Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle

Transcriptome Analysis of Cyclooctasulfur Oxidation and Reduction by the Neutrophilic Chemolithoautotrophic Sulfurovum indicum from Deep-Sea Hydrothermal Ecosystems

Chemolithoautotrophic Campylobacterota are widespread and predominant in worldwide hydrothermal vents, and they are key players in the turnover of zero-valence sulfur. However, at present, the mechanism of cyclooctasulfur activation and catabolism in Campylobacterota bacteria is not clearly understood. Here, we investigated these processes in a hydrothermal vent isolate named Sulfurovum indicum ST-419. A transcriptome analysis revealed that multiple genes related to biofilm formation were highly expressed during both sulfur oxidation and reduction. Additionally, biofilms containing cells and EPS coated on sulfur particles were observed by SEM, suggesting that biofilm formation may be involved in S0 activation in Sulfurovum species. Meanwhile, several genes encoding the outer membrane proteins of OprD family were also highly expressed, and among them, gene IMZ28_RS00565 exhibited significantly high expressions by 2.53- and 7.63-fold changes under both conditions, respectively, which may play a role in sulfur uptake. However, other mechanisms could be involved in sulfur activation and uptake, as experiments with dialysis bags showed that direct contact between cells and sulfur particles was not mandatory for sulfur reduction activity, whereas cell growth via sulfur oxidation did require direct contact. This indirect reaction could be ascribed to the role of H2S and/or other thiol-containing compounds, such as cysteine and GSH, which could be produced in the culture medium during sulfur reduction. In the periplasm, the sulfur-oxidation-multienzyme complexes soxABXY1Z1 and soxCDY2Z2 are likely responsible for thiosulfate oxidation and S0 oxidation, respectively. In addition, among the four psr gene clusters encoding polysulfide reductases, only psrA3B3C3 was significantly upregulated under the sulfur reduction condition, implying its essential role in sulfur reduction. These results expand our understanding of the interactions of Campylobacterota with the zero-valence sulfur and their adaptability to deep-sea hydrothermal environments.

Molecular Interactions, Structural Transitions and Alterations in SoxB Protein Due to SoxYZ Interaction from Two Distinct β-Proteobacteria: An In silico Approach Towards the Thiosulfate Oxidation and Recycling of SoxY Protein

Microbial oxidation-reduction reactions utilizing the environmental thiosulfate ions and mediated mainly by the sox operon are very much essential to maintain the sulfur balance in the environment. Majority of the previously documented wet laboratory studies show genetics behind the functionality of Sox proteins encoded by the sox operon. However, the molecular details of the involvements of the essential SoxB, SoxY and SoxZ proteins in the beta-proteobacteria have not yet been elucidated. In this work, an attempt was made to analyze the interaction profiles of the aforementioned SoxB, SoxY and SoxZ proteins to predict their roles in biological sulfur oxidation process. In order to establish the possible roles of these Sox proteins, we built the homology models of these proteins from the two different beta-proteobacteria Dechloromonas aromatica and Thiobacillus denitrificans. We then used molecular docking and simulation studies to further analyze the interaction profiles of these sox proteins. Our analyses revealed that SoxB protein from T. denitrificans exhibited steadier and stronger interactions with SoxYZ protein complex. On the other hand, SoxB protein from D. aromatica was found to exhibit a spontaneous interaction with greater ΔG values and therefore was well documented to exhibit a dual role. This is the first research article to discern the molecular level of interaction profiles of SoxB with SoxYZ protein complex in the beta-proteobacteria D. aromatica and T. denitrificans during the oxidations of thiosulfate. It would further prompt the future investigation into the mutational impact on the sequential interaction pattern in sox operon.

Insight into the Conformational Variations in SoxYZ Protein Complex from Two Different Members of the β-Proteobacterial Family Involved in Sulfur Oxidation

Sulfur anions serve as the important environmental pollutants. Microbes use hydrogen sulfide in different redox reactions and thus make the environment pollution-free. The sulfur redox processes are performed by a gene cluster called the sox operon, possessed by a diverse set of microorganisms. However, most of the previous studies were confined to α-proteobacteria. In this work, we tried to elucidate the mechanistic details of sulfur oxidation in β-proteobacteria. We compared the molecular mechanism of sulfur oxidation process using Dechloromonas aromatica and Thiobacillus denitrificans. Dechloromonas aromatica possesses the entire sox operon, whereas T. denitrificans lacks SoxCD. In both the organisms, SoxYZ complex formation is essential for thiosulfate oxidation. This SoxYZ protein complex interacts with SoxCD and SoxAX, respectively, for recycling the thiosulfate-bound SoxY protein. For this purpose, individual proteins were modeled via manifold modeling techniques. Protein-protein docking studies were executed to generate duo- and quadro-protein complexes. Different stability parameters such as free energy of folding, solvent accessibility area (for final complexes), and electrostatic surface potential (for SoxYZ complexes) were calculated and analyzed. Fifteen strengthening ionic interactions were accomplished in the SoxYZAX complex, whereas eight such interactions were observed in SoxYZCD complex. From the result, SoxYZAX complex was found to be more stable and interactive one. This study is the first of its kind that analyzes the comparative aspects of the binding interactions of the proteins involved in redox reactions of sulfur anions. This study may, therefore, be helpful in tailoring the microorganisms to function in a better way to remove the environmental sulfur pollutants.

