Molybdenum enzymes in bacteria and their maturation

Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T

Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.

A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.

Structure of recombinant formate dehydrogenase from Methylobacterium extorquens (MeFDH1)

Formate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties in the production of the enzyme have made elucidating its unique physicochemical properties challenging. Here, we purified recombinant Methylobacterium extorquens AM1 FDH (MeFDH1) and used cryo-electron microscopy to determine its structure. We resolved a heterodimeric MeFDH1 structure at a resolution of 2.8 Å, showing a noncanonical active site and a well-embedded Fe-S redox chain relay. In particular, the tungsten bis-molybdopterin guanine dinucleotide active site showed an open configuration with a flexible C-terminal cap domain, suggesting structural and dynamic heterogeneity in the enzyme.

History of Maturation of Prokaryotic Molybdoenzymes-A Personal View

In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.

Isolation, Genomic Sequence and Physiological Characterization of Parageobacillus sp. G301, an Isolate Capable of Both Hydrogenogenic and Aerobic Carbon Monoxide Oxidation

Prokaryotes that can oxidize carbon monoxide (CO oxidizers) can use this gas as a source of carbon or energy. They oxidize carbon monoxide with carbon monoxide dehydrogenases (CODHs): these are divided into nickel-containing CODH (Ni-CODH), which are sensitive to O2, and molybdenum-containing CODH (Mo-CODH), which can function aerobically. The oxygen conditions required for CO oxidizers to oxidize CO may be limited, as those which have been isolated and characterized so far contain either Ni- or Mo-CODH. Here, we report a novel CO oxidizer, Parageobacillus sp. G301, which is capable of CO oxidation using both types of CODH based on genomic and physiological characterization. This thermophilic, facultatively anaerobic Bacillota bacterium was isolated from the sediments of a freshwater lake. Genomic analyses revealed that strain G301 possessed both Ni-CODH and Mo-CODH. Genome-based reconstruction of its respiratory machinery and physiological investigations indicated that CO oxidation by Ni-CODH was coupled with H2 production (proton reduction), whereas CO oxidation by Mo-CODH was coupled with O2 reduction under aerobic conditions and nitrate reduction under anaerobic conditions. G301 would thus be able to thrive via CO oxidation under a wide range of conditions, from aerobic environments to anaerobic environments, even with no terminal electron acceptors other than protons. Comparative genome analyses revealed no significant differences in genome structures and encoded cellular functions, except for CO oxidation between CO oxidizers and non-CO oxidizers in the genus Parageobacillus; CO oxidation genes are retained exclusively for CO metabolism and related respiration. IMPORTANCE Microbial CO oxidation has received much attention because it contributes to global carbon cycling in addition to functioning as a remover of CO, which is toxic to many organisms. Some microbial CO oxidizers, including both bacteria and archaea, exhibit sister relationships with non-CO oxidizers even in genus-level monophyletic groups. In this study, we demonstrated that a new isolate, Parageobacillus sp. G301, is capable of both anaerobic (hydrogenogenic) and aerobic CO oxidation, which has not been previously reported. The discovery of this new isolate, which is versatile in CO metabolism, will accelerate research on CO oxidizers with diverse CO metabolisms, expanding our understanding of microbial diversity. Through comparative genomic analyses, we propose that CO oxidation genes are not essential genetic elements in the genus Parageobacillus, providing insights into the factors which shape the punctate distribution of CO oxidizers in the prokaryote tree, even in genus-level monophyletic groups.

PMo12 as a redox mediator for bio-reduction of Cr(VI): Promotor or inhibitor?

Slow reduction rate and low reduction ability were the main limitations of bio-reduction of Cr(VI). As an efficient redox mediator, how phosphomolybdic acid (PMo₁₂) affected bio-reduction of Cr(VI) was worthy of exploration. In this study, short-term and long-term effects of PMo₁₂ on Cr(VI) reduction were investigated to reveal the relevant mechanism. After evaluating the short-term effect of PMo₁₂ concentration from 0.05 to 1.00 mM on Cr(VI) bio-reduction, 0.50 mM was found to be optimum by improving Cr(VI) reduction rate by 16.3 % and microbial electron transport system activity (ETSA) by 43.0 % with Cr(VI) reduction efficiency of 100 % in short-term (22 h) batch experiments. By contrast, in long-term (28 days) continuous flow experiments, 0.50 mM PMo₁₂ exhibited serious inhibition on Cr(VI) bio-reduction. The cumulative toxicity of Mo, strong oxidative stress (reactive oxygen species increased by 16.5 %), the inhibition of extracellular polymeric substances production and the reduction of microbial activity were proved to be the main inhibition mechanism. In terms of microbial electron transport system, the main electron carriers including flavin mononucleotide (FMN), nitrate reductase (NAR), nitrite reductase (NIR) were seriously inhibited. BugBase analysis confirmed that the relative abundance of biofilm forming bacteria decreased after PMo₁₂ addition, and the relative abundance of oxidative stress tolerance bacteria continued to increase.

