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DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

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DMSO Reductase Family: Phylogenetics and Applications of Extremophiles International Journal of Molecular Sciences Review DMSO Reductase Family: Phylogenetics and Applications of Extremophiles Jose María Miralles-Robledillo , Javier Torregrosa-Crespo , Rosa María Martínez-Espinosa and Carmen Pire * Departamento de Agroquímica y Bioquímica, División de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Alicante, Carretera San Vicente del Raspeig s/n-03690 San Vicente del Raspeig, Alicante, Spain * Correspondence: [email protected] Received: 13 June 2019; Accepted: 5 July 2019; Published: 8 July 2019 Abstract: Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described. Keywords: dimethyl sulfoxide reductases; MoCo cofactor; redox reactions; biogeochemical cycles; N-cycle; phylogeny; nitrate reductase; perchlorate reductase 1. Introduction Molybdenum (Mo) is a transition metal that plays an essential role in metabolism in the three domains of life. It is a trace element; consequently, living beings require it in small doses. 4 The biologically available form of Mo is the oxyanion molybdate (MoO2− ) from which organisms take up Mo along their daily life [1]. Mo can be found as a cofactor at the active sites of enzymes in many organisms [2]. They are called molybdoenzymes and are involved in redox reactions of the global carbon, nitrogen, and sulfur cycles. Molybdoenzymes can show two different types of molybdenum cofactors: The iron-molybdenum cofactor (FeMoCo), which has only been identified in a bacterial nitrogenase, and the pterin-based cofactors (MoCo), which are widespread in all domains of life (Figure1)[ 2–4]. This last cofactor is the one of interest in this review due to its relationship with dimethyl sulfoxide reductases (DMSO reductases). Another different cofactor with a molybdenum/copper heterometallic cluster has been identified in a protein called “orange protein” from Desulfovibrio gigas, but its function is still unknown at the time of writing this work [5,6]. Therefore, information about it and the hypothetical family it belongs to has not been included due to the lack of information. The MoCo structure, as well as several genes participating in its biosynthesis, are conserved in plants, animals, fungi, archaea, and bacteria suggesting an evolutionary conserved pathway. Thus, at least the three first steps are shared by most organisms [1,7]: Synthesis of cPMP (cyclic pyranopterin monophosphate) from 50-GTP (guanosine triphosphate), conversion of cPMP in MPT (molybdopterin, or also called metal-binding pterin, the metal-free form of the MoCo), and addition of molybdenum to Int. J. Mol. Sci. 2019, 20, 3349; doi:10.3390/ijms20133349 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2019, 20, 3349 2 of 22 Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 2 of 22 form the MoCo (see Section3 for more details). It is noteworthy that molybdenum is not active in cells of molybdenum to form the MoCo (see Section 3 for more details). It is noteworthy that molybdenum until it forms the MoCo [4]. is not active in cells until it forms the MoCo [4]. (a) (b) FigureFigure 1.1. Molybdenum cofactors. ( aa)) The The iron-molybdenum cofactor (FeMoCo)(FeMoCo) of bacterial nitrogenasesnitrogenases andand (b(b) pyranopterin) pyranopterin molecule molecule from from which which the pterin-based the pterin-based cofactors cofactors (MoCo) are(MoCo) originated. are originated. Molecules drawnMolecules with drawn BioVIA with Draw BioVIA 2019 Draw [8]. 2019 [8]. ApartApart fromfrom Mo, Mo, there there are otherare other transition transition metals meta withls similar with biologicalsimilar biological roles, tungsten roles, (wolfram)tungsten (W)(wolfram) and vanadium (W) and (V)vanadium [9,10]. On(V) the [9,10]. one On hand, the vanadium one hand, isvanadium present alternatively is present alternatively to the FeMoCo to the in someFeMoCo nitrogenases, in some nitrogenases, as part of the as iron-vanadiumpart of the iron-vanadium cofactor (FeVCo) cofactor [10 (FeVCo)]. On the [10]. other On hand,the other tungsten hand, istungsten present is as present cofactor as incofactor tungsten in tungsten enzymes, enzyme sharings, asharing lot of resemblances a lot of resemblances with the with MoCo the of MoCo DMSO of reductasesDMSO reductases [11]. [11]. Biochemically,Biochemically, MoMo andand WW shareshare severalseveral similarities,similarities, suchsuch asas theirtheir analogousanalogous valencevalence electronelectron configurationconfiguration in allall oxidationoxidation states in almost all compounds and their similar atomic radii [12]. [12]. WhereasWhereas WW does does not not have have any any role role in in eukaryotic eukaryotic organisms, organisms, Mo Mo and and W areW relevantare relevant in prokaryotes in prokaryotes [13]. 