Crystal Structure of Adenylylsulfate Reductase from Desulfovibrio gigas Suggests a Potential Self-Regulation Mechanism Involving the C Terminus of the β-Subunit

Adenylylsulfate reductase (adenosine 5′-phosphosulfate [APS] reductase [APSR]) plays a key role in catalyzing APS to sulfite in dissimilatory sulfate reduction. Here, we report the crystal structure of APSR from Desulfovibrio gigas at 3.1-Å resolution. Different from the α₂β₂-heterotetramer of the Archaeoglobus fulgidus, the overall structure of APSR from D. gigas comprises six αβ-heterodimers that form a hexameric structure. The flavin adenine dinucleotide is noncovalently attached to the α-subunit, and two [4Fe-4S] clusters are enveloped by cluster-binding motifs. The substrate-binding channel in D. gigas is wider than that in A. fulgidus because of shifts in the loop (amino acid 326 to 332) and the α-helix (amino acid 289 to 299) in the α-subunit. The positively charged residue Arg160 in the structure of D. gigas likely replaces the role of Arg83 in that of A. fulgidus for the recognition of substrates. The C-terminal segment of the β-subunit wraps around the α-subunit to form a functional unit, with the C-terminal loop inserted into the active-site channel of the α-subunit from another αβ-heterodimer. Electrostatic interactions between the substrate-binding residue Arg282 in the α-subunit and Asp159 in the C terminus of the β-subunit affect the binding of the substrate. Alignment of APSR sequences from D. gigas and A. fulgidus shows the largest differences toward the C termini of the β-subunits, and structural comparison reveals notable differences at the C termini, activity sites, and other regions. The disulfide comprising Cys156 to Cys162 stabilizes the C-terminal loop of the β-subunit and is crucial for oligomerization. Dynamic light scattering and ultracentrifugation measurements reveal multiple forms of APSR upon the addition of AMP, indicating that AMP binding dissociates the inactive hexamer into functional dimers, presumably by switching the C terminus of the β-subunit away from the active site. The crystal structure of APSR, together with its oligomerization properties, suggests that APSR from sulfate-reducing bacteria might self-regulate its activity through the C terminus of the β-subunit.Sulfate-reducing bacteria (SRB) are a special group of prokaryotes that are found in sulfate-rich environments because of their ability to metabolize sulfate. SRB use sulfate as the final electron acceptor in various anaerobic environments, such as soil, oil fields, the sea, or the innards of animals or even human beings (10, 11, 19, 25, 33). Their ability to degrade sulfate offers protection against environmental pollution. SRB can remove sulfate and toxic heavy atoms from factory waste waters (12). The Desulfovibrio species is a much-studied representative of SRB, and Desulfovibrio gigas has been studied under many diverse conditions to elucidate metabolic pathways (23, 35).Sulfate reduction is one of the oldest forms of cellular metabolism. The reduction can be either assimilatory or dissimilatory. Sulfate is the terminal electron acceptor in dissimilatory reduction and the raw material for the biosynthesis of cysteine in assimilatory reduction. The latter type of reduction occurs in archaebacteria, bacteria, fungi, and plants via various pathways (17). For example, in Escherichia coli, the reduction initially catalyzes sulfate to adenosine 5′-phosphosulfate (APS) by ATP sulfurylase. APS is then phosphorylated by APS kinase to 3′-phosphate APS, which is then further reduced to sulfite by 3′-phosphate APS reductase (APSR). Finally, sulfite is reduced by sulfite reductase to sulfide, which condenses with O-acetylserine by O-acetylserine lyase to form cysteine. For comparison, in dissimilatory sulfate reduction, sulfate is first catalyzed by ATP sulfurylase to APS, which is then directly reduced by APSR to sulfite. Sulfite is subsequently reduced by dissimilatory sulfite reductase to the following three possible products: trithionite (S₃O₆²⁻), thiosulfate (S₂O₃²⁻), or sulfide (S²⁻).Adenylylsulfate reductase, also called APSR, plays an important role in catalyzing APS to AMP and sulfite in the dissimilatory sulfate reduction. APSR was first partially purified and characterized from Desulfovibrio desulfuricans (32). Multiple forms of APSR in Desulfovibrio vulgaris were observed in buffers under varied conditions (1) and were found in the cytoplasm of cells (18). APSR from D. gigas was first purified by Lampreia et al. (21) and showed a molecular mass of 400 kDa comprised of α- and β-subunits, corresponding to the molecular masses of 70 kDa and 23 kDa, respectively. One flavin adenine dinucleotide (FAD) and two [4Fe-4S] clusters per APSR have been observed and characterized by electron paramagnetic resonance and Mössbauer spectroscopy. The enzyme from D. gigas has been described as an α₂β complex involving one FAD and two [4Fe-4S] clusters (20). In D. vulgaris, APSR is apparently an α₂β₂ complex with a molecular mass of 186 kDa; only one Fe-S cluster is found in the αβ-heterodimer (31). Thus, the subunit and quaternary structures of APSR and their constitution of cofactors in terms of FAD and iron-sulfur clusters are still under debate. Only the enzyme from Archaeoglobus fulgidus has benefited from having an X-ray crystal structure. In this APSR, the functional unit has been shown to be the 1:1 αβ-heterodimer, containing two iron-sulfur clusters and one FAD in the structure (7). However, crystal packing shows that the asymmetric unit is an α₂β₂-heterotetramer.The catalytic mechanism of APSR can be divided into the transport of electrons and the cleavage of APS by FAD. Electron input to the FAD catalyzes the cleavage of APS, releasing AMP and sulfite. Although there have been a number of mechanisms proposed to explain the catalytic cleavage of APS to AMP and sulfite (7, 8, 13, 20, 34), many features of the postulated mechanism remain unsettled, including the proteinogenic hydrogen acceptor in the reaction, the conformational change in the enzyme induced by reduction/oxidation of the FAD cofactor, and the reasons for the observed multiple forms of APSR. The divergence between A. fulgidus and Desulfovibrio species also suggests an obvious distinction in the phylogeny of the α- and β-subunits of APSR.To clarify the difference between APSR from A. fulgidus and that from Desulfovibrio species, we have undertaken a structural study of APSR from D. gigas for comparison with the A. fulgidus enzyme. We have isolated and purified APSR directly from massive, anaerobically grown D. gigas cells for structure determination and characterization. The comparison of the structures and sequences revealing the notable differences at the C termini, activity sites, and other regions for the function is discussed. The structure of oxidized APSR from D. gigas provides much direct evidence about the subunit interactions and the role of the quaternary structure in the regulation of the catalytic mechanism.     