The History of the Molybdenum Cofactor-A Personal View

The transition element molybdenum (Mo) is an essential micronutrient for plants, animals, and microorganisms, where it forms part of the active center of Mo enzymes. To gain biological activity in the cell, Mo has to be complexed by a pterin scaffold to form the molybdenum cofactor (Moco). Mo enzymes and Moco are found in all kingdoms of life, where they perform vital transformations in the metabolism of nitrogen, sulfur, and carbon compounds. In this review, I recall the history of Moco in a personal view, starting with the genetics of Moco in the 1960s and 1970s, followed by Moco biochemistry and the description of its chemical structure in the 1980s. When I review the elucidation of Moco biosynthesis in the 1990s and the early 2000s, I do it mainly for eukaryotes, as I worked with plants, human cells, and filamentous fungi. Finally, I briefly touch upon human Moco deficiency and whether there is life without Moco.

Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily

Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria

Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.

Oxygen Atom Transfer Reactivity of Molybdenum(VI) Complexes Employing Pyrimidine- and Pyridine-2-thiolate Ligands

Four dioxidomolybdenum(VI) complexes of the general structure [MoO₂L₂] employing the S,N-bidentate ligands pyrimidine-2-thiolate (PymS, 1), pyridine-2-thiolate (PyS, 2), 4-methylpyridine-2-thiolate (4-MePyS, 3) and 6-methylpyridine-2-thiolate (6-MePyS, 4) were synthesized and characterized by spectroscopic means and single-crystal X-ray diffraction analysis (2-4). Complexes 1-4 were reacted with PPh₃ and PMe₃, respectively, to investigate their oxygen atom transfer (OAT) reactivity and catalytic applicability. Reduction with PPh₃ leads to symmetric molybdenum(V) dimers of the general structure [Mo₂O₃L₄] (6-9). Kinetic studies showed that the OAT from [MoO₂L₂] to PPh₃ is 5 times faster for the PymS system than for the PyS and 4-MePyS systems. The reaction of complexes 1-3 with PMe₃ gives stable molybdenum(IV) complexes of the structure [MoOL₂(PMe₃)₂] (10-12), while reduction of [MoO₂(6-MePyS)₂] (4) yields [MoO(6-MePyS)₂(PMe₃)] (13) with only one PMe₃ coordinated to the metal center. The activity of complexes 1-4 in catalytic OAT reactions involving Me₂SO and Ph₂SO as oxygen donors and PPh₃ as an oxygen acceptor has been investigated to assess the influence of the varied ligand frameworks on the OAT reaction rates. It was found that [MoO₂(PymS)₂] (1) and [MoO₂(6-MePyS)₂] (4) are similarly efficient catalysts, while complexes 2 and 3 are only moderately active. In the catalytic oxidation of PMe₃ with Me₂SO, complex 4 is the only efficient catalyst. Complexes 1-4 were also found to catalytically reduce NO₃^- with PPh₃, although their reactivity is inhibited by further reduced species such as NO, as exemplified by the formation of the nitrosyl complex [Mo(NO)(PymS)₃] (14), which was identified by single-crystal X-ray diffraction analysis. Computed ΔG^⧧ values for the very first step of the OAT were found to be lower for complexes 1 and 4 than for 2 and 3, explaining the difference in catalytic reactivity between the two pairs and revealing the requirement for an electron-deficient ligand system.

