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1.
Food Chem ; 448: 139182, 2024 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-38569413

RESUMEN

Amylosucrase (ASase) efficiently biosynthesizes α-glucoside using flavonoids as acceptor molecules and sucrose as a donor molecule. Here, ASase from Deinococcus wulumuqiensis (DwAS) biosynthesized more naringenin α-glucoside (NαG) with sucrose and naringenin as donor and acceptor molecules, respectively, than other ASases from Deinococcus sp. The biotransformation rate of DwAS to NαG was 21.3% compared to 7.1-16.2% for other ASases. Docking simulations showed that the active site of DwAS was more accessible to naringenin than those of others. The 217th valine in DwAS corresponded to the 221st isoleucine in Deinococcus geothermalis AS (DgAS), and the isoleucine possibly prevented naringenin from accessing the active site. The DwAS-V217I mutant had a significantly lower biosynthetic rate of NαG than DwAS. The kcat/Km value of DwAS with naringenin as the donor was significantly higher than that of DgAS and DwAS-V217I. In addition, NαG inhibited human intestinal α-glucosidase more efficiently than naringenin.


Asunto(s)
Proteínas Bacterianas , Biotransformación , Deinococcus , Flavanonas , Glucósidos , Glucosiltransferasas , Inhibidores de Glicósido Hidrolasas , Flavanonas/metabolismo , Flavanonas/química , Deinococcus/enzimología , Deinococcus/metabolismo , Deinococcus/química , Deinococcus/genética , Glucosiltransferasas/metabolismo , Glucosiltransferasas/química , Glucosiltransferasas/genética , Inhibidores de Glicósido Hidrolasas/química , Inhibidores de Glicósido Hidrolasas/metabolismo , Inhibidores de Glicósido Hidrolasas/farmacología , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Glucósidos/metabolismo , Glucósidos/química , Simulación del Acoplamiento Molecular , Cinética , alfa-Glucosidasas/metabolismo , alfa-Glucosidasas/química
2.
Nature ; 616(7956): 384-389, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-37020015

RESUMEN

The widespread TnpB proteins of IS200/IS605 transposon family have recently emerged as the smallest RNA-guided nucleases capable of targeted genome editing in eukaryotic cells1,2. Bioinformatic analysis identified TnpB proteins as the likely predecessors of Cas12 nucleases3-5, which along with Cas9 are widely used for targeted genome manipulation. Whereas Cas12 family nucleases are well characterized both biochemically and structurally6, the molecular mechanism of TnpB remains unknown. Here we present the cryogenic-electron microscopy structures of the Deinococcus radiodurans TnpB-reRNA (right-end transposon element-derived RNA) complex in DNA-bound and -free forms. The structures reveal the basic architecture of TnpB nuclease and the molecular mechanism for DNA target recognition and cleavage that is supported by biochemical experiments. Collectively, these results demonstrate that TnpB represents the minimal structural and functional core of the Cas12 protein family and provide a framework for developing TnpB-based genome editing tools.


Asunto(s)
Proteínas Asociadas a CRISPR , Elementos Transponibles de ADN , Deinococcus , Endonucleasas , Edición Génica , Proteínas Asociadas a CRISPR/química , Proteínas Asociadas a CRISPR/clasificación , Proteínas Asociadas a CRISPR/metabolismo , Proteínas Asociadas a CRISPR/ultraestructura , Sistemas CRISPR-Cas/genética , Microscopía por Crioelectrón , Deinococcus/enzimología , Deinococcus/genética , ADN/química , ADN/genética , ADN/metabolismo , ADN/ultraestructura , Elementos Transponibles de ADN/genética , Endonucleasas/química , Endonucleasas/clasificación , Endonucleasas/metabolismo , Endonucleasas/ultraestructura , Evolución Molecular , Edición Génica/métodos , ARN Guía de Sistemas CRISPR-Cas
3.
Nature ; 616(7956): 390-397, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-37020030

