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1.
J Biol Chem ; 299(10): 105222, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37673337

RESUMEN

Many microorganisms use both biological and nonbiological molecules as sources of carbon and energy. This resourcefulness means that some microorganisms have mechanisms to assimilate pollutants found in the environment. One such organism is Comamonas testosteroni, which metabolizes 4-methylbenzenesulfonate and 4-methylbenzoate using the TsaMBCD pathway. TsaM is a Rieske oxygenase, which in concert with the reductase TsaB consumes a molar equivalent of NADH. Following this step, the annotated short-chain dehydrogenase/reductase and aldehyde dehydrogenase enzymes TsaC and TsaD each regenerate a molar equivalent of NADH. This co-occurrence ameliorates the need for stoichiometric addition of reducing equivalents and thus represents an attractive strategy for integration of Rieske oxygenase chemistry into biocatalytic applications. Therefore, in this work, to overcome the lack of information regarding NADH recycling enzymes that function in partnership with Rieske non-heme iron oxygenases (Rieske oxygenases), we solved the X-ray crystal structure of TsaC to a resolution of 2.18 Å. Using this structure, a series of substrate analog and protein variant combination reactions, and differential scanning fluorimetry experiments, we identified active site features involved in binding NAD+ and controlling substrate specificity. Further in vitro enzyme cascade experiments demonstrated the efficient TsaC- and TsaD-mediated regeneration of NADH to support Rieske oxygenase chemistry. Finally, through in-depth bioinformatic analyses, we illustrate the widespread co-occurrence of Rieske oxygenases with TsaC-like enzymes. This work thus demonstrates the utility of these NADH recycling enzymes and identifies a library of short-chain dehydrogenase/reductase enzyme prospects that can be used in Rieske oxygenase pathways for in situ regeneration of NADH.


Asunto(s)
Proteínas Bacterianas , Comamonas testosteroni , Oxigenasas , Aldehído Deshidrogenasa/metabolismo , NAD/metabolismo , Oxigenasas/metabolismo , Especificidad por Sustrato , Comamonas testosteroni/enzimología , Comamonas testosteroni/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/genética , Proteínas de Hierro no Heme/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Estructura Terciaria de Proteína , Modelos Moleculares , Estabilidad Proteica , Biología Computacional
2.
Curr Opin Chem Biol ; 72: 102228, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36402006

RESUMEN

Ox-/thiazoline groups in nonribosomal peptides are formed by a variant of peptide-forming condensation domains called heterocyclization (Cy) domains and appear in a range of pharmaceutically important natural products and virulence factors. Recent cryo-EM, crystallographic, and NMR studies of Cy domains make it opportune to revisit outstanding questions regarding their molecular mechanisms. This review covers structural and dynamical findings about Cy domains that will inform future bioengineering efforts and our understanding of natural product synthesis.


Asunto(s)
Péptido Sintasas , Péptidos , Ciclización , Péptido Sintasas/metabolismo , Dominios Proteicos
3.
J Biol Chem ; 298(10): 102454, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36063993

RESUMEN

Nonribosomal peptide synthetase heterocyclization (Cy) domains generate biologically important oxazoline/thiazoline groups found in natural products, including pharmaceuticals and virulence factors such as some siderophores. Cy domains catalyze consecutive condensation and cyclodehydration reactions, although the mechanism is unknown. To better understand Cy domain catalysis, here we report the crystal structure of the second Cy domain (Cy2) of yersiniabactin synthetase from the causative agent of the plague, Yersinia pestis. Our high-resolution structure of Cy2 adopts a conformation that enables exploration of interactions with the extended thiazoline-containing cyclodehydration intermediate and the acceptor carrier protein (CP) to which it is tethered. We also report complementary electrostatic interfaces between Cy2 and its donor CP that mediate donor binding. Finally, we explored domain flexibility through normal mode analysis and identified small-molecule fragment-binding sites that may inform future antibiotic design targeting Cy function. Our results suggest how CP binding may influence global Cy conformations, with consequences for active-site remodeling to facilitate the separate condensation and cyclodehydration steps as well as potential inhibitor development.