Kβ X-Ray Emission Spectroscopic Study of a Second-Row Transition Metal (Mo) and Its Application to Nitrogenase-Related Model Complexes

In recent years, X-ray emission spectroscopy (XES) in the Kβ (3p-1s) and valence-to-core (valence-1s) regions has been increasingly used to study metal active sites in (bio)inorganic chemistry and catalysis, providing information about the metal spin state, oxidation state and the identity of coordinated ligands. However, to date this technique has been limited almost exclusively to first-row transition metals. In this work, we present an extension of Kβ XES (in both the 4p-1s and valence-to-1s [or VtC] regions) to the second transition row by performing a detailed experimental and theoretical analysis of the molybdenum emission lines. It is demonstrated in this work that Kβ2 lines are dominated by spin state effects, while VtC XES of a 4d transition metal provides access to metal oxidation state and ligand identity. An extension of Mo Kβ XES to nitrogenase-relevant model complexes shows that the method is sufficiently sensitive to act as a spectator probe for redox events that are localized at the Fe atoms. Mo VtC XES thus has promise for future applications to nitrogenase, as well as a range of other Mo-containing biological cofactors. Further, the clear assignment of the origins of Mo VtC XES features opens up the possibility of applying this method to a wide range of second-row transition metals, thus providing chemists with a site-specific tool for the elucidation of 4d transition metal electronic structure.

Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor

Regulation of the expression of the gene for chlorite dismutase (cld), located on the chlorate reduction composite transposon of the chlorate reducer Ideonella dechloratans, was studied. A 200 bp upstream sequence of the cld gene, and mutated and truncated versions thereof, was used in a reporter system in Escherichia coli. It was found that a sequence within this upstream region, which is nearly identical to the canonical FNR-binding sequence of E. coli, is necessary for anaerobic induction of the reporter gene. Anaerobic induction was regained in an FNR-deficient strain of E. coli when supplemented either with the fnr gene from E. coli or with a candidate fnr gene cloned from I. dechloratans. In vivo transcription of the suggested fnr gene of I. dechloratans was demonstrated by qRT-PCR. Based on these results, the cld promoter of I. dechloratans is suggested to be a class II-activated promoter regulated by an FNR-type protein of I. dechloratans. No fnr-type genes have been found on the chlorate reduction composite transposon of I. dechloratans, making anaerobic upregulation of the cld gene after a gene transfer event dependent on the presence of an fnr-type gene in the recipient.

Functional mononuclear molybdenum enzymes: challenges and triumphs in molecular cloning, expression, and isolation

Mononuclear molybdenum enzymes catalyze a variety of reactions that are essential in the cycling of nitrogen, carbon, arsenic, and sulfur. For decades, the structure and function of these crucial enzymes have been investigated to develop a fundamental knowledge for this vast family of enzymes and the chemistries they carry out. Therefore, obtaining abundant quantities of active enzyme is necessary for exploring this family's biochemical capability. This mini-review summarizes the methods for overexpressing mononuclear molybdenum enzymes in the context of the challenges encountered in the process. Effective methods for molybdenum cofactor synthesis and incorporation, optimization of expression conditions, improving isolation of active vs. inactive enzyme, incorporation of additional prosthetic groups, and inclusion of redox enzyme maturation protein chaperones are discussed in relation to the current molybdenum enzyme literature. This article summarizes the heterologous and homologous expression studies providing underlying patterns and potential future directions.

The biosynthesis of the molybdenum cofactors in Escherichia coli

The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5'-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.

Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress

Tolerance to acid is of dual importance for the food-borne pathogen Listeria monocytogenes: acids are used as a preservative, and gastric acid is one of the first defenses within the host. There are considerable differences in the acid tolerance of strains. Here we present the transcriptomic response of acid-tolerant field strains of L. monocytogenes to HCl at pH 3.0. RNAseq revealed significant differential expression of genes involved in phosphotransferase systems, oxidative phosphorylation, cell morphology, motility, and biofilm formation. Genes in the acetoin biosynthesis pathway were upregulated, suggesting that L. monocytogenes shifts to metabolizing pyruvate to acetoin under organic acid stress. We also identified the formation of cell aggregates in microcolonies as a potential relief strategy. A motif search within the first 150 bp upstream of differentially expressed genes identified a novel potential regulatory sequence that may have a function in the regulation of virulence gene expression. Our data support a model where an excess of intracellular H+ ions is counteracted by pumping H+ out of the cytosol via cytochrome C under reduced activity of the ATP synthase. The observed morphological changes suggest that acid stress may cause cells to aggregate in biofilm microcolonies to create a more favorable microenvironment. Additionally, HCl stress in the host stomach may serve as (i) a signal to downregulate highly immunogenic flagella, and (ii) as an indicator for the imminent contact with host cells which triggers early stage virulence genes.

