of Magnetococcus sp. (Nav Ms) through constant pH methodology in explicit solvent and free energy perturbation calculations. We find that at physiological pH the fully deprotonated as well as singly and doubly protonated states of the SF appear feasible, and that the calculated pKa decreases with each additional bound ion, suggesting that a decrease in the number of ions in the pore can lead to protonation of the SF. Previous molecular dynamics simulations have suggested that protonation can lead to a decrease in the conductance, but no pKa calculations were performed. We confirm a decreased ionic population of the pore with protonation, and also observe structural symmetry breaking triggered by protonation; the SF of the deprotonated channel is closest to the C4 symmetry observed in crystal structures of the open state, while the SF of protonated states display greater levels of asymmetry which could lead to transition to the inactivated state which possesses a C2 symmetry in the crystal structure. We speculate that the decrease in the number of ions near the mouth of the channel, due to either random fluctuations or ion depletion due to conduction, could be a self-regulatory mechanism resulting in a nonconducting state that functionally resembles inactivated states.


Asunto(s)
Alphaproteobacteria/química , Proteínas Bacterianas/química , Protones , Sodio/química , Canales de Sodio Activados por Voltaje/química , Alphaproteobacteria/metabolismo , Proteínas Bacterianas/metabolismo , Sitios de Unión , Cationes Monovalentes , Cristalografía por Rayos X , Concentración de Iones de Hidrógeno , Transporte Iónico , Cinética , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica en Hélice alfa , Dominios y Motivos de Interacción de Proteínas , Sodio/metabolismo , Termodinámica , Canales de Sodio Activados por Voltaje/metabolismo
4.
EMBO J ; 35(8): 820-30, 2016 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-26873592

RESUMEN

Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na(+) ≈ Li(+) â‰« K(+), Ca(2+), Mg(2+)) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.


Asunto(s)
Canales de Sodio/química , Canales de Sodio/metabolismo , Sodio/metabolismo , Alphaproteobacteria/química , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Cationes/metabolismo , Cristalografía por Rayos X , Ácido Glutámico/genética , Células HEK293 , Humanos , Activación del Canal Iónico , Modelos Moleculares , Mutación , Técnicas de Placa-Clamp , Permeabilidad , Conformación Proteica , Canales de Sodio/genética , Electricidad Estática
5.
Int J Syst Evol Microbiol ; 70(12): 6444-6449, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33174831

RESUMEN

A Gram-stain-negative and aerobic bacterial strain, designated as JL3514T, was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10-50 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-9 % (w/v) NaCl (optimum, 2 %). Strain JL3514T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family Erythrobacteraceae, namely Croceibacterium atlanticum (96.1 %), Pelagerythrobacter marensis (96.0 %), Tsuneonella rigui (96.0 %) and Altericroceibacterium xinjiangense (96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, C17 : 1 ω6c, C14 : 0 2-OH and C12 : 0. The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514T to represent a novel genus of the family Erythrobacteraceae, with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514T (=KCTC 62623T=MCCC 1K03561T).


Asunto(s)
Alphaproteobacteria/clasificación , Filogenia , Agua de Mar/microbiología , Alphaproteobacteria/química , Alphaproteobacteria/genética , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Especificidad de la Especie , Taiwán
6.
Int J Mol Sci ; 21(15)2020 Aug 03.
Artículo en Inglés | MEDLINE | ID: mdl-32756387

RESUMEN

Members of the Sphingomonadales are renowned for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). However, little is known about the regulatory mechanisms of the degradative pathway. Using cross-feeding bioassay, a functional LuxI/LuxR-type acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) system was identified from Croceicoccus naphthovorans PQ-2, a member of the order Sphingomonadales. Inactivation of the QS system resulted in a significant decrease in PAHs degradation. The QS system positively controlled the expression of three PAH-degrading genes (ahdA1e, xylE and xylG) and a regulatory gene ardR, which are located on the large plasmid. Interestingly, the transcription levels of these three PAH-degrading genes were significantly down-regulated in the ardR mutant. In addition, bacterial cell surface hydrophobicity and cell morphology were altered in the QS-deficient mutant. Therefore, the QS system in strain PQ-2 positively regulates PAH degradation via two mechanisms: (i) by induction of PAH-degrading genes directly and/or indirectly; and (ii) by an increase of bacterial cell surface hydrophobicity. The findings of this study improve our understanding of how the QS system influences the degradation of PAHs, therefore facilitating the development of new strategies for the bioremediation of PAHs.