RESUMEN

The class 2 type V CRISPR effector Cas12 is thought to have evolved from the IS200/IS605 superfamily of transposon-associated TnpB proteins1. Recent studies have identified TnpB proteins as miniature RNA-guided DNA endonucleases2,3. TnpB associates with a single, long RNA (ωRNA) and cleaves double-stranded DNA targets complementary to the ωRNA guide. However, the RNA-guided DNA cleavage mechanism of TnpB and its evolutionary relationship with Cas12 enzymes remain unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of Deinococcus radiodurans ISDra2 TnpB in complex with its cognate ωRNA and target DNA. In the structure, the ωRNA adopts an unexpected architecture and forms a pseudoknot, which is conserved among all guide RNAs of Cas12 enzymes. Furthermore, the structure, along with our functional analysis, reveals how the compact TnpB recognizes the ωRNA and cleaves target DNA complementary to the guide. A structural comparison of TnpB with Cas12 enzymes suggests that CRISPR-Cas12 effectors acquired an ability to recognize the protospacer-adjacent motif-distal end of the guide RNA-target DNA heteroduplex, by either asymmetric dimer formation or diverse REC2 insertions, enabling engagement in CRISPR-Cas adaptive immunity. Collectively, our findings provide mechanistic insights into TnpB function and advance our understanding of the evolution from transposon-encoded TnpB proteins to CRISPR-Cas12 effectors.


Asunto(s)
Proteínas Bacterianas , Microscopía por Crioelectrón , Elementos Transponibles de ADN , Deinococcus , Endodesoxirribonucleasas , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/ultraestructura , Proteínas Asociadas a CRISPR/química , Proteínas Asociadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , ADN/química , ADN/genética , ADN/metabolismo , ADN/ultraestructura , Elementos Transponibles de ADN/genética , ARN Guía de Sistemas CRISPR-Cas/química , ARN Guía de Sistemas CRISPR-Cas/genética , ARN Guía de Sistemas CRISPR-Cas/metabolismo , ARN Guía de Sistemas CRISPR-Cas/ultraestructura , Endodesoxirribonucleasas/química , Endodesoxirribonucleasas/metabolismo , Endodesoxirribonucleasas/ultraestructura , Deinococcus/enzimología , Deinococcus/genética , Especificidad por Sustrato
4.
Nature ; 599(7886): 692-696, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34619744

RESUMEN

Transposition has a key role in reshaping genomes of all living organisms1. Insertion sequences of IS200/IS605 and IS607 families2 are among the simplest mobile genetic elements and contain only the genes that are required for their transposition and its regulation. These elements encode tnpA transposase, which is essential for mobilization, and often carry an accessory tnpB gene, which is dispensable for transposition. Although the role of TnpA in transposon mobilization of IS200/IS605 is well documented, the function of TnpB has remained largely unknown. It had been suggested that TnpB has a role in the regulation of transposition, although no mechanism for this has been established3-5. A bioinformatic analysis indicated that TnpB might be a predecessor of the CRISPR-Cas9/Cas12 nucleases6-8. However, no biochemical activities have been ascribed to TnpB. Here we show that TnpB of Deinococcus radiodurans ISDra2 is an RNA-directed nuclease that is guided by an RNA, derived from the right-end element of a transposon, to cleave DNA next to the 5'-TTGAT transposon-associated motif. We also show that TnpB could be reprogrammed to cleave DNA target sites in human cells. Together, this study expands our understanding of transposition mechanisms by highlighting the role of TnpB in transposition, experimentally confirms that TnpB is a functional progenitor of CRISPR-Cas nucleases and establishes TnpB as a prototype of a new system for genome editing.


Asunto(s)
Elementos Transponibles de ADN/genética , Deinococcus/enzimología , Deinococcus/genética , Desoxirribonucleasa I/genética , Desoxirribonucleasa I/metabolismo , ARN/genética , Secuencia de Bases , Proteínas Asociadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , Escherichia coli/genética , Edición Génica , Células HEK293 , Humanos , Motivos de Nucleótidos
5.
Sci Rep ; 11(1): 21106, 2021 10 26.
Artículo en Inglés | MEDLINE | ID: mdl-34702889