Seasonal characterization and dosimetry-assisted risk assessment of indoor particulate matter (PM10-2.5, PM2.5-0.25, and PM0.25) collected in different schools

Inhalation of particulate matter (PM) has been linked to serious adverse health effects, such as asthma, cardiovascular diseases and lung cancer. In the present study, coarse (PM_10-2.5), accumulation mode (PM_2.5-0.25), and quasi-ultrafine (PM_0.25) particulates were collected inside twelve educative centers of Tarragona County (Catalonia, Spain) during two seasons (cold and warm). Chemical characterization of PM, as well as risk assessment were subsequently conducted in order to evaluate respiratory and digestive risks during school time for children. Levels and chemical composition of PM were very different among the 12 centers. Average PM levels were higher during the cold season, as well as the concentrations of most toxic metals. In most schools, PM levels were below the daily PM₁₀ threshold established in the regulation (50 μg/m³), with the exception of school number 1 during the cold season. On average, and regardless of season, coarse PM was highly influenced by mineral matter, while organic matter and elemental carbon were prevalent in quasi-ultrafine PM. The concentrations of the toxic elements considered by the legislation (As, Cd, Pb, and Ni) were below their correspondent regulatory annual limits. Calculated risks were below the safety thresholds, being fine fractions (PM_2.5-0.25 and PM_0.25) the main contributors to both digestive and respiratory risks.

New insights into the molecular physiology of sulfoxide reduction in bacteria

Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. In bacteria MSR proteins are often found in the cytoplasm but in some bacteria, including pathogenic Neisseria, Streptococci, and Haemophilus they are extracytoplasmic. Mutants lacking MSR proteins are often sensitive to oxidative stress and in pathogens exhibit decreased virulence as indicated by reduced survival in host cell or animal model systems. Molybdenum enzymes are also known to reduce S-oxides and traditionally their physiological role was considered to be in anaerobic respiration using dimethylsulfoxide (DMSO) as an electron acceptor. However, it now appears that some enzymes (MtsZ) of the DMSO reductase family of Mo enzymes use methionine sulfoxide as preferred physiological substrate and thus may be involved in scavenging/recycling of this amino acid. Similarly, an enzyme (MsrP/YedY) of the sulfite oxidase family of Mo enzymes has been shown to be involved in repair of methionine sulfoxides in periplasmic proteins. Again, some mutants deficient in Mo-dependent sulfoxide reductases exhibit reduced virulence, and there is evidence that these Mo enzymes and some MSR systems are induced by hypochlorite produced by the innate immune system. This review describes recent advances in the understanding of the molecular microbiology of MSR systems and the broadening of the role of Mo-dependent sulfoxide reductase to encompass functions beyond anaerobic respiration.

Bioenergetic aspects of archaeal and bacterial hydrogen metabolism

Hydrogenases are metal-containing biocatalysts that reversibly convert protons and electrons to hydrogen gas. This reaction can contribute in different ways to the generation of the proton motive force (PMF) of a cell. One means of PMF generation involves reduction of protons on the inside of the cytoplasmic membrane, releasing H₂ gas, which being without charge is freely diffusible across the cytoplasmic membrane, where it can be re-oxidized to release protons. A second route of PMF generation couples transfer of electrons derived from H₂ oxidation to quinone reduction and concomitant proton uptake at the membrane-bound heme cofactor. This redox-loop mechanism, as originally formulated by Mitchell, requires a second, catalytically distinct, enzyme complex to re-oxidize quinol and release the protons outside the cell. A third way of generating PMF is also by electron transfer to quinones but on the outside of the membrane while directly drawing protons through the entire membrane. The cofactor-less membrane subunits involved are proposed to operate by a conformational mechanism (redox-linked proton pump). Finally, PMF can be generated through an electron bifurcation mechanism, whereby an exergonic reaction is tightly coupled with an endergonic reaction. In all cases the protons can be channelled back inside through a F₁F₀-ATPase to convert the 'energy' stored in the PMF into the universal cellular energy currency, ATP. New and exciting discoveries employing these mechanisms have recently been made on the bioenergetics of hydrogenases, which will be discussed here and placed in the context of their contribution to energy conservation.