Asunto(s)
Alphaproteobacteria/metabolismo , Proteínas Bacterianas/genética , Hidrocarburos Policíclicos Aromáticos/química , Proteínas Represoras/genética , Transactivadores/genética , Factores de Transcripción/genética , Acil-Butirolactonas/metabolismo , Alphaproteobacteria/química , Proteínas Bacterianas/química , Biodegradación Ambiental , Regulación Bacteriana de la Expresión Génica/genética , Hidrocarburos Policíclicos Aromáticos/metabolismo , Percepción de Quorum , Proteínas Represoras/química , Transactivadores/química , Factores de Transcripción/química
7.
Biochem Biophys Res Commun ; 512(3): 564-570, 2019 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-30914200

RESUMEN

Baeyer-Villiger monooxygenase (BVMO) catalyzes insertion of an oxygen atom into aliphatic or cyclic ketones with high regioselectivity. The BVMOs from Parvibaculum lavamentivorans (BVMOParvi) and Oceanicola batsensis (BVMOOcean) are interesting because of their homologies, with >40% sequence identity, and reaction with the same cyclic ketones with a methyl moiety to give different products. The revealed BVMOParvi structure shows that BVMOParvi forms a two-domain structure like other BVMOs. It has two inserted residues, compared with BVMOOcean, that form a bulge near the bound flavin adenine dinucleotide in the active site. Furthermore, this bulge is linked to a nearby α-helix via a disulfide bond, probably restricting access of the bulky methyl group of the substrate to this bulge. Another sequence motif at the entrance of the active site (Ala-Ser in BVMOParvi and Ser-Thr in BVMOOcean) allows a large volume in BVMOParvi. These minute differences may discriminate a substrate orientation in both BVMOs from the initial substrate binding pocket to the final oxygenation site, resulting in the inserted oxygen atom being in different positions of the same substrate.


Asunto(s)
Alphaproteobacteria/metabolismo , Proteínas Bacterianas/metabolismo , Cetonas/metabolismo , Oxigenasas de Función Mixta/metabolismo , Alphaproteobacteria/química , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Dominio Catalítico , Cristalografía por Rayos X , Ciclización , Cetonas/química , Oxigenasas de Función Mixta/química , Modelos Moleculares , NADP/metabolismo , Oxígeno/metabolismo , Conformación Proteica , Especificidad por Sustrato
8.
J Proteome Res ; 17(4): 1615-1623, 2018 04 06.
Artículo en Inglés | MEDLINE | ID: mdl-29466012

RESUMEN

The reaction center (RC) from the phototrophic bacterium Blastochloris viridis was the first integral membrane protein complex to have its structure determined by X-ray crystallography and has been studied extensively since then. It is composed of four protein subunits, H, M, L, and C, as well as cofactors, including bacteriopheophytin (BPh), bacteriochlorophyll (BCh), menaquinone, ubiquinone, heme, carotenoid, and Fe. In this study, we utilized mass spectrometry-based proteomics to study this protein complex via bottom-up sequencing, intact protein mass analysis, and native MS ligand-binding analysis. Its primary structure shows a series of mutations, including an unusual alteration and extension on the C-terminus of the M-subunit. In terms of quaternary structure, proteins such as this containing many cofactors serve to test the ability to introduce native-state protein assemblies into the gas phase because the cofactors will not be retained if the quaternary structure is seriously perturbed. Furthermore, this specific RC, under native MS, exhibits a strong ability not only to bind the special pair but also to preserve the two peripheral BCh's.