RESUMEN

RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response. It is also used in the context of biotechnological applications in recombinase polymerase isothermal amplification (RPA). In this work, we studied the biological properties of seven RecA variants, in particular their recombinogenic activity and their ability to induce the SOS response, to better understand the structure-function relationship of RecA and the effect of combined mutations. We also investigated the biochemical properties of RecA variants that may be useful for the development of biotechnological applications. We showed that Dickeya dadantii RecA (DdRecA) had an optimum strand exchange activity at 30 °C and in the presence of a dNTP mixture that inhibited Escherichia coli RecA (EcRecA). The differences between the CTD and C-tail of the EcRecA and DdRecA domains could explain the altered behaviour of DdRecA. D. radiodurans RecA (DrRecA) was unable to perform recombination and activation of the SOS response in an E. coli context, probably due to its inability to interact with E. coli recombination accessory proteins and SOS LexA repressor. DrRecA strand exchange activity was totally inhibited in the presence of chloride ions but worked well in acetate buffer. The overproduction of Pseudomonas aeruginosa RecA (PaRecA) in an E. coli context was responsible for a higher SOS response and defects in cellular growth. PaRecA was less inhibited by the dNTP mixture than EcRecA. Finally, the study of three variants, namely, EcPa, EcRecAV1 and EcRecAV2, that contained a combination of mutations that, taken independently, are described as improving recombination, led us to raise new hypotheses on the structure-function relationship and on the monomer-monomer interactions that perturb the activity of the protein as a whole.


Asunto(s)
Proteínas de Unión al ADN/química , Deinococcus/enzimología , Dickeya/enzimología , Proteínas de Escherichia coli/química , Escherichia coli/enzimología , Pseudomonas aeruginosa/enzimología , Rec A Recombinasas/química , Proteínas de Unión al ADN/genética , Deinococcus/genética , Dickeya/genética , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Pseudomonas aeruginosa/genética , Rec A Recombinasas/genética , Especificidad de la Especie
6.
J Microbiol Biotechnol ; 31(12): 1692-1700, 2021 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-34584041

RESUMEN

Glycosylation of resveratrol was carried out by using the amylosucrase of Deinococcus geothermalis, and the glycosylated products were tested for their solubility, chemical stability, and biological activities. We synthesized and identified these two major glycosylated products as resveratrol-4'-O-α-glucoside and resveratrol-3-O-α-glucoside by nuclear magnetic resonance analysis with a ratio of 5:1. The water solubilities of the two resveratrol-α-glucoside isomers (α-piceid isomers) were approximately 3.6 and 13.5 times higher than that of ß-piceid and resveratrol, respectively, and they were also highly stable in buffered solutions. The antioxidant activity of the α-piceid isomers, examined by radical scavenging capability, showed it to be initially lower than that of resveratrol, but as time passed, the α-piceid isomers' activity reached a level similar to that of resveratrol. The α-piceid isomers also showed better inhibitory activity against tyrosinase and melanin synthesis in B16F10 melanoma cells than ß-piceid. The cellular uptake of the α-piceid isomers, which was assessed by ultra-performance liquid chromatography (UPLC) analysis of the cell-free extracts of B16F10 melanoma cells, demonstrated that the glycosylated form of resveratrol was gradually converted to resveratrol inside the cells. These results indicate that the enzymatic glycosylation of resveratrol could be a useful method for enhancing the bioavailability of resveratrol.


Asunto(s)
Antioxidantes/metabolismo , Deinococcus/enzimología , Glucosiltransferasas/metabolismo , Resveratrol/metabolismo , Animales , Antioxidantes/química , Disponibilidad Biológica , Línea Celular Tumoral , Glucósidos/química , Glucósidos/metabolismo , Glicosilación , Melaninas/metabolismo , Ratones , Monofenol Monooxigenasa/antagonistas & inhibidores , Proteínas Recombinantes/metabolismo , Resveratrol/química , Solubilidad
7.
Nat Commun ; 12(1): 4394, 2021 07 20.
Artículo en Inglés | MEDLINE | ID: mdl-34285211

RESUMEN

Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While Agp1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes suggest the use of light-controllable histidine kinases and phosphatases for optogenetics.