Asunto(s)
Dominio Catalítico , Péptido Sintasas , Yersinia pestis , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas Portadoras/metabolismo , Péptido Sintasas/química , Péptido Sintasas/metabolismo , Sideróforos/metabolismo , Yersinia pestis/química , Yersinia pestis/enzimología
4.
Sci Adv ; 8(28): eabn6549, 2022 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-35857508

RESUMEN

Biological activity is governed by the timely redistribution of molecular interactions, and static structural snapshots often appear insufficient to provide the molecular determinants that choreograph communication. This conundrum applies to multidomain enzymatic systems called nonribosomal peptide synthetases (NRPSs), which assemble simple substrates into complex metabolites, where a dynamic domain organization challenges rational design to produce new pharmaceuticals. Using a nuclear magnetic resonance (NMR) atomic-level readout of biochemical transformations, we demonstrate that global structural fluctuations help promote substrate-dependent communication and allosteric responses, and impeding these global dynamics by a point-site mutation hampers allostery and molecular recognition. Our results establish global structural dynamics as sensors of molecular events that can remodel domain interactions, and they provide new perspectives on mechanisms of allostery, protein communication, and NRPS synthesis.

5.
Nucleic Acids Res ; 50(6): 3001-3017, 2022 04 08.
Artículo en Inglés | MEDLINE | ID: mdl-34522950

RESUMEN

The DNAs of bacterial viruses are known to contain diverse, chemically complex modifications to thymidine that protect them from the endonuclease-based defenses of their cellular hosts, but whose biosynthetic origins are enigmatic. Up to half of thymidines in the Pseudomonas phage M6, the Salmonella phage ViI, and others, contain exotic chemical moieties synthesized through the post-replicative modification of 5-hydroxymethyluridine (5-hmdU). We have determined that these thymidine hypermodifications are derived from free amino acids enzymatically installed on 5-hmdU. These appended amino acids are further sculpted by various enzyme classes such as radical SAM isomerases, PLP-dependent decarboxylases, flavin-dependent lyases and acetyltransferases. The combinatorial permutations of thymidine hypermodification genes found in viral metagenomes from geographically widespread sources suggests an untapped reservoir of chemical diversity in DNA hypermodifications.


Asunto(s)
Bacteriófagos , Liasas , Aminoácidos/metabolismo , Bacteriófagos/genética , ADN/metabolismo , Timidina/metabolismo
6.
J Biol Chem ; 297(1): 100823, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34029591

RESUMEN

Bacterial two-component flavin-dependent monooxygenases cleave the stable C-S bond of environmental and anthropogenic organosulfur compounds. The monooxygenase MsuD converts methanesulfonate (MS-) to sulfite, completing the sulfur assimilation process during sulfate starvation, but the mechanism of this conversion remains unclear. To explore the mechanism of C-S bond cleavage, we report a series of crystal structures of MsuD from Pseudomonas fluorescens in different liganded states. This report provides the first crystal structures of an alkanesulfonate monooxygenase with a bound flavin and alkanesulfonate, elucidating the roles of the active site lid, the protein C terminus, and an active site loop in flavin and/or alkanesulfonate binding. These structures position MS- closest to the flavin N5 position, consistent with an N5-(hydro)peroxyflavin mechanism rather than a classical C4a-(hydro)peroxyflavin mechanism. A fully enclosed active site is observed in the ternary complex, mediated by interchain interaction of the C terminus at the tetramer interface. These structures identify an unexpected function of the protein C terminus in this protein family in stabilizing tetramer formation and the alkanesulfonate-binding site. Spurred by interest from the crystal structures, we conducted biochemical assays and molecular docking that redefine MsuD as a small- to medium-chain alkanesulfonate monooxygenase. Functional mutations verify the sulfonate-binding site and reveal the critical importance of the protein C terminus for monooxygenase function. These findings reveal a deeper understanding of MsuD's functionality at the molecular level and consequently how it operates within its role as part of the sulfur assimilation pathway.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Oxigenasas de Función Mixta/química , Oxigenasas de Función Mixta/metabolismo , Multimerización de Proteína , Pseudomonas fluorescens/enzimología , Secuencia de Aminoácidos , Sitios de Unión , Dominio Catalítico , Mononucleótido de Flavina/metabolismo , Mesilatos/metabolismo , Modelos Moleculares , Especificidad por Sustrato , Azufre/metabolismo
7.
Genome Biol Evol ; 12(11): 2183-2195, 2020 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-33210146