Asunto(s)
Proteínas Bacterianas/química , Espectrometría de Masas/métodos , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Alphaproteobacteria/química , Bacterioclorofilas/metabolismo , Unión Proteica , Estabilidad Proteica , Estructura Cuaternaria de Proteína , Proteómica/métodos
9.
Anal Biochem ; 550: 8-14, 2018 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-29649471

RESUMEN

In the present work, Principal coordinate analysis (PCoA) is introduced to develop a robust model to classify the chromatographic data sets of peptidoglycan sample. PcoA captures the heterogeneity present in the data sets by using the dissimilarity matrix as input. Thus, in principle, it can even capture the subtle differences in the bacterial peptidoglycan composition and can provide a more robust and fast approach for classifying the bacterial collection and identifying the novel cell wall targets for further biological and clinical studies. The utility of the proposed approach is successfully demonstrated by analysing the two different kind of bacterial collections. The first set comprised of peptidoglycan sample belonging to different subclasses of Alphaproteobacteria. Whereas, the second set that is relatively more intricate for the chemometric analysis consist of different wild type Vibrio Cholerae and its mutants having subtle differences in their peptidoglycan composition. The present work clearly proposes a useful approach that can classify the chromatographic data sets of chromatographic peptidoglycan samples having subtle differences. Furthermore, present work clearly suggest that PCoA can be a method of choice in any data analysis workflow.


Asunto(s)
Alphaproteobacteria/química , Pared Celular/química , Peptidoglicano/análisis , Vibrio cholerae/química , Alphaproteobacteria/metabolismo , Pared Celular/metabolismo , Cromatografía/métodos , Peptidoglicano/metabolismo , Vibrio cholerae/metabolismo
10.
Langmuir ; 34(45): 13713-13724, 2018 11 13.
Artículo en Inglés | MEDLINE | ID: mdl-30394747

RESUMEN

New biomimetic magnetite nanoparticles (hereafter BMNPs) with sizes larger than most common superparamagnetic nanoparticles were produced in the presence of the recombinant MamC protein from Magnetococcus marinus MC-1 and functionalized with doxorubicin (DOXO) intended as potential drug nanocarriers. Unlike inorganic magnetite nanoparticles, in BMNPs the MamC protein controls their size and morphology, providing them with magnetic properties consistent with a large magnetic moment per particle; moreover, it provides the nanoparticles with novel surface properties. BMNPs display the isoelectric point at pH 4.4, being strongly negatively charged at physiological pH (pH 7.4). This allows both (i) their functionalization with DOXO, which is positively charged at pH 7.4, and (ii) the stability of the DOXO-surface bond and DOXO release to be pH dependent and governed by electrostatic interactions. DOXO adsorption follows a Langmuir-Freundlich model, and the coupling of DOXO to BMNPs (binary biomimetic nanoparticles) is very stable at physiological pH (maximum release of 5% of the drug adsorbed). Conversely, when pH decreases, these electrostatic interactions weaken, and at pH 5, DOXO is released up to ∼35% of the amount initially adsorbed. The DOXO-BMNPs display cytotoxicity on the GTL-16 human gastric carcinoma cell line in a dose-dependent manner, reaching about ∼70% of mortality at the maximum amount tested, while the nonloaded BMNPs are fully cytocompatible. The present data suggest that BMNPs could be useful as potential drug nanocarriers with a drug adsorption-release governed by changes in local pH values.


Asunto(s)
Proteínas Bacterianas/química , Materiales Biomiméticos/química , Doxorrubicina/química , Portadores de Fármacos/química , Nanopartículas de Magnetita/química , Adsorción , Alphaproteobacteria/química , Proteínas Bacterianas/toxicidad , Materiales Biomiméticos/toxicidad , Línea Celular Tumoral , Portadores de Fármacos/síntesis química , Portadores de Fármacos/toxicidad , Liberación de Fármacos , Hemólisis/efectos de los fármacos , Humanos , Concentración de Iones de Hidrógeno , Nanopartículas de Magnetita/toxicidad , Tamaño de la Partícula , Proteínas Recombinantes/química , Proteínas Recombinantes/toxicidad , Propiedades de Superficie
11.
Nature ; 486(7401): 130-4, 2012 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-22678295

