Structural Evolution of the Ancient Enzyme, Dissimilatory Sulfite Reductase

Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme diversified into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving sulfate/sulfite reducing organismal (SRO) lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.

Role of Nanoparticles Synthesized from Bacteria as Antimicroorganism: A Review

Nanoparticles are one of the most important technologies of today and the future. This groundbreaking technology is considered a very significant domain among all the fields of science due to its tangible capacity in improving products, treating diseases, serving mankind in all spheres of life, and realizing future scientific revolutions in the fields of physics, chemistry, biology, engineering, and other sciences. Therefore, it is truly necessary to take advantage of the distinct properties of nanomaterials. Hence, synthesized nanoparticles have been shown to be enjoying anti-proliferating antioxidant, anti-migration, antioagulant and anti-cancer antipathogenic characteristics in the laboratory. Accordingly, this study came to prominence in this field. The biochemical equipment used in nanoparticle bacterial biosynthesis was subsequently proven. Many of these biochemical types of equipment have been used as part of a cellular detoxification resistance mechanism that involves altering inorganic ions solubility by reducing and/or precipitating soluble toxic to insoluble non-toxic nanostructures. Microorganisms, such as bacteria, are used as an environmentally responsible strategy, and an alternative in the method of chemical agents when nanoparticles are synthesized. Extracellular as well as intracellular biocatalytic (including possible excretion) synthesis involves mainly oxidreductase enzymes like NADH dependent reductase nitrate NADPH, NADPH sulphite reductase alfa (NADPH dependent on sulfite reductase) and cells.

Level of Sulfite Oxidase Activity Affects Sulfur and Carbon Metabolism in Arabidopsis

Molybdenum cofactor containing sulfite oxidase (SO) enzyme is an important player in protecting plants against exogenous toxic sulfite. It was also demonstrated that SO activity is essential to cope with rising dark-induced endogenous sulfite levels and maintain optimal carbon and sulfur metabolism in tomato plants exposed to extended dark stress. The response of SO and sulfite reductase to direct exposure of low and high levels of sulfate and carbon was rarely shown. By employing Arabidopsis wild-type, sulfite reductase, and SO-modulated plants supplied with excess or limited carbon or sulfur supply, the current study demonstrates the important role of SO in carbon and sulfur metabolism. Application of low and excess sucrose, or sulfate levels, led to lower biomass accumulation rates, followed by enhanced sulfite accumulation in SO impaired mutant compared with wild-type. SO-impairment resulted in the channeling of sulfite to the sulfate reduction pathway, resulting in an overflow of organic S accumulation. In addition, sulfite enhancement was followed by oxidative stress contributing as well to the lower biomass accumulation in SO-modulated plants. These results indicate that the role of SO is not limited to protection against elevated sulfite toxicity but to maintaining optimal carbon and sulfur metabolism in Arabidopsis plants.

The Ion-Translocating NrfD-Like Subunit of Energy-Transducing Membrane Complexes

Several energy-transducing microbial enzymes have their peripheral subunits connected to the membrane through an integral membrane protein, that interacts with quinones but does not have redox cofactors, the so-called NrfD-like subunit. The periplasmic nitrite reductase (NrfABCD) was the first complex recognized to have a membrane subunit with these characteristics and consequently provided the family's name: NrfD. Sequence analyses indicate that NrfD homologs are present in many diverse enzymes, such as polysulfide reductase (PsrABC), respiratory alternative complex III (ACIII), dimethyl sulfoxide (DMSO) reductase (DmsABC), tetrathionate reductase (TtrABC), sulfur reductase complex (SreABC), sulfite dehydrogenase (SoeABC), quinone reductase complex (QrcABCD), nine-heme cytochrome complex (NhcABCD), group-2 [NiFe] hydrogenase (Hyd-2), dissimilatory sulfite-reductase complex (DsrMKJOP), arsenate reductase (ArrC) and multiheme cytochrome c sulfite reductase (MccACD). The molecular structure of ACIII subunit C (ActC) and Psr subunit C (PsrC), NrfD-like subunits, revealed the existence of ion-conducting pathways. We performed thorough primary structural analyses and built structural models of the NrfD-like subunits. We observed that all these subunits are constituted by two structural repeats composed of four-helix bundles, possibly harboring ion-conducting pathways and containing a quinone/quinol binding site. NrfD-like subunits may be the ion-pumping module of several enzymes. Our data impact on the discussion of functional implications of the NrfD-like subunit-containing complexes, namely in their ability to transduce energy.

Diversity and distribution of sulfate-reducing bacteria and its ecological effect in Shimen Realgar Mine

Microbial sulfate reduction, a vital mechanism for microorganisms living in anaerobic, sulfate-rich environments, is an essential aspect of the sulfur biogeochemical cycle. However, there has been no detailed investigation of the diversity and distribution of SRBs and its effect in Shimen Realgar Mine, which is characterized as a hot research area rich in sulfate. To elucidate this issue, soils sample from Shimen Realgar Mine were collected. Further, a total of 55 new or new-type dissimilatory sulfite reductase genes and 5 new families of DrsAB proteins were successfully identified, which demonstrate the rich and unique diversity of the sulfate reducing microbes in this environment. We also isolate a novel DSRP strain, Desulfotomaculum sp. JL90 from the soils, which can efficiently respiratory reduces sulfate and arsenate. JL90 also can promote the generation of yellow precipitations in the presence of multiple electron acceptors (both contain sulfate and As(V) in the cultures). Moreover, microbial community compositions also indicated the biogenesis contribution of SRBs to the Shimen realgar mine. The results of this study provided a new insight into the diversity and distribution of SRBs and its ecological effect in Shimen Realgar Mine.