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

Bacterial genes for molybdenum-containing and tungsten-containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA-binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate-specific transporting systems as well as molybdo/tungsto-enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten-containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten-specific ABC-type transporter tupABC genes under tungsten-replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.

The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria

The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.

Proteomic Adaptation of Australian Epidemic Bordetella pertussis

Bordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from cluster II (non-ptxP3/non-prn2). Cluster I was mostly responsible for the 2008-2012 Australian epidemic and was found to have higher fitness compared to cluster II using an in vivo mouse competition assay, regardless of host's immunization status. This study aimed to identify proteomic differences that explain higher fitness in cluster I using isobaric tags for relative and absolute quantification (iTRAQ), and high-resolution multiple reaction monitoring (MRM-hr). A few key differences in the whole cell and secretome were identified between the cluster I and II strains tested. In the whole cell, nine proteins were upregulated (>1.2 fold change, q < 0.05) and three were downregulated (<0.8 fold change, q < 0.05) in cluster I. One downregulated protein was BP1569, a TLR2 agonist for Th1 immunity. In the secretome, 12 proteins were upregulated and 1 was downregulated which was Bsp22, a type III secretion system (T3SS) protein. Furthermore, there was a trend of downregulation in three T3SS effectors and other virulence factors. Three proteins were upregulated in both whole cell and supernatant: BP0200, molybdate ABC transporter (ModB), and tracheal colonization factor A (TcfA). Important expression differences in lipoprotein, T3SS, and transport proteins between the cluster I and II strains were identified. These differences may affect immune evasion, virulence and metabolism, and play a role in increased fitness of cluster I.

Assembly pathway of a bacterial complex iron sulfur molybdoenzyme

Protein folding and assembly into macromolecule complexes within the living cell are complex processes requiring intimate coordination. The biogenesis of complex iron sulfur molybdoenzymes (CISM) requires use of a system specific chaperone - a redox enzyme maturation protein (REMP) - to help mediate final folding and assembly. The CISM dimethyl sulfoxide (DMSO) reductase is a bacterial oxidoreductase that utilizes DMSO as a final electron acceptor for anaerobic respiration. The REMP DmsD strongly interacts with DMSO reductase to facilitate folding, cofactor-insertion, subunit assembly and targeting of the multi-subunit enzyme prior to membrane translocation and final assembly and maturation into a bioenergetic catalytic unit. In this article, we discuss the biogenesis of DMSO reductase as an example of the participant network for bacterial CISM maturation pathways.

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation

The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen.

Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), can persist for years and even decades in the lungs of its human host. Here we report that a unique M. tuberculosis gene cluster involved in the synthesis of the molybdenum cofactor, a cofactor for several oxidoreductases including the nitrate reductase, allows this major pathogen to respire nitrate and to persist in a dormant state under hypoxia, a stress condition encountered in lung TB lesions. Strikingly the M. tuberculosis ancestor, which most likely was an environmental harmless bacterium, acquired this gene cluster, together with its hypoxia-responsive transcriptional regulator, horizontally from neighboring bacteria. Our results uncover a key step in M. tuberculosis evolution towards pathogenicity.

Oxidative stress in ageing and disease development studied by FT-IR spectroscopy

FT-IR spectroscopy was used to investigate the effect of oxidative stress and to approach the mechanism on cancer bone demineralization, aortic valve mineralization and heterotopic ossification on disease development. The FT-IR spectra obtained from paediatric, adult bone and ex vivo irradiated adult healthy bone with a dose of 20Gy were compared with those of healthy bone. The increase of band intensity changes of vasCH_2,vsCH₂ in the region 3000-2850cm^-1 depended on aging, the disease progression and the dose of irradiation. The bands at 3080cm^-1 and 1744cm^-1, which originate from olefinic terminal bond (v=CH) and ester carbonyl group (vROCO), respectively, indicate the influence of oxidative stress on lipid degradation and peroxidation, respectively. The new bands at about 1690cm^-1 and 1516cm^-1 denote the presence of β-sheet conformation of the proteins due to the diseases, confirming the increasing amount of lipophilic environment and fibril formation. Comparison of the FT-IR spectra of calcified aortic valve and hip heterotopic ossification with that of normal bones showed that in the bone-like formation the peroxide anion free radicals play an important role in the disease.