RESUMEN

Voltage-gated sodium (Na(v)) channels are essential for the rapid depolarization of nerve and muscle, and are important drug targets. Determination of the structures of Na(v) channels will shed light on ion channel mechanisms and facilitate potential clinical applications. A family of bacterial Na(v) channels, exemplified by the Na(+)-selective channel of bacteria (NaChBac), provides a useful model system for structure-function analysis. Here we report the crystal structure of Na(v)Rh, a NaChBac orthologue from the marine alphaproteobacterium HIMB114 (Rickettsiales sp. HIMB114; denoted Rh), at 3.05 Å resolution. The channel comprises an asymmetric tetramer. The carbonyl oxygen atoms of Thr 178 and Leu 179 constitute an inner site within the selectivity filter where a hydrated Ca(2+) resides in the crystal structure. The outer mouth of the Na(+) selectivity filter, defined by Ser 181 and Glu 183, is closed, as is the activation gate at the intracellular side of the pore. The voltage sensors adopt a depolarized conformation in which all the gating charges are exposed to the extracellular environment. We propose that Na(v)Rh is in an 'inactivated' conformation. Comparison of Na(v)Rh with Na(v)Ab reveals considerable conformational rearrangements that may underlie the electromechanical coupling mechanism of voltage-gated channels.


Asunto(s)
Alphaproteobacteria/química , Proteínas Bacterianas/química , Activación del Canal Iónico , Canales de Sodio/química , Secuencia de Aminoácidos , Proteínas Bacterianas/metabolismo , Cristalización , Cristalografía por Rayos X , Células HEK293 , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Canales de Sodio/metabolismo , Relación Estructura-Actividad
12.
Antonie Van Leeuwenhoek ; 111(10): 1767-1775, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-29536278

RESUMEN

A Gram-stain negative, aerobic, motile, non-spore-forming and rod-shaped bacterial strain, designated YIM 730227T, was isolated from a soil sample, collected from Karak district, Khyber-Pakhtun-Khwa, Pakistan. The bacterium was characterized using a polyphasic taxonomic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strain YIM 730227T is closely related to Phenylobacterium lituiforme FaiI3T (97.5% sequence similarity), Phenylobacterium muchangponense A8T (97.4%), Phenylobacterium panacis DCY109T (97.1%), Phenylobacterium immobile ET (97.1%) and Phenylobacterium composti 4T-6T (97.0%), while also sharing 98.0% sequence similarity with Phenylobacterium hankyongense HKS-05T after NCBI blast, showing it represents a member of the family Caulobacteraceae. The major respiratory quinone was Q-10 and the major fatty acids were C16:0, summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c), C18:1ω7c 11-methyl and C17:0. The polar lipids were phosphatidylglycerol, unidentified glycolipids, phospholipid and unidentified lipid. The G + C content of the genomic DNA was 68.2 mol%. The DNA-DNA relatedness values of strain YIM 730227T with P. hankyongense HKS-05T, P. lituiforme FaiI3T, P. muchangponense A8T, P. panacis DCY109T, P. immobile ET and P. composti 4T-6T were 31.3 ± 0.6, 26.1 ± 0.2, 24.3 ± 0.1, 21.8 ± 0.9, 19.8 ± 0.6 and 18.2 ± 1.1%, respectively, values lower than 70%. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of 16S rRNA gene sequences and the biochemical characteristics indicated that the strain YIM 730227T represents a novel member of the genus Phenylobacterium, for which the name Phenylobacterium terrae sp. nov. (type strain YIM 730227T = KCTC62324T = CGMCC 1.16326T) is proposed.