Molecular dynamics study of the conformations of glycosidic linkages in sialic acid modified ganglioside GM3 analogues

The objective of the present study is to model the analogues of monosialoganglioside (GM3) by making modifications in its sialic acid residue with different substitutions in aqueous environment and to determine their structural stability based upon computational molecular dynamics. Molecular mechanics and molecular dynamics investigation was carried out to study the conformational preferences of the analogues of GM3. Dynamic simulations were carried out on the analogues of GM3 varying in the substituents at C-1, C-4, C-5, C-8 and C-9 positions of their sialic acid or Neuraminic acid (NeuAc) residue. The analogues are soaked in a periodic box of TIP3P water as solvent and subjected to a 10 ns molecular dynamics (MD) simulation using AMBER ff03 and gaff force fields with 30 ps equilibration. The analogue of GM3 with 9-N-succNeuAc (analogue5, C9 substitution) was observed to have the lowest energy of -6112.5 kcal/mol. Graphical analysis made on the MD trajectory reveals the direct and water mediated hydrogen bonds existing in these sialic acid analogues. The preferable conformations for glycosidic linkages of GM3 analogues found in different minimum energy regions in the conformational maps were identified. This study sheds light on the conformational preferences of GM3 analogues which may be essential for the design of GM3 analogues as inhibitors for different ganglioside specific pathogenic proteins such as bacterial toxins, influenza toxins and neuraminidases.

Mutation study of DsrM from Allochromatium vinosum using the amino acid sequences

Sulfur metabolism is one of the oldest known environmental processes. The operon involved in this process is called the dsr operon. The vital role of the operon is to maintain the environmental sulfur balance. The dsr operon of proteobacteria consists of 15 genes, viz. dsrABEFHCMKLJOPNRS. The proteins encoded by the dsr operon are essential for the transfer of sulfur globules from periplasm to cytosol and oxidation of the stored sulfur. In the present study we tried to analyze the probable molecular details of the DsrM proteins from a diverse set of microbial species using their sequence information. There are certain mutations in the sequences of the DsrM proteins from the different proteobacterial species. The effects of mutations in the sequences of DsrM proteins were predicted from the evolutionary point of view. This is so far the first report of its kind. Our study would therefore enable the researches to predict the hitherto unknown biochemistry of sulfur oxidation using the amino acid sequences of the DsrM proteins.

DOT2: Macromolecular docking with improved biophysical models

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.

Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle

Microbial redox reactions of inorganic sulfur compounds are one of the important reactions for the recycling of sulfur to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse microorganisms. The sulfur oxidizing gene cluster (sox) of α-proteobacteria, Allochromatium vinosum comprises two divergently transcribed units. The central players of this process are SoxY, SoxZ and SoxL. SoxY is sulfur compound binder which binds to sulfur anions with the help of SoxZ. SoxL is a rhodanese like protein, which then cleaves off the sulfur substrate from the SoxYZ complex to recycle the SoxY and SoxZ. In the present work, homology modeling has been employed to build the three dimensional structures of SoxY, SoxZ and SoxL. With the help of docking simulations the amino acid residues of these proteins involved in the interactions have been identified. The interactions between the SoxY, SoxZ and SoxL proteins are mediated mainly through hydrogen bonding. Strong positive fields created by the SoxZ and SoxL proteins are found to be responsible for the binding and removal of the sulfur anion. The probable biochemical mechanism of sulfur anion oxidation process has been identified.

The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri

BACKGROUND

Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018.

METHODOLOGY/PRINCIPAL FINDINGS

Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Sulfuromonas denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae, and those of the deep-sea vent Epsilonproteobacteria Sulfurovum and Nitratiruptor. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in S. denitrificans, W. succinogenes, Sulfurovum, and/or Nitratiruptor, or are unique to the subdivision. In addition, the analyses indicated also that a substantial proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where <70% of the genes were present in at least two strains.

CONCLUSION/SIGNIFICANCE

The presence of pathways and loci associated often with non-host-associated organisms, as well as genes associated with virulence, suggests that A. butzleri is a free-living, water-borne organism that might be classified rightfully as an emerging pathogen. The genome sequence and analyses presented in this study are an important first step in understanding the physiology and genetics of this organism, which constitutes a bridge between the environment and mammalian hosts.