Anaerobic Formate and Hydrogen Metabolism

Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.

[MoO2]2+-Mediated Oxygen Atom Transfer via an Unusual Lewis Acid Mechanism

Density functional theory is applied to the study of the oxygen atom transfer reaction from sulfoxide (DMSO) to phosphine (PMe₃) catalyzed by the [MoO₂]²⁺ active core. In this work, two fundamentally different roles are explored for this dioxometal complex in the first step of the catalytic cycle: as an oxidizing agent and as a Lewis acid. The latter turns out to be the favored pathway for the oxygen atom transfer. This finding may have more general implications for similar reactions catalyzed by the same [MoO₂]²⁺ core.

Discovery of piperonal-converting oxidase involved in the metabolism of a botanical aromatic aldehyde

Piperonal-catabolizing microorganisms were isolated from soil, the one (strain CT39-3) exhibiting the highest activity being identified as Burkholderia sp. The piperonal-converting enzyme involved in the initial step of piperonal metabolism was purified from strain CT39-3. Gene cloning of the enzyme and a homology search revealed that the enzyme belongs to the xanthine oxidase family, which comprises molybdoenzymes containing a molybdopterin cytosine dinucleotide cofactor. We found that the piperonal-converting enzyme acts on piperonal in the presence of O₂, leading to formation of piperonylic acid and H₂O₂. The growth of strain CT39-3 was inhibited by higher concentrations of piperonal in the culture medium. Together with this finding, the broad substrate specificity of this enzyme for various aldehydes suggests that it would play an important role in the defense mechanism against antimicrobial compounds derived from plant species.

Redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism

A major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. This holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. This large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (Mo/W-bisPGD) and Fe/S clusters. Here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational changes accompanying Mo/W-bisPGD and Fe/S cofactors insertion. Identified conformational changes are shown to be essential for recognition of the dedicated chaperone involved in cofactors insertion. A solvent-exposed salt bridge is shown to play a key role in enzyme folding after cofactors insertion. Furthermore, this salt bridge is shown to be strictly conserved within this prokaryotic molybdoenzyme family as deduced from a phylogenetic analysis issued from 3D structure-guided multiple sequence alignment. A biochemical analysis with a distantly-related member of the family, respiratory complex I, confirmed the critical importance of the salt bridge for folding. Overall, our results point to a conserved cofactors insertion mechanism within the Mo/W-bisPGD family.

Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock

Ruminal methane production is among the main targets for greenhouse gas (GHG) mitigation for the animal agriculture industry. Many compounds have been evaluated for their efficacy to suppress enteric methane production by ruminal microorganisms. Of these, nitrate as an alternative hydrogen sink has been among the most promising, but it suffers from variability in efficacy for reasons that are not understood. The accumulation of nitrite, which is poisonous when absorbed into the animal’s circulation, is also variable and poorly understood. This review identifies large gaps in our knowledge of rumen microbial ecology that handicap the further development and safety of nitrate as a dietary additive. Three main bacterial species have been associated historically with ruminal nitrate reduction, namely Wolinella succinogenes, Veillonella parvula, and Selenomonas ruminantium, but others almost certainly exist in the largely uncultivated ruminal microbiota. Indications are strong that ciliate protozoa can reduce nitrate, but the significance of their role relative to bacteria is not known. The metabolic fate of the reduced nitrate has not been studied in detail. It is important to be sure that nitrate metabolism and efforts to enhance rates of nitrite reduction do not lead to the evolution of the much more potent GHG, nitrous oxide. The relative importance of direct inhibition of archaeal methanogenic enzymes by nitrite or the efficiency of capture of hydrogen by nitrate reduction in lowering methane production is also not known, nor are nitrite effects on other members of the microbiota. How effective would combining mitigation methods be, based on our understanding of the effects of nitrate and nitrite on the microbiome? Answering these fundamental microbiological questions is essential in assessing the potential of dietary nitrate to limit methane emissions from ruminant livestock.