Asunto(s)
Alphaproteobacteria/clasificación , Alphaproteobacteria/aislamiento & purificación , Microbiología del Suelo , Alphaproteobacteria/química , Alphaproteobacteria/genética , Técnicas de Tipificación Bacteriana , Tipificación Molecular , Pakistán , Fenotipo , Filogenia , ARN Ribosómico 16S/genética
13.
Proc Natl Acad Sci U S A ; 111(23): 8428-33, 2014 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-24850863

RESUMEN

Voltage-gated sodium channels are important targets for the development of pharmaceutical drugs, because mutations in different human sodium channel isoforms have causal relationships with a range of neurological and cardiovascular diseases. In this study, functional electrophysiological studies show that the prokaryotic sodium channel from Magnetococcus marinus (NavMs) binds and is inhibited by eukaryotic sodium channel blockers in a manner similar to the human Nav1.1 channel, despite millions of years of divergent evolution between the two types of channels. Crystal complexes of the NavMs pore with several brominated blocker compounds depict a common antagonist binding site in the cavity, adjacent to lipid-facing fenestrations proposed to be the portals for drug entry. In silico docking studies indicate the full extent of the blocker binding site, and electrophysiology studies of NavMs channels with mutations at adjacent residues validate the location. These results suggest that the NavMs channel can be a valuable tool for screening and rational design of human drugs.


Asunto(s)
Alphaproteobacteria/metabolismo , Proteínas Bacterianas/metabolismo , Canal de Sodio Activado por Voltaje NAV1.1/metabolismo , Canales de Sodio/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Sitios de Unión/genética , Cristalografía por Rayos X , Células HEK293 , Humanos , Activación del Canal Iónico/efectos de los fármacos , Activación del Canal Iónico/genética , Activación del Canal Iónico/fisiología , Lamotrigina , Potenciales de la Membrana/efectos de los fármacos , Potenciales de la Membrana/fisiología , Modelos Moleculares , Datos de Secuencia Molecular , Mutación , Canal de Sodio Activado por Voltaje NAV1.1/química , Canal de Sodio Activado por Voltaje NAV1.1/genética , Estructura Terciaria de Proteína , Homología de Secuencia de Aminoácido , Bloqueadores de los Canales de Sodio/metabolismo , Bloqueadores de los Canales de Sodio/farmacología , Canales de Sodio/química , Canales de Sodio/genética , Triazinas/metabolismo , Triazinas/farmacología
14.
J Biol Chem ; 290(52): 30806-12, 2015 Dec 25.
Artículo en Inglés | MEDLINE | ID: mdl-26534965

RESUMEN

Lasso peptide isopeptidase is an enzyme that specifically hydrolyzes the isopeptide bond of lasso peptides, rendering these peptides linear. To carry out a detailed structure-activity analysis of the lasso peptide isopeptidase AtxE2 from Asticcacaulis excentricus, we solved NMR structures of its substrates astexin-2 and astexin-3. Using in vitro enzyme assays, we show that the C-terminal tail portion of these peptides is dispensable with regards to isopeptidase activity. A collection of astexin-2 and astexin-3 variants with alanine substitutions at each position within the ring and the loop was constructed, and we showed that all of these peptides except for one were cleaved by the isopeptidase. Thus, much like the lasso peptide biosynthetic enzymes, lasso peptide isopeptidase has broad substrate specificity. Quantitative analysis of the cleavage reactions indicated that alanine substitutions in loop positions of these peptides led to reduced cleavage, suggesting that the loop is serving as a recognition element for the isopeptidase.


Asunto(s)
Alphaproteobacteria/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Liasas de Carbono-Nitrógeno/química , Liasas de Carbono-Nitrógeno/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Biocatálisis , Liasas de Carbono-Nitrógeno/genética , Cristalografía por Rayos X , Modelos Moleculares , Péptidos/química , Péptidos/metabolismo , Especificidad por Sustrato
15.
Biochim Biophys Acta ; 1854(10 Pt A): 1425-37, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26093111