RESUMEN

In addition to known genes, much of the human genome is transcribed into RNA. Chance formation of novel open reading frames (ORFs) can lead to the translation of myriad new proteins. Some of these ORFs may yield advantageous adaptive de novo proteins. However, widespread translation of noncoding DNA can also produce hazardous protein molecules, which can misfold and/or form toxic aggregates. The dynamics of how de novo proteins emerge from potentially toxic raw materials and what influences their long-term survival are unknown. Here, using transcriptomic data from human and five other primates, we generate a set of transcribed human ORFs at six conservation levels to investigate which properties influence the early emergence and long-term retention of these expressed ORFs. As these taxa diverged from each other relatively recently, we present a fine scale view of the evolution of novel sequences over recent evolutionary time. We find that novel human-restricted ORFs are preferentially located on GC-rich gene-dense chromosomes, suggesting their retention is linked to pre-existing genes. Sequence properties such as intrinsic structural disorder and aggregation propensity-which have been proposed to play a role in survival of de novo genes-remain unchanged over time. Even very young sequences code for proteins with low aggregation propensities, suggesting that genomic regions with many novel transcribed ORFs are concomitantly less likely to produce ORFs which code for harmful toxic proteins. Our data indicate that the survival of these novel ORFs is largely stochastic rather than shaped by selection.


Asunto(s)
Evolución Molecular , Sistemas de Lectura Abierta , Primates/genética , Animales , ADN Intergénico , Humanos , Transcriptoma
8.
Genome Biol Evol ; 12(7): 1099-1188, 2020 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-32442304

RESUMEN

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.


Asunto(s)
Especiación Genética , Genoma de los Insectos , Interacciones Huésped-Parásitos/genética , Himenópteros/genética , Secuencia de Aminoácidos , Animales , Secuencia Conservada , Elementos Transponibles de ADN , Femenino , Dosificación de Gen , Glicoproteínas/genética , Herbivoria/genética , Inmunidad/genética , Proteínas de Insectos/genética , Masculino , Familia de Multigenes , Receptores Odorantes/genética , Conducta Social , Visión Ocular/genética
9.
Biochem Biophys Res Commun ; 522(1): 107-112, 2020 01 29.
Artículo en Inglés | MEDLINE | ID: mdl-31753487

RESUMEN

Methyl sulfur compounds are a rich source of environmental sulfur for microorganisms, but their use requires redox systems. The bacterial sfn and msu operons contain two-component flavin-dependent monooxygenases for dimethylsulfone (DMSO2) assimilation: SfnG converts DMSO2 to methanesulfinate (MSI-), and MsuD converts methanesulfonate (MS-) to sulfite. However, the enzymatic oxidation of MSI- to MS- has not been demonstrated, and the function of the last enzyme of the msu operon (MsuC) is unresolved. We employed crystallographic and biochemical studies to identify the function of MsuC from Pseudomonas fluorescens. The crystal structure of MsuC adopts the acyl-CoA dehydrogenase fold with putative binding sites for flavin and MSI-, and functional assays of MsuC in the presence of its oxidoreductase MsuE, FMN, and NADH confirm the enzymatic generation of MS-. These studies reveal that MsuC converts MSI- to MS- in sulfite biosynthesis from DMSO2.


Asunto(s)
Proteínas Bacterianas/metabolismo , Pseudomonas fluorescens/enzimología , Azufre/química , Acil-CoA Deshidrogenasa/metabolismo , Sitios de Unión , Cristalografía por Rayos X , Dimerización , Dimetilsulfóxido/química , Flavinas/química , Espectroscopía de Resonancia Magnética , Mesilatos/química , Simulación del Acoplamiento Molecular , Oxidorreductasas/metabolismo , Oxígeno/química , Estructura Secundaria de Proteína , Relación Estructura-Actividad , Sulfuros/química , Sulfonas/química , Tiofenos/química
10.
Protein Sci ; 28(1): 202-215, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-30341796

