Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi

Computational studies on metabolic pathways of Coxiella burnetii to combat Q fever: A roadmap to vaccine development

Coxiella burnetii (Cbu) is the gram-negative intracellular pathogen responsible for deadly zoonotic infection, Q fever. The pathogen is environmentally stable and distributed throughout the world which is sustained in nature by chronic infection of ruminants. The epidemiological studies on Q fever indicates it as emerging public health problem in various countries and it is imperative to promptly identify an appropriate therapeutic solution for this pathogen. In the current study, metabolic pathways of Cbu were analysed by the combination of multiple computational tools for the prediction of suitable therapeutic candidates. We have identified 25 metabolic pathways which were specific to Cbu containing 287 unique proteins. A total of 141 proteins which were either virulent, essential or resistant were shortlisted that do not show homology with the host proteins and considered as potential targets for drug and vaccine development. The potential therapeutic targets were classified in to seven functional classes, i.e., metabolism, transport, gene expression and regulation, signal transduction, antimicrobial resistance, stress response regulator and unknown. The majority of the proteins were found to be present in metabolism and transport class. The functional annotation showed the predominant presence of proteins containing HATPase_c, Beta-lactamase, GerE, ACR_tran, PP-binding, CsrA domains. We have identified Type I secretion outer membrane protein for the design of multi-epitope subunit vaccine using reverse vacciniology approach. Four B cell epitopes, six MHC-I epitopes and four MHC-II epitopes were identified which are non-toxic, non-allergen and highly antigenic. The multi-epitope subunit vaccine construct was 327 amino acid residues long which include adjuvant, B cell epitopes, MHC-I epitopes and MHC-II epitopes. The Cholera enterotoxin subunit B is included as an adjuvant in the N terminal of vaccine construct which will help to produce a strong immune response to the vaccine. The multi-epitope vaccine construct was non-toxic, non-allergen and probable antigen having molecular weight 35.13954 kDa, aliphatic index 85.50, theoretical PI 9.65, GRAVY -0.001, and instability index of 28.37. The tertiary structure of the vaccine construct was modeled and physiochemical properties were predicted. After validation and refinement of tertiary structure the molecular docking of vaccine exhibited strong binding with TLR2, TLR3, TLR4, TLR5 and TLR8. The TLRs and vaccine construct formed hydrogen bonds, salt bridges and non-bonded contacts with all TLR receptors. The in-silico immune simulations showed the ability to trigger primary immune response as shown by increment in B-cell and T-cell population. The research paves the way for more effective control of zoonotic disease Q fever.

Deciphering Rickettsia conorii metabolic pathways: A treasure map to therapeutic targets

Indian tick typhus is an infectious disease caused by intracellular gram-negative bacteria Rickettsia conorii (R. conorii). The bacterium is transmitted to humans through bite of infected ticks and sometimes by lice, fleas or mites. The disease is restricted to some areas with few cases but in last decade it is re-emerging with large number of cases from different areas of India. The insight in to genetic makeup of bacterial pathogens can be derived from their metabolic pathways. In the current study 18 metabolic pathways were found to be unique to the pathogen (R. conorii). A comprehensive analysis revealed 163 proteins implicated in 18 unique metabolic pathways of R. conorii. 140 proteins were reported to be essential for the bacterial survival, 46 were found virulent and 10 were found involved in resistance which can enhance the bacterial pathogenesis. The functional analysis of unique metabolic pathway proteins showed the abundance of plasmid conjugal transfer TrbL/VirB6, aliphatic acid kinase short chain, signal transduction response regulator receiver and components of type IV transporter system domains. The proteins were classified into six broad categories on the basis of predicted domains, i.e., metabolism, transport, gene expression and regulation, antimicrobial resistance, cell signalling and proteolysis. Further, in silico analysis showed that 88 proteins were suitable therapeutic targets which do not showed homology with host proteins. The 43 proteins showed hits with the DrugBank database showing their druggable nature and remaining 45 proteins were classified as novel drug targets that require further validation. The study will help to provide the better understanding of pathogens survival and embark on the development of successful therapies for the management of Indian tick typhus.

Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8

The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BACKGROUND

The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS

To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION

Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

Orientia tsutsugamushi OtDUB Is Expressed and Interacts with Adaptor Protein Complexes during Infection

Orientia tsutsugamushi is an etiologic agent of scrub typhus, a globally emerging rickettsiosis that can be fatal. The bacterium's obligate intracellular lifestyle requires its interaction with host eukaryotic cellular pathways. The proteins it employs to do so and their functions during infection are understudied. Recombinant versions of the recently characterized O. tsutsugamushi deubiquitylase (OtDUB) exhibit high-affinity ubiquitin binding, mediate guanine nucleotide exchange to activate Rho GTPases, bind clathrin adaptor protein complexes 1 and 2, and bind the phospholipid phosphatidylserine. Whether OtDUB is expressed and its function during O. tsutsugamushi infection have yet to be explored. Here, OtDUB expression, location, and interactome during infection were examined. O. tsutsugamushi transcriptionally and translationally expresses OtDUB throughout infection of epithelial, monocytic, and endothelial cells. Results from structured illumination microscopy, surface trypsinization of intact bacteria, and acetic acid extraction of non-integral membrane proteins indicate that OtDUB peripherally associates with the O. tsutsugamushi cell wall and is at least partially present on the bacterial surface. Analyses of the proteins with which OtDUB associates during infection revealed several known O. tsutsugamushi cell wall proteins and others. It also forms an interactome with adapter protein complex 2 and other endosomal membrane traffic regulators. This study documents the first interactors of OtDUB during O. tsutsugamushi infection and establishes a strong link between OtDUB and the host endocytic pathway.

mebipred: identifying metal binding potential in protein sequence

Motivation

metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability.

Results

we developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred’s utility in analyzing microbiome metal requirements.

Availability and implementation

mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Functional assignment to hypothetical proteins in Orientia tsutsugamushistrain Ikeda

Orientia tsutsugamushi(O. tsutsugamushi) is an intracellular bacterial pathogen which causes zoonosis scrub typhus in humans. Genome of O. tsutsugamushi strain Ikeda contains 214 hypothetical proteins (HPs) which is nearly 20% of the total proteins. Domain and family based functional analysis of HPs results in the annotation of 44 hypothetical proteins. The annotated HPs were classified in to five main classes namely, gene expression and regulation, transport, metabolism, cell signaling and proteolysis. Thus, computational analysis of HPs helps to understand their putative roles in various biological and cellular processes, including pathogenesis for further consideration as potential therapeutic targets.

Differential analysis of Orientia tsutsugamushi genomes for therapeutic target identification and possible intervention through natural product inhibitor screening

Orientia tsutsugamushi (Ott) is a causative agent of scrub typhus, and one of the emerging pathogens that could affect a large human population. It is one of the misdiagnosed and under-reported, febrile illnesses that infects various body organs (skin, heart, lung, kidney, and brain). The control of this infection is hampered due to the lack of drugs or vaccine against it. This study was undertaken to identify potential drug targets from the core genome of Ott and investigate novel natural product inhibitors against them. Hence, the available genomes for 22 strains of Ott were downloaded from the PATRIC database, and pan-genomic analysis was performed. Only 202 genes were present in the core region. Among these, 94 were identified as essential, 32 non-homologous to humans, nine non-homologous to useful gut flora and a single gene dapD as a drug target. Product of this gene (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase) was modeled and docked against traditional Indian (Ayurvedic) and Chinese phytochemical libraries, with best hits selected for docking, based on multiple target-drug/s interactions and minimum energy scores. ADMET profiling and molecular dynamics simulation was performed for top three compounds from each library to assess the toxicity and stability, respectively. We presume that these compounds (ZINC8214635, ZINC32793028, ZINC08101133, ZINC85625167, ZINC06018678, and ZINC13377938) could be successful inhibitors of Ott. However, in-depth experimental and clinical research is needed for further validation.

Pan-proteome profiling of emerging and re-emerging zoonotic pathogen Orientia tsutsugamushi for getting insight into microbial pathogenesis

With the occurrence and evolution of antibiotic and multidrug resistance in bacteria most of the existing remedies are becoming ineffective. The pan-proteome exploration of the bacterial pathogens helps to identify the wide spectrum therapeutic targets which will be effective against all strains in a species. The current study is focused on the pan-proteome profiling of zoonotic pathogen Orientia tsutsugamushi (Ott) for the identification of potential therapeutic targets. The pan-proteome of Ott is estimated to be extensive in nature that has 1429 protein clusters, out of which 694 were core, 391 were accessory, and 344 were unique. It was revealed that 622 proteins were essential, 222 proteins were virulent factors, and 42 proteins were involved in antibiotic resistance. The potential therapeutic targets were further classified into eleven broad classes among which gene expression and regulation, transport, and metabolism were dominant. The biological interactome analysis of therapeutic targets revealed that an ample amount of interactions were present among the proteins involved in DNA replication, ribosome assembly, cellwall metabolism, cell division, and antimicrobial resistance. The predicted therapeutic targets from the pan-proteome of Ott are involved in various biological processes, virulence, and antibiotic resistance; hence envisioned as potential candidates for drug discovery to combat scrub typhus.