RESUMEN

The genome of the α-proteobacterium Pseudaminobacter salicylatoxidans codes for a ferrous iron containing ring-fission dioxygenase which catalyzes the 1,2-cleavage of (substituted) salicylate(s), gentisate (2,5-dihydroxybenzoate), and 1-hydroxy-2-naphthoate. Sequence alignments suggested that the "salicylate 1,2-dioxygenase" (SDO) from this strain is homologous to gentisate 1,2-dioxygenases found in bacteria, archaea and fungi. In the present study the catalytic mechanism of the SDO and gentisate 1,2-dioxygenases in general was analyzed based on sequence alignments, mutational and previously performed crystallographic studies and mechanistic comparisons with "extradiol- dioxygenases" which cleave aromatic nuclei in the 2,3-position. Different highly conserved amino acid residues that were supposed to take part in binding and activation of the organic substrates were modified in the SDO by site-specific mutagenesis and the enzyme variants subsequently analyzed for the conversion of salicylate, gentisate and 1-hydroxy-2-naphthoate. The analysis of enzyme variants which carried exchanges in the positions Arg83, Trp104, Gly106, Gln108, Arg127, His162 and Asp174 demonstrated that Arg83 and Arg127 were indispensable for enzymatic activity. In contrast, residual activities were found for variants carrying mutations in the residues Trp104, Gly106, Gln108, His162, and Asp174 and some of these mutants still could oxidize gentisate, but lost the ability to convert salicylate. The results were used to suggest a general reaction mechanism for gentisate-1,2-dioxygenases and to assign to certain amino acid residues in the active site specific functions in the cleavage of (substituted) salicylate(s).


Asunto(s)
Alphaproteobacteria/química , Aminoácidos/química , Proteínas Bacterianas/química , Dioxigenasas/química , Alphaproteobacteria/enzimología , Secuencia de Aminoácidos , Aminoácidos/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Dioxigenasas/genética , Dioxigenasas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Gentisatos/química , Gentisatos/metabolismo , Cinética , Datos de Secuencia Molecular , Mutación , Naftoles/química , Naftoles/metabolismo , Oxidación-Reducción , Conformación Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Salicilatos/química , Salicilatos/metabolismo , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Relación Estructura-Actividad , Especificidad por Sustrato
16.
J Am Chem Soc ; 138(29): 9193-204, 2016 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-27337563

RESUMEN

Peptidoglycan is a fundamental structure for most bacteria. It contributes to the cell morphology and provides cell wall integrity against environmental insults. While several studies have reported a significant degree of variability in the chemical composition and organization of peptidoglycan in the domain Bacteria, the real diversity of this polymer is far from fully explored. This work exploits rapid ultraperformance liquid chromatography and multivariate data analysis to uncover peptidoglycan chemical diversity in the Class Alphaproteobacteria, a group of Gram negative bacteria that are highly heterogeneous in terms of metabolism, morphology and life-styles. Indeed, chemometric analyses revealed novel peptidoglycan structures conserved in Acetobacteria: amidation at the α-(l)-carboxyl of meso-diaminopimelic acid and the presence of muropeptides cross-linked by (1-3) l-Ala-d-(meso)-diaminopimelate cross-links. Both structures are growth-controlled modifications that influence sensitivity to Type VI secretion system peptidoglycan endopeptidases and recognition by the Drosophila innate immune system, suggesting relevant roles in the environmental adaptability of these bacteria. Collectively our findings demonstrate the discriminative power of chemometric tools on large cell wall-chromatographic data sets to discover novel peptidoglycan structural properties in bacteria.


Asunto(s)
Pared Celular/metabolismo , Biología Computacional , Drosophila melanogaster/inmunología , Inmunidad Innata/efectos de los fármacos , Peptidoglicano/metabolismo , Peptidoglicano/farmacología , Alphaproteobacteria/química , Alphaproteobacteria/citología , Animales , Drosophila melanogaster/efectos de los fármacos , Endopeptidasas/metabolismo
17.
Appl Environ Microbiol ; 82(17): 5298-308, 2016 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-27342553

RESUMEN

UNLABELLED: 1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. IMPORTANCE: Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.