RESUMEN

7-Carboxy-7-deazaguanine synthase, QueE, catalyzes the radical mediated ring contraction of 6-carboxy-5,6,7,8-tetrahydropterin, forming the characteristic pyrrolopyrimidine core of all 7-deazaguanine natural products. QueE is a member of the S-adenosyl-L-methionine (AdoMet) radical enzyme superfamily, which harnesses the reactivity of radical intermediates to perform challenging chemical reactions. Members of the AdoMet radical enzyme superfamily utilize a canonical binding motif, a CX3 CXϕC motif, to bind a [4Fe-4S] cluster, and a partial (ß/α)6 TIM barrel fold for the arrangement of AdoMet and substrates for catalysis. Although variations to both the cluster-binding motif and the core fold have been observed, visualization of drastic variations in the structure of QueE from Burkholderia multivorans called into question whether a re-haul of the defining characteristics of this superfamily was in order. Surprisingly, the structure of QueE from Bacillus subtilis revealed an architecture more reminiscent of the classical AdoMet radical enzyme. With these two QueE structures revealing varying degrees of alterations to the classical AdoMet fold, a new question arises: what is the purpose of these alterations? Here, we present the structure of a third QueE enzyme from Escherichia coli, which establishes the middle range of the spectrum of variation observed in these homologs. With these three homologs, we compare and contrast the structural architecture and make hypotheses about the role of these structural variations in binding and recognizing the biological reductant, flavodoxin. Broader impact statement: We know more about how enzymes are tailored for catalytic activity than about how enzymes are tailored to react with a physiological reductant. Here, we consider structural differences between three 7-carboxy-7-deazaguanine synthases and how these differences may be related to the interaction between these enzymes and their biological reductant, flavodoxin.


Asunto(s)
Liasas de Carbono-Nitrógeno/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimología , Proteínas Hierro-Azufre/química , Secuencias de Aminoácidos , Cristalografía por Rayos X , Flavodoxina , Dominios Proteicos , Especificidad por Sustrato
11.
BMC Bioinformatics ; 18(1): 111, 2017 Feb 16.
Artículo en Inglés | MEDLINE | ID: mdl-28209129

RESUMEN

BACKGROUND: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses. RESULTS: We present a new software pipeline, Orthograph, that addresses and solves the above problems and implements useful features for a wide range of comparative genomic and transcriptomic analyses. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. We demonstrate the performance of our approach on de novo-sequenced and assembled transcript libraries of 24 species of apoid wasps (Hymenoptera: Aculeata) as well as on published genomic datasets. CONCLUSION: With Orthograph, we implemented a best reciprocal hit approach to reference-based orthology prediction for coding nucleotide sequences such as RNAseq data. Orthograph is flexible, easy to use, open source and freely available at https://mptrsen.github.io/Orthograph . Additionally, we release 24 de novo-sequenced and assembled transcript libraries of apoid wasp species.


Asunto(s)
Genómica/métodos , Familia de Multigenes/genética , Sistemas de Lectura Abierta/genética , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de Proteína/métodos , Programas Informáticos , Animales , Genoma/genética , Transcriptoma/genética , Avispas/genética
12.
J Am Chem Soc ; 139(5): 1912-1920, 2017 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-28045519

RESUMEN

Radical S-adenosyl-l-methionine (SAM) enzymes are widely distributed and catalyze diverse reactions. SAM binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster and is reductively cleaved to generate a 5'-deoxyadenosyl radical, which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes a key step in the biosynthesis of 7-deazapurine containing natural products. 6-Carboxypterin (6-CP), an oxidized analogue of the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase. Under reducing conditions that would promote the reductive cleavage of SAM, 6-CP is turned over to 6-deoxyadenosylpterin (6-dAP), presumably by radical addition of the 5'-deoxyadenosine followed by oxidative decarboxylation to the product. By contrast, in the absence of the strong reductant, dithionite, the carboxylate of 6-CP is esterified to generate 6-carboxypterin-5'-deoxyadenosyl ester (6-CP-dAdo ester). Structural studies with 6-CP and SAM also reveal electron density consistent with the ester product being formed in crystallo. The differential reactivity of 6-CP under reducing and nonreducing conditions highlights the ability of radical SAM enzymes to carry out both polar and radical transformations in the same active site.