Identification of protein-protein interactions between the TatB and TatC subunits of the twin-arginine translocase system and respiratory enzyme specific chaperones

The Twin-arginine translocation (Tat) pathway serves for translocation of fully folded proteins across the cytoplasmic membrane in bacterial and chloroplast thylakoid membranes. The Escherichia coli Tat system consists of three core components: TatA, TatB, and TatC. The TatB and TatC subunits form the receptor complex for Tat dependent proteins. The TatB protein is composed of a single transmembrane helix and cytoplasmic domain. The structure of TatC revealed six transmembrane helices. Redox Enzyme Maturation Proteins (REMPs) are system specific chaperones, which play roles in the maturation of Tat dependent respiratory enzymes. Here we applied the in vivo bacterial two-hybrid technique to investigate interaction of REMPs with the TatBC proteins, finding that all but the formate dehydrogenase REMP dock to TatB or TatC. We focused on the NarJ subfamily, where DmsD--the REMP for dimethyl sulfoxide reductase in E. coli--was previously shown to interact with TatB and TatC. We found that these REMPs interact with TatC cytoplasmic loops 1, 2 and 4, with the exception of NarJ, that only interacts with 1 and 4. An in vitro isothermal titration calorimetry study was applied to confirm the evidence of interactions between TatC fragments and DmsD chaperone. Using a peptide overlapping array, it was shown that the different NarJ subfamily REMPs interact with different regions of the TatB cytoplasmic domains. The results demonstrate a role of REMP chaperones in targeting respiratory enzymes to the Tat system. The data suggests that the different REMPs may have different mechanisms for this task.

Biogenesis of Escherichia coli DMSO Reductase: A Network of Participants for Protein Folding and Complex Enzyme Maturation

Protein folding and structure have been of interest since the dawn of protein chemistry. Following translation from the ribosome, a protein must go through various steps to become a functional member of the cellular society. Every protein has a unique function in the cell and is classified on this basis. Proteins that are involved in cellular respiration are the bioenergetic workhorses of the cell. Bacteria are resilient organisms that can survive in diverse environments by fine tuning these workhorses. One class of proteins that allow survival under anoxic conditions are anaerobic respiratory oxidoreductases, which utilize many different compounds other than oxygen as its final electron acceptor. Dimethyl sulfoxide (DMSO) is one such compound. Respiration using DMSO as a final electron acceptor is performed by DMSO reductase, converting it to dimethyl sulfide in the process. Microbial respiration using DMSO is reviewed in detail by McCrindle et al. (Adv Microb Physiol 50:147-198, 2005). In this chapter, we discuss the biogenesis of DMSO reductase as an example of the participant network for complex iron-sulfur molybdoenzyme maturation pathways.

Distribution and dynamics of OXPHOS complexes in the bacterial cytoplasmic membrane

Oxidative phosphorylation (OXPHOS) is an essential process for most living organisms mostly sustained by protein complexes embedded in the cell membrane. In order to thrive, cells need to quickly respond to changes in the metabolic demand or in their environment. An overview of the strategies that can be employed by bacterial cells to adjust the OXPHOS outcome is provided. Regulation at the level of gene expression can only provide a means to adjust the OXPHOS outcome to long-term trends in the environment. In addition, the actual view is that bioenergetic membranes are highly compartmentalized structures. This review discusses what is known about the spatial organization of OXPHOS complexes and the timescales at which they occur. As exemplified with the commensal gut bacterium Escherichia coli, three levels of spatial organization are at play: supercomplexes, membrane microdomains and polar assemblies. This review provides a particular focus on whether dynamic spatial organization can fine-tune the OXPHOS through the definition of specialized functional membrane microdomains. Putative mechanisms responsible for spatio-temporal regulation of the OXPHOS complexes are discussed. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.

Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae

Mononuclear molybdenum enzymes of the dimethylsulfoxide (DMSO) reductase family occur exclusively in prokaryotes, and a loss of some these enzymes has been linked to a loss of bacterial virulence in several cases. The MobA protein catalyzes the final step in the synthesis of the molybdenum guanine dinucleotide (MGD) cofactor that is exclusive to enzymes of the DMSO reductase family. MobA has been proposed as a potential target for control of virulence since its inhibition would affect the activities of all molybdoenzymes dependent upon MGD. Here, we have studied the phenotype of a mobA mutant of the host-adapted human pathogen Haemophilus influenzae. H. influenzae causes and contributes to a variety of acute and chronic diseases of the respiratory tract, and several enzymes of the DMSO reductase family are conserved and highly expressed in this bacterium. The mobA mutation caused a significant decrease in the activities of all Mo-enzymes present, and also resulted in a small defect in anaerobic growth. However, we did not detect a defect in in vitro biofilm formation nor in invasion and adherence to human epithelial cells in tissue culture compared to the wild-type. In a murine in vivo model, the mobA mutant showed only a mild attenuation compared to the wild-type. In summary, our data show that MobA is essential for the activities of molybdenum enzymes, but does not appear to affect the fitness of H. influenzae. These results suggest that MobA is unlikely to be a useful target for antimicrobials, at least for the purpose of treating H. influenzae infections.

