Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus

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.

The epidemiology, diagnosis and management of scrub typhus disease in China

Thirty-nine years ago, scrub typhus (ST), a disease, was not among the China's notifiable diseases. However, ST has reemerged to become a growing public health issue in the southwest part of China. The major factors contributing to an increased incidence and prevalence of this disease include rapid globalization, urbanization, expansion of humans into previously uninhabited areas, and climate change. The clinical manifestation of ST also consists of high fever, headache, weakness, myalgia, rash, and an eschar. In severe cases, complications (e.g. multi-organ failure, jaundice, acute renal failure, pneumonitis, myocarditis, and even death) can occur. The diagnosis of ST is mainly based on serological identification by indirect immunofluorescence assay and other molecular methods. Furthermore, several groups of antibiotics (e.g. tetracycline, chloramphenicol, macrolides, and rifampicin) are currently effective in treating this disease. This fact suggests the need for robust early diagnostic techniques, increased surveillance, and prompt treatment, and develop future vaccine.

In silico characterization of hypothetical proteins from Orientia tsutsugamushi str. Karp uncovers virulence genes

Scrub typhus also known as bush typhus is a disease with symptoms similar to Chikungunya infection. It is caused by a gram-negative bacterium Orientia tsutsugamushi which resides in its vertebrate host, Mites. The genome of Orientia tsutsugamushi str. Karp encodes for 1,563 proteins, of which 344 are characterized as hypothetical ones. In the present study, we tried to identify the probable functions of these 344 hypothetical proteins (HPs). All the characterized hypothetical proteins (HPs) belong to the various protein classes like enzymes, transporters, binding proteins, metabolic process and catalytic activity and kinase activity. These hypothetical proteins (HPs) were further analyzed for virulence factors with 62 proteins identified as the most virulent proteins among these hypothetical proteins (HPs). In addition, we studied the protein sequence similarity network for visualizing functional trends across protein superfamilies from the context of sequence similarity and it shows great potential for generating testable hypotheses about protein structure-function relationships. Furthermore, we calculated toplogical properties of the network and found them to obey network power law distributions showing a fractal nature. We also identifed two highly interconnected modules in the main network which contained five hub proteins (KJV55465, KJV56211, KJV57212, KJV57203 and KJV57216) having 1.0 clustering coefficient. The structural modeling (2D and 3D structure) of these five hub proteins was carried out and the catalytic site essential for its functioning was analyzed. The outcome of the present study may facilitate a better understanding of the mechanism of virulence, pathogenesis, adaptability to host and up-to-date annotations will make unknown genes easy to identify and target for experimentation. The information on the functional attributes and virulence characteristic of these hypothetical proteins (HPs) are envisaged to facilitate effective development of novel antibacterial drug targets of Orientia tsutsugamushi.

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

Metal ions are involved in many essential biological processes and are crucial for the survival of all organisms. Identification of metal-binding proteins (MBPs) of human affecting pathogens may provide the blueprint for understanding biological metal usage and their putative roles in pathogenesis. This study is focused on the analysis of MBPs from Orientia tsutsugamushi (Ott), a causal agent of scrub typhus in humans. A total of 321 proteins were predicted as putative MBPs, based on sequence search and three-dimensional structure analysis. Majority of proteins could bind with magnesium, and the order of metal binding was Mg > Ca > Zn > Mn > Fe > Cd > Ni > Co > Cu, respectively. The predicted MBPs were functionally classified into nine broad classes. Among them, gene expression and regulation, metabolism, cell signaling, and transport classes were dominant. It was noted that the putative MBPs were localized in all subcellular compartments of Ott, but majorly found in the cytoplasm. Additionally, it was revealed that out of 321 predicted MBPs 245 proteins were putative bacterial toxins and among them, 98 proteins were nonhomologous to human proteome. Sixty putative MBPs showed the ability to interact with drug or drug-like molecules, which indicate that they may be used as broad-spectrum drug targets. These predicted MBPs from Ott could play vital role(s) in various cellular activities and virulence, hence may serve as plausible therapeutic targets to design metal-based drugs to curtail its infection.

Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa

Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant-pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant-pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.

Intellectual Property Rights in Animal Biotechnology

Intellectual property is the foundation of innovations. The science of animal biotechnology has progressed vastly during past three decades. Vaccines, antibodies, gene-editing, or transgenic animals as model for investigating human diseases and producing recombinant therapeutics, and the bioinformatics methods are the innovative intellectual outcomes.

Highlights

Animal biotechnology is oriented toward developing products at commercial scale

IPRs are essential components of animal biotechnology research and development.