Asunto(s)
Alphaproteobacteria/aislamiento & purificación , Dicloruros de Etileno/metabolismo , Agua Subterránea/microbiología , Plásmidos/genética , Contaminantes Químicos del Agua/metabolismo , Xanthobacter/aislamiento & purificación , Alphaproteobacteria/química , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Secuencia de Aminoácidos , Australia , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Clonación Molecular , Datos de Secuencia Molecular , Plásmidos/metabolismo , Alineación de Secuencia , Contaminación Química del Agua , Xanthobacter/química , Xanthobacter/genética , Xanthobacter/metabolismo
18.
Photosynth Res ; 128(1): 35-43, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26482589

RESUMEN

Light-harvesting capacity was investigated in six species of aerobic anoxygenic phototrophic (AAP) bacteria using absorption spectroscopy, fluorescence emission spectroscopy, and pigment analyses. Aerobically grown AAP cells contained approx. 140-1800 photosynthetic reaction centers per cell, an order of magnitude less than purple non-sulfur bacteria grown semiaerobically. Three of the studied AAP species did not contain outer light-harvesting complexes, and the size of their reaction center core complexes (RC-LH1 core complexes) varied between 29 and 36 bacteriochlorophyll molecules. In AAP species containing accessory antennae, the size was frequently reduced, providing between 5 and 60 additional bacteriochlorophyll molecules. In Roseobacter litoralis, it was found that cells grown at a higher light intensity contained more reaction centers per cell, while the size of the light-harvesting complexes was reduced. The presented results document that AAP species have both the reduced number and size of light-harvesting complexes which is consistent with the auxiliary role of phototrophy in this bacterial group.


Asunto(s)
Alphaproteobacteria/metabolismo , Gammaproteobacteria/metabolismo , Complejos de Proteína Captadores de Luz/química , Complejos de Proteína Captadores de Luz/metabolismo , Aerobiosis , Alphaproteobacteria/química , Bacterioclorofilas/metabolismo , Gammaproteobacteria/química , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Proteínas del Complejo del Centro de Reacción Fotosintética/metabolismo , Procesos Fototróficos
19.
Appl Microbiol Biotechnol ; 100(13): 5829-38, 2016 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-26932546

RESUMEN

The catalytic activity of hexahistidine-tagged organophosphorus hydrolase (His6-OPH) in hydrolytic reactions of methylphosphonic acid (MPA) and its monoesters and diesters being decomposition products of R-VX was demonstrated for the first time. The catalytic constants of enzyme in such reactions were determined. The mechanism of C-P bond cleavage in the MPA by His6-OPH was proposed. Such reaction was estimated to be carried out with the soluble and nanocapsulated forms of His6-OPH. His6-OPH was demonstrated to be capable of degrading the key organophosphorus components of reaction masses (RMs) that are produced by the chemical detoxification of R-VX and RMs are multi-substrate mixtures for this enzyme. The kinetic model describing the behaviour of His6-OPH in RMs was proposed and was shown to adequately fit experimental points during degradation of the real samples of RMs.


Asunto(s)
Alphaproteobacteria/enzimología , Arildialquilfosfatasa/química , Proteínas Bacterianas/química , Organofosfonatos/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/genética , Arildialquilfosfatasa/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Biocatálisis , Histidina/genética , Histidina/metabolismo , Hidrólisis , Cinética , Oligopéptidos/genética , Oligopéptidos/metabolismo , Organofosfonatos/química , Especificidad por Sustrato
20.
Planta Med ; 82(13): 1143-52, 2016 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-27220082

RESUMEN

This review presents the state of knowledge on the medicinal potential of bacteria associated with lichens. In fact, besides the classical symbiotic partners (photobiont and mycobiont) forming the lichen thallus, associated bacteria have been recently described as a third partner. Various studies demonstrated the diversity of these communities with a predominance of Alphaproteobacteria. Bacterial groups more relevant for secondary metabolite synthesis have also been revealed. This article summarizes studies reporting the abilities of these communities to produce metabolites with relevant bioactivities. The biotechnological interest of these bacteria for drug discovery is highlighted regarding the production of compounds with therapeutic potential. Special focus is given to the synthesis of the most promising compound, uncialamycin, a potent enediyne isolated from a Streptomyces sp. associated with Cladonia uncialis.


Asunto(s)
Alphaproteobacteria/química , Antraquinonas/uso terapéutico , Líquenes/microbiología , Alphaproteobacteria/aislamiento & purificación , Antraquinonas/síntesis química , Antraquinonas/química , Antraquinonas/aislamiento & purificación , Descubrimiento de Drogas , Streptomyces/química
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