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

Pyranopterin Coordination Controls Molybdenum Electrochemistry in Escherichia coli Nitrate Reductase

We test the hypothesis that pyranopterin (PPT) coordination plays a critical role in defining molybdenum active site redox chemistry and reactivity in the mononuclear molybdoenzymes. The molybdenum atom of Escherichia coli nitrate reductase A (NarGHI) is coordinated by two PPT-dithiolene chelates that are defined as proximal and distal based on their proximity to a [4Fe-4S] cluster known as FS0. We examined variants of two sets of residues involved in PPT coordination: (i) those interacting directly or indirectly with the pyran oxygen of the bicyclic distal PPT (NarG-Ser(719), NarG-His(1163), and NarG-His(1184)); and (ii) those involved in bridging the two PPTs and stabilizing the oxidation state of the proximal PPT (NarG-His(1092) and NarG-His(1098)). A S719A variant has essentially no effect on the overall Mo(VI/IV) reduction potential, whereas the H1163A and H1184A variants elicit large effects (ΔEm values of -88 and -36 mV, respectively). Ala variants of His(1092) and His(1098) also elicit large ΔEm values of -143 and -101 mV, respectively. An Arg variant of His(1092) elicits a small ΔEm of +18 mV on the Mo(VI/IV) reduction potential. There is a linear correlation between the molybdenum Em value and both enzyme activity and the ability to support anaerobic respiratory growth on nitrate. These data support a non-innocent role for the PPT moieties in controlling active site metal redox chemistry and catalysis.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Behavior of anionic molybdenum(IV, VI) and tungsten(IV, VI) complexes containing bulky hydrophobic dithiolate ligands and intramolecular NH···S hydrogen bonds in nonpolar solvents

Molybdenum(IV, VI) and tungsten(IV, VI) complexes, (Et4N)2[M(IV)O{1,2-S2-3,6-(RCONH)2C6H2}2] and (Et4N)2[M(VI)O2{1,2-S2-3,6-(RCONH)2C6H2}2] (M = Mo, W; R = (4-(t)BuC6H4)3C), with bulky hydrophobic dithiolate ligands containing NH···S hydrogen bonds were synthesized. These complexes are soluble in nonpolar solvents like toluene, which allows the detection of unsymmetrical coordination structures and elusive intermolecular interactions in solution. The (1)H NMR spectra of the complexes in toluene-d8 revealed an unsymmetrical coordination structure, and proximity of the counterions to the anion moiety was suggested at low temperatures. The oxygen-atom-transfer reaction between the molybdenum(IV) complex and Me3NO in toluene was considerably accelerated in nonpolar solvents, and this increase was attributed to the favorable access of the substrate to the active center in the hydrophobic environment.

Phylogenomics of Mycobacterium Nitrate Reductase Operon

NarGHJI operon encodes a nitrate reductase that can reduce nitrate to nitrite. This process enhances bacterial survival by nitrate respiration under anaerobic conditions. NarGHJI operon exists in many bacteria, especially saprophytic bacteria living in soil which play a key role in the nitrogen cycle. Most actinomycetes, including Mycobacterium tuberculosis, possess NarGHJI operons. M. tuberculosis is a facultative intracellular pathogen that expands in macrophages and has the ability to persist in a non-replicative form in granuloma lifelong. Nitrogen and nitrogen compounds play crucial roles in the struggle between M. tuberculosis and host. M. tuberculosis can use nitrate as a final electron acceptor under anaerobic conditions to enhance its survival. In this article, we reviewed the mechanisms regulating nitrate reductase expression and affecting its activity. Potential genes involved in regulating the nitrate reductase expression in M. tuberculosis were identified. The conserved NarG might be an alternative mycobacterium taxonomic marker.