Asunto(s)
Proteínas Bacterianas/metabolismo , Histidina Quinasa/metabolismo , Monoéster Fosfórico Hidrolasas/metabolismo , Fotorreceptores Microbianos/metabolismo , Transducción de Señal/efectos de la radiación , Agrobacterium/enzimología , Proteínas Bacterianas/ultraestructura , Deinococcus/enzimología , Histidina Quinasa/ultraestructura , Luz , Simulación de Dinámica Molecular , Monoéster Fosfórico Hidrolasas/ultraestructura , Fotorreceptores Microbianos/ultraestructura , Dominios Proteicos
8.
Int J Mol Sci ; 22(11)2021 May 25.
Artículo en Inglés | MEDLINE | ID: mdl-34070642

RESUMEN

Urate oxidase initiates the uric acid degradation pathways and is extensively used for protein drug development for gout therapy and serum uric acid diagnosis. We first present the biochemical and structural elucidation of a urate oxidase from the extremophile microorganism Deinococcus radiodurans (DrUox). From enzyme characterization, DrUox showed optimal catalytic ability at 30 °C and pH 9.0 with high stability under physiological conditions. Only the Mg2+ ion moderately elevated its activity, which indicates the characteristic of the cofactor-free urate oxidase family. Of note, DrUox is thermostable in mesophilic conditions. It retains almost 100% activity when incubated at 25 °C and 37 °C for 24 h. In this study, we characterized a thermostable urate oxidase, DrUox with high catalytic efficiency and thermal stability, which strengthens its potential for medical applications.


Asunto(s)
Proteínas Bacterianas , Deinococcus , Gota/tratamiento farmacológico , Hiperuricemia/tratamiento farmacológico , Urato Oxidasa , Animales , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/uso terapéutico , Deinococcus/enzimología , Deinococcus/genética , Humanos , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/uso terapéutico , Urato Oxidasa/química , Urato Oxidasa/genética , Urato Oxidasa/uso terapéutico
9.
Sci Rep ; 11(1): 10939, 2021 05 25.
Artículo en Inglés | MEDLINE | ID: mdl-34035321

RESUMEN

Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4-11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.


Asunto(s)
Reparación del ADN , Deinococcus/genética , Inestabilidad Genómica , Mutación , Rec A Recombinasas/genética , Roturas del ADN de Doble Cadena , Análisis Mutacional de ADN , ADN Bacteriano/metabolismo , Deinococcus/enzimología , Genoma Bacteriano , Eliminación de Secuencia
10.
Mar Genomics ; 57: 100832, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33867118

RESUMEN

The general features and genomic characteristics of gram-positive Deinococcus sp. D7000 isolated from the hadal region of Mariana Trench Challenger Deep were analyzed in this study. Deinococcus sp. D7000 has a genome consisting of 4,558,742 bp, including one chromosome and nine plasmids. This strain exhibits extracellular protease activity under low temperatures. Among 4328 protein-coding sequences (CDSs), 47 encode serine peptidases. Multiple annotation analysis was used to identify two genes encoding extracellular subtilases. In addition, three types of extracellular secretion transporter systems were found upon pathway construction and analysis. Genome analysis offers insights into the putative pathway of extracellular protease and application prospect of Deinococcus sp. D7000 in enzyme development.


Asunto(s)
Deinococcus/genética , Genoma Bacteriano , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Deinococcus/enzimología , Océano Pacífico , Péptido Hidrolasas/genética , Péptido Hidrolasas/metabolismo , Secuenciación Completa del Genoma
11.
Biochimie ; 185: 22-32, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33727139