Prognostic Value of Red Blood Cell Distribution Width for Patients with Heart Failure: A Systematic Review and Meta-Analysis of Cohort Studies

Aims

Multiple studies have investigated the prognostic role of red blood cell distribution width (RDW) for patients with heart failure (HF), but the results have been inconsistent. The aim of the present study was to estimate the impact of RDW on the prognosis of HF by performing a systematic review and meta-analysis.

Methods and Results

The Embase, PubMed, and Web of Science databases were searched up to November 16, 2013 to identify eligible cohort studies. The quality of each study was assessed using the Newcastle-Ottawa Scale (NOS). The association between RDW, either on admission or at discharge, and HF outcomes (all-cause mortality [ACM], heart transplantation, cardiovascular mortality, and rehospitalization, etc.) were reviewed. The overall hazard ratio (HR) for the effect of RDW on ACM was pooled using a random-effects model, and the publication bias was evaluated using funnel plots and Eggers'' tests. Seventeen studies, with a total of 18288 HF patients, were included for systematic review. All eligible studies indicated that RDW on admission and RDW at discharge, as well as its change during treatment, were of prognostic significance for HF patients. The HR for the effect of a 1% increase in baseline RDW on ACM was 1.10 (95% confidence interval: 1.07–1.13), based on pooling of nine studies that provided related data. However, publication bias was observed among these studies.