Asunto(s)
Proteínas Bacterianas/metabolismo , Productos Biológicos/metabolismo , Liasas de Carbono-Nitrógeno/metabolismo , Purinas/biosíntesis , S-Adenosilmetionina/metabolismo , Proteínas Bacterianas/química , Biocatálisis , Productos Biológicos/química , Liasas de Carbono-Nitrógeno/química , Cristalografía por Rayos X , Radicales Libres/química , Radicales Libres/metabolismo , Modelos Moleculares , Estructura Molecular , Purinas/química , S-Adenosilmetionina/química
13.
Proc Natl Acad Sci U S A ; 113(44): 12432-12437, 2016 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-27791103

RESUMEN

Epothilones are thiazole-containing natural products with anticancer activity that are biosynthesized by polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) enzymes EpoA-F. A cyclization domain of EpoB (Cy) assembles the thiazole functionality from an acetyl group and l-cysteine via condensation, cyclization, and dehydration. The PKS carrier protein of EpoA contributes the acetyl moiety, guided by a docking domain, whereas an NRPS EpoB carrier protein contributes l-cysteine. To visualize the structure of a cyclization domain with an accompanying docking domain, we solved a 2.03-Å resolution structure of this bidomain EpoB unit, comprising residues M1-Q497 (62 kDa) of the 160-kDa EpoB protein. We find that the N-terminal docking domain is connected to the V-shaped Cy domain by a 20-residue linker but otherwise makes no contacts to Cy. Molecular dynamic simulations and additional crystal structures reveal a high degree of flexibility for this docking domain, emphasizing the modular nature of the components of PKS-NRPS hybrid systems. These structures further reveal two 20-Å-long channels that run from distant sites on the Cy domain to the active site at the core of the enzyme, allowing two carrier proteins to dock with Cy and deliver their substrates simultaneously. Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified. Surprisingly, these residues do not map to the location of the conserved HHxxxDG motif in the structurally homologous NRPS condensation (C) domain. Thus, although both C and Cy domains have the same basic fold, their active sites appear distinct.


Asunto(s)
Epotilonas/química , Péptido Sintasas/química , Sintasas Poliquetidas/química , Dominios Proteicos , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Vías Biosintéticas/genética , Dominio Catalítico , Cristalografía por Rayos X , Ciclización , Epotilonas/metabolismo , Modelos Moleculares , Myxococcales/genética , Myxococcales/metabolismo , Péptido Sintasas/genética , Péptido Sintasas/metabolismo , Sintasas Poliquetidas/genética , Sintasas Poliquetidas/metabolismo , Unión Proteica , Homología de Secuencia de Aminoácido , Tiazoles/química , Tiazoles/metabolismo
14.
BMC Genomics ; 17(1): 861, 2016 Nov 03.
Artículo en Inglés | MEDLINE | ID: mdl-27809783

RESUMEN

BACKGROUND: Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. RESULTS: Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection. CONCLUSIONS: Our results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods.


Asunto(s)
Artrópodos/genética , Proteínas de Unión al ADN/genética , Evolución Molecular , Elementos Aisladores , Transcriptoma , Animales , Drosophila melanogaster/genética , Elementos de Facilitación Genéticos , Perfilación de la Expresión Génica , Filogenia
15.
Nucleic Acids Res ; 44(20): 9965-9976, 2016 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-27638883

RESUMEN

Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet the final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), was only recently identified. QueG is a cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces the hypermodified nucleoside Q in situ on four tRNAs. To understand how QueG is able to perform epoxide reduction, an unprecedented reaction for a Cbl-dependent enzyme, we have determined a series of high resolution structures of QueG from Bacillus subtilis Our structure of QueG bound to a tRNATyr anticodon stem loop shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site. We find Q bound directly above the Cbl, consistent with a reaction mechanism that involves the formation of a covalent Cbl-tRNA intermediate. Using protein film electrochemistry, we show that two [4Fe-4S] clusters adjacent to the Cbl have redox potentials in the range expected for Cbl reduction, suggesting how Cbl can be activated for nucleophilic attack on oQ. Together, these structural and electrochemical data inform our understanding of Cbl dependent nucleic acid modification.