RESUMEN

Deinococcus radiodurans survives extraordinary doses of ionizing radiation and desiccation that cause numerous DNA strand breaks. D. radiodurans DNA polymerase A (DrPolA) is essential for reassembling the shattered genome, while its biochemical property has not been fully demonstrated. In this study, we systematically examined the enzymatic activities of DrPolA and characterized its unique features. DrPolA contains an N-terminal nuclease domain (DrPolA-NTD) and a C-terminal Klenow fragment (KlenDr). Compared with the Klenow fragment of E. coli Pol I, KlenDr shows higher fidelity despite the lacking of 3'-5' exonuclease proofreading activity and prefers double-strand DNA rather than Primer-Template substrates. Apart from the well-annotated 5'-3' exonuclease and flap endonuclease activities, DrPolA-NTD displays approximately 140-fold higher gap endonuclease activity than its homolog in E. coli and Human FEN1. Its 5'-3' exonuclease activity on ssDNA, gap endonuclease, and Holliday junction cleavage activities are greatly enhanced by Mn2+. The DrPolA-NTD deficient strain shows increased sensitivity to UV and gamma-ray radiation. Collectively, our results reveal distinct biochemical characteristics of DrPolA during DNA degradation and re-synthesis, which provide new insight into the outstanding DNA repair capacity of D. radiodurans.


Asunto(s)
Proteínas Bacterianas/química , ADN Polimerasa III/química , ADN Bacteriano/química , Deinococcus/enzimología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , ADN Polimerasa III/genética , ADN Polimerasa III/metabolismo , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , Deinococcus/genética , Humanos
12.
Biochem Biophys Res Commun ; 539: 42-47, 2021 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-33421767

RESUMEN

In this report, we describe a truncated Deinococcus radiodurans 1-deoxy-D-xylulose-5-phosphate synthase (DXS) protein that retains enzymatic activity, while slowing protein degradation and showing improved crystallization properties. With modern drug-design approaches relying heavily on the elucidation of atomic interactions of potential new drugs with their targets, the need for co-crystal structures with the compounds of interest is high. DXS itself is a promising drug target, as it catalyzes the first reaction in the 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway for the biosynthesis of the universal precursors of terpenes, which are essential secondary metabolites. In contrast to many bacteria and pathogens, which employ the MEP pathway, mammals use the distinct mevalonate-pathway for the biosynthesis of these precursors, which makes all enzymes of the MEP-pathway potential new targets for the development of anti-infectives. However, crystallization of DXS has proven to be challenging: while the first X-ray structures from Escherichia coli and D. radiodurans were solved in 2004, since then only two additions have been made in 2019 that were obtained under anoxic conditions. The presented site of truncation can potentially also be transferred to other homologues, opening up the possibility for the determination of crystal structures from pathogenic species, which until now could not be crystallized. This manuscript also provides a further example that truncation of a variable region of a protein can lead to improved structural data.


Asunto(s)
Deinococcus/enzimología , Escherichia coli/enzimología , Proteínas Mutantes/química , Transferasas/química , Secuencia de Aminoácidos , Cristalografía por Rayos X/métodos , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Mutación , Elementos Estructurales de las Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Homología de Secuencia , Transferasas/genética , Transferasas/metabolismo
13.
J Microbiol Biotechnol ; 31(1): 43-50, 2021 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-33046683

RESUMEN

A newly cloned 4-α-glucanotransferase (αGT) from Deinococcus geothermalis and two typical bacterial αGTs from Thermus scotoductus and Escherichia coli (MalQ) were investigated. Among 4 types of catalysis, the cyclization activity of αGTs that produces cycloamylose (CA), a valuable carbohydrate making inclusion complexes, was intensively studied. The new αGT, DgαGT, showed close protein sequence to the αGT from T. scotoductus (TsαGT). MalQ was clearly separated from the other two αGTs in the phylogenetic and the conserved regions analyses. The reaction velocities of disproportionation, cyclization, coupling, and hydrolysis of three αGTs were determined. Intriguingly, MalQ exhibited more than 100-fold lower cyclization activity than the others. To lesser extent, the disproportionation activity of MalQ was relatively low. DgαGT and TsαGT showed similar kinetics results, but TsαGT had nearly 10-fold lower hydrolysis activity than DgαGT. Due to the very low cyclizing activity of MalQ, DgαGT and TsαGT were selected for further analyses. When amylose was treated with DgαGT or TsαGT, CA with a broad DP range was generated immediately. The DP distribution of CA had a bimodal shape (DP 7 and 27 as peaks) for the both enzymes, but larger DPs of CA quickly decreased in the DgαGT. Cyclomaltopentaose, a rare cyclic sugar, was produced at early reaction stage and accumulated as the reactions went on in the both enzymes, but the increase was more profound in the TsαGT. Taken together, we clearly demonstrated the catalytic differences between αGT groups from thermophilic and pathogenic bacteria that and showed that αGTs play different roles depending on their lifestyle.