2 Tungstate[13]. Tungstate (WO4 (WO− ) is4− the2) is biologically the biologically available availa formble form of W of and W isand present is present in lower in lower concentrations concentrations than 4 MoOthan 2MoO− in2 oceans.−4 in oceans. Under Under euxinic euxinic conditions conditions such as such those as characterizing those characterizing hydrothermal hydrothermal vents (similar vents conditions(similar conditions to the ancient to the Earth),ancient MoEarth), forms Mo MoS forms2, whichMoS2, which is insoluble, is insoluble, whilst whilst W forms W forms soluble soluble salts 2 (WS 4− ) available−2 for microorganisms [11,13,14]. This fact could explain why, under these conditions, salts− (WS−4 ) available for microorganisms [11,13,14]. This fact could explain why, under these weconditions, can find we hyperthermophilic can find hyperthe archaea,rmophilic which archaea, are dependentwhich are dependent on W instead on W of instead Mo [13 ].of AnotherMo [13]. remarkableAnother remarkable aspect about aspect the about relationship the relationship between Mobetween and W Mo (and and directly W (and related directly to related their chemical to their similarity)chemical similarity) is the fact is that the some fact enzymes,that some suchenzyme as DMSOs, such reductases, as DMSO reductases, can use W insteadcan use of W Mo instead in their of cofactorsMo in their when cofactors Mo is when at lower Mo concentration. is at lower concentration. It is probably It is due probably to the similarity due to the between similarity W between cofactor (WCo,W cofactor tungsten-enzymes) (WCo, tungsten-enzymes) and Mo cofactor and (MoCo, Mo co molybdoenzymes)factor (MoCo, molybdoe [1,11,13nzymes),15]. However, [1,11,13,15]. some enzymesHowever, (even some in enzymes the same (even family) in the can same only usefamily one) orcan the only other use despite one or their the other similarities, despite so their the discriminationsimilarities, so mechanismthe discrimination in these mechanism enzymes would in these be enzymes very efficient would [1, 13be]. very efficient [1,13]. ThisThis reviewreview is is an an attempt attempt to compileto compile the knowledgethe knowledge about theabout enzymes the enzymes that contain that Mocontain cofactors, Mo focusingcofactors, on focusing the DMSO on the reductases DMSO reductases family for theirfamily biological for their rolebiological in anaerobic role in respiration.anaerobic respiration.The types ofThe anaerobic types of respirationanaerobic respiration that they carry that out,they theircarryposition out, their in position the bacterial in the/archaeal bacterial/archaeal phylogeny, thephylogeny, phylogenetic the phylogeneticrelationship relationship between di ffbetweenerent DMSO different reductases, DMSO reductases, and their roleand intheir the role nitrogen in the cycle,nitrogen as wellcycle, as as their well potential as their potential applications applications in bioremediation, in bioremediation, are reviewed. are reviewed. 2. Biosynthesis of the Bis-MGD Cofactor and Maturation of Molybdoenzymes 2. Biosynthesis of the Bis-MGD Cofactor and Maturation of Molybdoenzymes The coordination and structure of the MoCo in DMSO reductases differentiate them from the The coordination and structure of the MoCo in DMSO reductases differentiate them from the rest of molybdoenzymes and tungsten-enzymes families and give to these enzymes their specific rest of molybdoenzymes and tungsten-enzymes families and give to these enzymes their specific functionalities. However, despite the existence of a wide range of cofactors in molybdoenzymes functionalities. However, despite the existence of a wide range of cofactors in molybdoenzymes and and tungsto-enzymes, the first three reactions for the biosynthesis of the molybdenum cofactor are tungsto-enzymes, the first three reactions for the biosynthesis of the molybdenum cofactor are shared shared among all families [1,3,16,17]. DMSO reductases
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