Asunto(s)
Procesamiento Postranscripcional del ARN , ARN de Transferencia/química , ARN de Transferencia/genética , Vitamina B 12/química , Anticodón , Bacillus subtilis/genética , Enlace de Hidrógeno , Hierro/química , Modelos Moleculares , Conformación Molecular , Conformación de Ácido Nucleico , Nucleósido Q/análogos & derivados , Nucleósido Q/química , Unión Proteica , Estabilidad del ARN , ARN Bacteriano/química , ARN Bacteriano/genética , ARN Bacteriano/metabolismo , ARN de Transferencia/metabolismo , Ribonucleasas/química , Ribonucleasas/metabolismo , Azufre/química , Vitamina B 12/metabolismo
16.
Genome Biol Evol ; 8(12): 3784-3793, 2016 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-28062756

RESUMEN

RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders. We inferred the phylogenetic origin of insect-specific RNAi pathway genes and also identified several hitherto unrecorded gene expansions using whole-body transcriptome data from the international 1KITE (1000 Insect Transcriptome Evolution) project as well as other resources such as i5K (5000 Insect Genome Project). Specifically, we traced the origin of the double stranded RNA binding protein R2D2 to the last common ancestor of winged insects (Pterygota), the loss of Sid-1/Tag-130 orthologs in Antliophora (fleas, flies and relatives, and scorpionflies in a broad sense), and confirm previous evidence for the splitting of the Argonaute proteins Aubergine and Piwi in Brachyceran flies (Diptera, Brachycera). Our study offers new reference points for future experimental research on RNAi-related pathway genes in insects.


Asunto(s)
Evolución Molecular , Insectos/genética , Filogenia , Interferencia de ARN , Animales , Proteínas Argonautas/genética , Proteínas de Drosophila/genética , Genoma de los Insectos , Proteínas de Insectos/genética , Factores de Iniciación de Péptidos/genética , Proteínas de Unión al ARN/genética , Transducción de Señal/genética
17.
Proc Biol Sci ; 282(1821): 20151777, 2015 12 22.
Artículo en Inglés | MEDLINE | ID: mdl-26674944

RESUMEN

Cleptoparasitic wasps and bees smuggle their eggs into the nest of a host organism. Here the larvae of the cleptoparasite feed upon the food provision intended for the offspring of the host. As cleptoparasitism incurs a loss of fitness for the host organism (offspring of the host fail to develop), hosts of cleptoparasites are expected to exploit cues that alert them to potential cleptoparasite infestation. Cuticular hydrocarbons (CHCs) could serve as such cues, as insects inevitably leave traces of them behind when entering a nest. By mimicking the host's CHC profile, cleptoparasites can conceal their presence and evade detection by their host. Previous studies have provided evidence of cleptoparasites mimicking their host's CHC profile. However, the impact of this strategy on the evolution of the host's CHC profile has remained unexplored. Here, we present results from our investigation of a host-cleptoparasite system consisting of a single mason wasp species that serves syntopically as the host to three cuckoo wasp species. We found that the spiny mason wasp (Odynerus spinipes) is able to express two substantially different CHC profiles, each of which is seemingly mimicked by a cleptoparasitic cuckoo wasp (i.e. Chrysis mediata and Pseudospinolia neglecta). The CHC profile of the third cuckoo wasp (Chrysis viridula), a species not expected to benefit from mimicking its host's CHC profile because of its particular oviposition strategy, differs from the two CHC profiles of its host. Our results corroborate the idea that the similarity of the CHC profiles between cleptoparasitic cuckoo wasps and their hosts are the result of chemical mimicry. They further suggest that cleptoparasites may represent a hitherto unappreciated force that drives the evolution of their hosts' CHCs.