Asunto(s)
Bacterias/enzimología , Bacterias/metabolismo , Sistema de la Enzima Desramificadora del Glucógeno/química , Sistema de la Enzima Desramificadora del Glucógeno/metabolismo , Secuencia de Aminoácidos , Amilosa , Carbohidratos , Catálisis , Ciclización , Ciclodextrinas/metabolismo , Deinococcus/enzimología , Escherichia coli/enzimología , Sistema de la Enzima Desramificadora del Glucógeno/clasificación , Sistema de la Enzima Desramificadora del Glucógeno/genética , Cinética , Filogenia , Thermus/enzimología
14.
Int J Mol Sci ; 21(19)2020 Oct 07.
Artículo en Inglés | MEDLINE | ID: mdl-33036395

RESUMEN

Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.


Asunto(s)
Adenosina Trifosfato/química , Proteínas Bacterianas/química , Deinococcus/enzimología , Modelos Moleculares , Conformación Molecular , Rec A Recombinasas/química , Imagen Individual de Molécula , Adenosina Trifosfato/metabolismo , Proteínas Bacterianas/metabolismo , ADN de Cadena Simple/química , ADN de Cadena Simple/metabolismo , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Hidrólisis , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Rec A Recombinasas/metabolismo , Imagen Individual de Molécula/métodos
15.
Enzyme Microb Technol ; 141: 109648, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-33051009

RESUMEN

Amylosucrase (ASase, EC.4.2.1.4) is well-known for its distinguishable property of transglycosylation of many flavonoids and phenolics. Quercetin has diverse biological functions, however, its use is limited due to poor solubility and bioavailability. ASase derived from Deinococcus geothermalis (DGAS) showed conditional preference for producing unusual quercetin glucosides (QGs). DGAS produced a variety of QGs including quercetin monoglucosides (QG1), diglucosides (QG2 and QG2'), and triglucoside from quercetin and sucrose. The newly synthesized QG2' was recognized as a novel quercetin isomaltoside with an α-1,6 linkage branched at the -OH of C4' in quercetin by mass and nuclear magnetic resonance spectra. With a higher conversion yield from quercetin to QGs (60-92%), the optimum conditions for producing QG2' were examined under various pH and sucrose concentrations by response surface methodology. QG2' was predominantly produced under acidic conditions (pH 5.0) and at high sucrose concentrations (1000-1500 mM). In contrast, QG1 was generated as an intermediate of consecutive glycosylation. Kinetic evaluations indicated that considerable differences of transglycosylation velocities were caused by the pH and buffer salts of the reaction, which had a 3.9-fold higher overall performance (kcat/K'm) of generating QG2' at pH 5 compared to at pH 7. A rationale of unusual transglycosylations was demonstrated with a molecular docking simulation. Taken together, our study demonstrated that ASase can be used to synthesize unusually branched flavonoid glycosides from flavonol aglycones with clear patterns by modulating reaction conditions.


Asunto(s)
Proteínas Bacterianas/metabolismo , Deinococcus/enzimología , Glucosiltransferasas/metabolismo , Glicósidos/metabolismo , Quercetina/metabolismo , Proteínas Bacterianas/química , Glucosiltransferasas/química , Glicósidos/química , Glicosilación , Concentración de Iones de Hidrógeno , Cinética , Simulación del Acoplamiento Molecular , Estructura Molecular , Quercetina/química , Solubilidad , Sacarosa/metabolismo
16.
Biochem Biophys Res Commun ; 529(4): 869-875, 2020 09 03.
Artículo en Inglés | MEDLINE | ID: mdl-32819591