Conclusions

HF patients with higher RDW may have poorer prognosis than those with lower RDW. Further studies are needed to explore the potential mechanisms underlying this association.     

Correction to: Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae,isolated from a surface seawater sample

Antonie van Leeuwenhoek -     

Classification and evolution of metazoan traces at a topological level

Topological fidelity of metazoan traces formed by metazoan behaviour is little influenced by compaction, diagenesis, continuous soft-sediment deformation and biostratinomy, substrate consistency, etc., whereas all of these can greatly alter the Euclidean geometric attributes of metazoan traces. Morphological characteristics of trace fossils can be distinguished and described objectively by both topological and Euclidean geometric parameters. The former constitute the basis of ichnoorder and ichnofamily. On the basis of topological criteria, metazoan traces can be classified as 4 ichnoorders and 22 ichnofamilies, consisting of 9 basic and 3 combined topological configurations. At a topological level, the behavioural diversity and complexity indicated by metazoan topoichnotaxa remain fairly stable in the Phanerozoic. All ichnoorders, 75% of ichnofamilies and all 9 basic topological configurations of metazoan traces are formed in the late Neoproterozoic, and all ichnofamilies, a combination of topological configurations and the most complex and highest level of topological configurations of metazoan traces, occurred in the early Cambrian. The evolution of metazoan traces can be expressed in three ranks. Changes at ichnoorder level constitute the first evolution, which is associated with the advent of kingdoms (animalia and plantae, etc.) and phyla (Ediacara and bilaterian, etc.), and the first level of palaeoecological and palaeoenvironmental changes, such as the appearance or disappearance of an ecosystem (Precambrian biomat). The first evolution terminated in the late Neoproterozoic. Changes at the ichnofamily level constitute the second evolution, which is associated with the advent of important phyla such as coelomate animal explosion and the second level of palaeoecological and palaeoenvironmental changes, such as structural changes within an ecosystem. The second evolution terminated in the early Cambrian. Changes at the ichnogeneric and ichnospecific levels constitute the third evolution, which is associated with the appearance or disappearance of the organic taxa lower than phylum, such as dinosaurs and birds, etc., and the third and fourth levels of palaeoecological and palaeoenvironmental changes, such as community-type level changes, within an established ecological structure and community level. The third evolution has been taking place since the Proterozoic.     

Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae,isolated from a surface seawater sample

A Gram-stain-negative, light yellow pigmented, non-motile and aerobic bacterial strain, designated HHU E2-1 ^T, was isolated from a surface seawater sample. The 16S rRNA gene sequence analysis indicated that HHU E2-1 ^T shared the highest sequence similarity to the type strain Qipengyuania gaetbuli DSM 16225 ^T (96.90%), which belongs to the family Erythrobacteraceae. Combined phylogeny of 288 single-copy orthologous gene clusters, analysis of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI) and evolutionary distances suggested that HHU E2-1 ^T can be considered as a member of the genus Altererythrobacter based on the recently proposed standard for defining genera of Erythrobacteraceae. Strain HHU E2-1 ^T grew at 15–35 °C and pH 5.0–8.0, with optimum growth at 28 °C and pH 7.0. Tolerance to NaCl was up to 4% (w/v) with optimum growth in 2–3% NaCl. The major fatty acids (>?10%) were C_18:1ω7c11-methyl, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The predominant isoprenoid quinone was ubiquinone-10. The genomic G?+?C content was 57.40%. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, HHU E2-1 ^T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter flava sp. nov. is proposed. The type strain is HHU E2-1 ^T (=?CGMCC 1.17394 ^T?=?KCTC 72835 ^T?=?MCCC 1K04226^T).