Asunto(s)
Hidrocarburos/química , Avispas/química , Avispas/parasitología , Comunicación Animal , Animales , Evolución Biológica , Señales (Psicología) , Interacciones Huésped-Parásitos , Odorantes , Análisis de Secuencia de ADN , Especificidad de la Especie , Avispas/fisiología
18.
J Diabetes Res ; 2014: 624939, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25054159

RESUMEN

PURPOSE: To investigate cardiomyopathy in offspring in a mouse model of pregestational type 1 diabetic pregnancy. METHODS: Pregestational diabetes was induced with STZ administration in female C57BL6/J mice that were subsequently mated with healthy C57BL6/J males. Offspring were sacrificed at embryonic day 18.5 and 6-week adolescent and 12-week adult stages. The size and number of cardiomyocyte nuclei and also the extent of collagen deposition within the hearts of diabetic and control offspring were assessed following cardiac tissue staining with either haematoxylin and eosin or Picrosirius red and subsequently quantified using automated digital image analysis. RESULTS: Offspring from diabetic mice at embryonic day 18.5 had a significantly higher number of cardiomyocyte nuclei present compared to controls. These nuclei were also significantly smaller than controls. Collagen deposition was shown to be significantly increased in the hearts of diabetic offspring at the same age. No significant differences were found between the groups at 6 and 12 weeks. CONCLUSIONS: Our results from offspring of type 1 diabetic mice show increased myocardial collagen deposition in late gestation and have increased myocardial nuclear counts (hyperplasia) as opposed to increased myocardial nuclear size (hypertrophy) in late gestation. These changes normalize postpartum after removal from the maternal intrauterine environment.


Asunto(s)
Cardiomiopatías/etiología , Diabetes Gestacional/fisiopatología , Modelos Animales de Enfermedad , Corazón/embriología , Animales , Cardiomiopatías/fisiopatología , Núcleo Celular/metabolismo , Colágeno/metabolismo , Diabetes Mellitus Experimental/complicaciones , Diabetes Mellitus Tipo 1/fisiopatología , Femenino , Cardiopatías Congénitas/fisiopatología , Masculino , Ratones , Ratones Endogámicos C57BL , Miocitos Cardíacos/patología , Embarazo , Preñez
19.
Nat Chem Biol ; 10(2): 106-12, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24362703

RESUMEN

7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg(2+)-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a member of the AdoMet radical superfamily, which employs the 5'-deoxyadenosyl radical from reductive cleavage of AdoMet to initiate chemistry. To provide a mechanistic rationale for this elaborate transformation, we present the crystal structure of a QueE along with structures of pre- and post-turnover states. We find that substrate binds perpendicular to the [4Fe-4S]-bound AdoMet, exposing its C6 hydrogen atom for abstraction and generating the binding site for Mg(2+), which coordinates directly to the substrate. The Burkholderia multivorans structure reported here varies from all other previously characterized members of the AdoMet radical superfamily in that it contains a hypermodified (ß6/α3) protein core and an expanded cluster-binding motif, CX14CX2C.


Asunto(s)
Magnesio/química , Manganeso/química , Modelos Moleculares , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo , Sodio/química , Sitios de Unión , Burkholderia/enzimología , Radicales Libres/química , Radicales Libres/metabolismo , Enlace de Hidrógeno/efectos de los fármacos , Magnesio/farmacología , Manganeso/farmacología , Estructura Molecular , Estructura Terciaria de Proteína , Sodio/farmacología
20.
Obes Facts ; 6(2): 134-45, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23571656

RESUMEN

The incidence of obesity, increased weight gain and the popularity of high-fat / high-sugar diets are seriously impacting upon the global population. Billions of individuals are affected, and although diet and lifestyle are of paramount importance to the development of adult obesity, compelling evidence is emerging which suggests that maternal obesity and related disorders may be passed on to the next generation by non-genetic means. The processes acting within the uteri of obese mothers may permanently predispose offspring to a diverse plethora of diseases ranging from obesity and diabetes to psychiatric disorders. This review aims to summarise some of the molecular mechanisms and active processes currently known about maternal obesity and its effect on foetal and neonatal physiology and metabolism. Complex and multifactorial networks of molecules are intertwined and culminate in a pathologically synergistic manner to cause disruption and disorganisation of foetal physiology. This altered phenotype may potentiate the cycle of intergenerational transmission of obesity and related disorders.


Asunto(s)
Epigénesis Genética , Fenómenos Fisiologicos Nutricionales Maternos , Obesidad/etiología , Fenotipo , Efectos Tardíos de la Exposición Prenatal , Adulto , Femenino , Feto , Humanos , Fenómenos Fisiologicos Nutricionales Maternos/genética , Obesidad/genética , Embarazo , Efectos Tardíos de la Exposición Prenatal/genética
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