RESUMEN

Deinococcus radiodurans is a Gram positive bacterium the capability of which to withstand high doses of ionizing radiations is well known. Physiologically speaking, D. radiodurans is a proteolytic prokaryote able to express and secrete quite a number of proteases, and to use amino acids as an energy source. When considering this, it is surprising that little information is available on the biochemical components responsible for the uptake of peptides in D. radiodurans. Here we report on the purification and characterization of an ABC peptide transporter, isolated from D. radiodurans cells grown in tryptone-glucose-yeast extract (TGY) medium. In particular, we show here that the action of this transporter (denoted DR1571, SwissProt data bank accession number Q9RU24 UF71_DEIRA) is exerted on peptides containing at least 3 amino acids. Further, using tetra-peptides as model systems, we were able to observe that the DR1571 protein does not bind to peptides containing phenylalanine or valine, but associates with high efficiency to tetra-glycine, and with moderate affinity to tetra-peptides containing arginine or aspartate.


Asunto(s)
Transportadoras de Casetes de Unión a ATP/metabolismo , Proteínas Bacterianas/metabolismo , Deinococcus/enzimología , Oligopéptidos/metabolismo , Transportadoras de Casetes de Unión a ATP/genética , Transportadoras de Casetes de Unión a ATP/aislamiento & purificación , Proteínas Bacterianas/genética , Proteínas Bacterianas/aislamiento & purificación , Sitios de Unión , Deinococcus/genética , Pruebas de Enzimas , Expresión Génica , Cinética , Peso Molecular , Oligopéptidos/química , Unión Proteica , Especificidad por Sustrato
17.
Int J Biol Macromol ; 164: 902-910, 2020 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-32693146

RESUMEN

RecD family helicases play an important role in prokaryotic genome stability and serve as the structural models for studying superfamily 1B (SF1B) helicases. However, RecD-catalyzed duplex DNA unwinding behavior and the underlying mechanism are still elusive. RecD family helicases share a common proto-helicase with eukaryotic Pif1 family helicases, which are well known for their outstanding G-quadruplex (G4) unwinding ability. However, there are still controversial points as to whether and how RecD helicases unfold G4 structures. Here, single-molecule fluorescence resonance energy transfer (smFRET) and magnetic tweezers (MT) were used to study Deinococcus radiodurans RecD2 (DrRecD2)-mediated duplex DNA unwinding and resolution of G4 structures. A symmetric, repetitive unwinding phenomenon was observed on duplex DNA, revealed from the strand switch and translocation of one monomer. Furthermore, we found that DrRecD2 was able to unwind both parallel and antiparallel G4 structures without obvious topological preferences. Surprisingly, the unwinding properties of RecD on duplex and G4 DNA are different from those of Pif1. The findings provide an example, in which the patterns of two molecules derived from a common ancestor deviate during evolution, and they are of significance for understanding the unwinding mechanism and function of SF1B helicases.


Asunto(s)
Proteínas Bacterianas/química , ADN Helicasas/química , Deinococcus/enzimología , G-Cuádruplex , Proteínas de Saccharomyces cerevisiae/química , Catálisis , Dicroismo Circular , ADN de Cadena Simple/química , Transferencia Resonante de Energía de Fluorescencia/métodos , Inestabilidad Genómica , Magnetismo
18.
J Microbiol Biotechnol ; 30(9): 1436-1442, 2020 Sep 28.
Artículo en Inglés | MEDLINE | ID: mdl-32522959

RESUMEN

Amylosucrase (ASase, E.C. 2.4.1.4) is capable of efficient glucose transfer from sucrose, acting as the sole donor molecule, to various functional acceptor compounds, such as polyphenols and flavonoids. An ASase variant from Deinococcus geothermalis, in which the 226th alanine is replaced with asparagine (DgAS-A226N), shows increased polymerization activity due to changes in the flexibility of the loop near the active site. In this study, we further investigated how the mutation modulates the enzymatic activity of DgAS using molecular dynamics and docking simulations to evaluate interactions between the enzyme and phenolic compounds. The computational analysis revealed that the A226N mutation could induce and stabilize structural changes near the substratebinding site to increase glucose transfer efficiency to phenolic compounds. Kinetic parameters of DgAS-A226N and WT DgAS were determined with sucrose and 4-methylumbelliferone (MU) as donor and acceptor molecules, respectively. The kcat/Km value of DgAS-A226N with MU (6.352 mM-1min-1) was significantly higher than that of DgAS (5.296 mM-1min-1). The enzymatic activity was tested with a small phenolic compound, hydroquinone, and there was a 1.4-fold increase in α-arbutin production. From the results of the study, it was concluded that DgAS-A226N has improved acceptor specificity toward small phenolic compounds by way of stabilizing the active conformation of these compounds.


Asunto(s)
Deinococcus/enzimología , Glucosiltransferasas/química , Glucosiltransferasas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Deinococcus/genética , Glucosa/metabolismo , Glucosiltransferasas/genética , Hidroquinonas , Cinética , Simulación del Acoplamiento Molecular , Sacarosa/metabolismo
19.
J Photochem Photobiol B ; 205: 111843, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32146269

RESUMEN

UV exposure could induce carcinogenic mutation in human cells, including CPD (Cyclobutane pyrimidine dimer), and 6-4 pp (6-4 photoproduct) DNA damages. Spiting the active BER (Base Excision Repair) system of human cells, it lacks initiator glycosylase, rendering these damages to be only repaired through NER (Nucleotide Excision Repair) system. Some microorganisms such as Deinococcus radiodurans bacteria have a BER system for repairing these damages with an enzyme coded by the uvsE gene. This study evaluated the efficacy of the recombinant UVSE protein for repairing the CPD and 6-4 pp DNA damages in human cells. At the current study, the optimized sequence of the uvsE gene was synthesized and expressed in Hek293T cell line. The identity of protein was ascertained through ELISA assay and the stability of expression was measured via qPCR. The human Hek293T cells with the recombinant protein and without it were exposed to the UV light, and the repair of DNA damages was analyzed in both conditions using CPD and 6-4PP ELISA Combo Kit. The results indicated that uvsE gene was successfully colonized and expressed and expression showed to be stable. Hek293T cells with recombinant uvsE gene showed efficacy at repairing 80% of CPD and 85% of 6-4 photoproducts during one hour, and more than 95% of damages over 4 h' repair time. Considering the outcome of this study, it could be concluded that the uvsE recombinant product is highly effective at repairing both CPD and 6-4 pp damages and could be considered as a preventive agent for UV-induced skin cancers.


Asunto(s)
Proteínas Bacterianas/genética , Enzimas Reparadoras del ADN/genética , Reparación del ADN , Deinococcus/enzimología , Rayos Ultravioleta/efectos adversos , Daño del ADN , Células HEK293 , Humanos , Dímeros de Pirimidina
20.
Enzyme Microb Technol ; 135: 109505, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32146930

RESUMEN

Amylosucrase (ASase) has great industrial potential owing to its multifunctional activities, including transglucosylation, polymerization, and isomerization. In the present study, the properties of Deinococcus geothermalis ASase (DGAS) expressed in Corynebacterium glutamicum (cDGAS) and purified via Ni-NTA affinity chromatography were compared to those of DGAS expressed in Escherichia coli (eDGAS). The pH profile of cDGAS was similar to that of eDGAS, whereas the temperature profile of cDGAS was lower than that of eDGAS. The melting temperature of both enzymes did not differ significantly. Interestingly, polymerization activity was slightly lower in cDGAS than in eDGAS, whereas luteolin (an acceptor molecule) transglucosylation activity in cDGAS was 10 % higher than that in eDGAS. Analysis of protein secondary structure via circular dichroism spectroscopy revealed that cDGAS had a lower strand/helix ratio than eDGAS. The present results indicate that cDGAS is of greater industrial significance than eDGAS.


Asunto(s)
Proteínas Bacterianas/metabolismo , Corynebacterium glutamicum/metabolismo , Deinococcus/enzimología , Glucósidos/biosíntesis , Glucosiltransferasas/metabolismo , Luteolina/biosíntesis , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Corynebacterium glutamicum/genética , Deinococcus/genética , Estabilidad de Enzimas , Escherichia coli/genética , Escherichia coli/metabolismo , Glucosiltransferasas/química , Glucosiltransferasas/genética , Ingeniería Metabólica
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