Pan-proteome profiling of emerging and re-emerging zoonotic pathogen Orientia tsutsugamushi for getting insight into microbial pathogenesis
Introduction
The acute febrile zoonotic disease “scrub typhus” is caused by the intracellular bacterium Orientia tsutsugamushi (Ott), which threatens about one billion and infect nearly one million people across the globe [1,2]. Orientia tsutsugamushi is an obligate intracellular gram-negative bacterium that belongs to order Rickettsiales and family Rickettsiaceae. The species name of the bacterium is obtained from the Japanese word “tsutsuga” meaning “disease” and “mushi” means “mite” [3]. The pathogenic bacterium is transmitted to humans by feeding larvae of trombiculid mites (genus Leptotrombidium) and mite also serves as the reservoir of Ott [4]. The microorganism spreads through blood and lymphatic fluid, causing symptoms like rash, fever, and elevated levels of liver enzymes and C-reactive protein [5].
Scrub typhus is one of the oldest vector-borne diseases endemic to the “tsutsugamushi triangle” in Asia-Pacific. The tsutsugamushi triangle covers about eight million sq km area including Northern Australia, Northern Japan, Taiwan, Russia, China, Philippines, South Korea, India, Nepal, and Afghanistan [6]. The disease is endemic in the tsutsugamushi triangle but cases also reported from South America, Middle East, Africa, and Europe, shows the wider geographical distribution of the Orientia genus [5,7]. Furthermore, scrub typhus is considered a neglected zoonotic disease but has an ever-widening impact throughout the world.
Scrub typhus is an endemic and emerging and re-emerging infectious disease in India. During the Second World War scrub typhus broke out in an epidemic form in West Bengal and Assam states of India [8]. The disease can simultaneously lead to various other health complications, i.e., neurological, respiratory, hematological, and cardiac problems [9]. Moreover, scrub typhus is the major cause of acute encephalitis syndrome among Indian children [10].
Centre for Disease Control and Prevention (CDC) mentioned that no satisfactory vaccine had been developed yet for scrub typhus. There are some antibiotics currently available to treat scrub typhus, though; uncertain evidences of antibiotic resistance have been documented [[11], [12], [13]]. The present need is to design effective control measures to eradicate scrub typhus due to its non-specific representation and high mortality rate [3].
Closely related bacterial species share large number of genes; however, some variable genes concentrate bacterial species gene pool due to genetic diversity and further expand species pan-genome [14,15]. The notion of bacterial pan-genome was established about 15 years back and can be defined as the entire genic content of all strains in a species [[16], [17], [18]]. The three components of pan-genome are: (i) core genome composed of genes present in all strains, (ii) accessory genome consisting set of genes absent from one or more strains, and (iii) unique genome confined to individual strain [[16], [17], [18]].
Scientists used a single reference genome of each species in the early period of the genomic era for various genetic analyses [15,19]. The development and expansion of next generation sequencing (NGS) technologies broaden our perceptive on microbial genetics, physiology, and functional diversity at the metagenomic echelon which makes realization to the scientific community that it is not sufficient to extract all the genetic information from a single reference genome [14,15,17]. The large datasets provided by these sequencing technologies further assist in-depth analysis of intra-species comparisons and diversity from various prospects like understanding the genetic variations in and among pathogenic groups and designing therapeutic targets [15,17,20]. Although, genetic diversity is measurable at genetic level, yet, the best impact is obtained by analyzing “protein”, i.e., functional unit of the cell [21]. Therefore, the use of proteomics approaches is offered as one of the most favorable or convenient way to get insight into the complex functional diversity across bacterial species. A rising analytical approach “pan-proteomics” seeks to evaluate expressed and translated pan-genome [21,22]. Thus, pan-proteomics is presented as an extension of the pan-genome paradigm which permits both qualitative and quantitative proteome comparison, among the species [21,22]. Further, it is well documented that analyses of the pan-proteome not only aids in measuring genetic variations and classification of strain types, but also helps in the identification of vaccine or drug targets and determination of their mode of actions [[21], [22], [23], [24], [25]].
Currently, most of the existing therapies are becoming ineffective with the occurrence and evolution of multidrug and antibiotic resistance in bacterial species [26]. Thus, the need for the current time is to explore the pan-proteome of the bacterial pathogens to identify wide-spectrum therapeutic targets which will be effective against most of the closely linked bacterial species [27,28]. Furthermore, computational biology has emerged as a promising approach for analyzing the genome and proteome sequence data [29,30]. The bioinformatics approaches are more efficient, cost effective, less time consuming, and provides extensive knowledge regarding complete biological systems [[31], [32], [33]]. The current study provided here is focused on in silico identification of probable therapeutic targets from the pan-proteome of eight completely sequenced strains of Ott.
Section snippets
Data extraction
The complete genome assembly has maximum information regarding the genetic makeup of the pathogen. Hence, the whole proteome sequence data of 8 completely sequenced strains of intracellular pathogens “Ott” was retrieved from the RefSeq database accessible at National Centre for Biotechnology Information (NCBI). RefSeq is an open-access comprehensive, well-annotated, non-redundant, and curated collection of reference sequences including nucleotides and proteins [34]. The detailed description of
Pan-proteome profiling of Ott
The pan-proteome approach, which is an extension of pan-genome, was applied for the prioritization of therapeutic targets in which the ortholog clustering of all the protein sequences present in 8 complete proteomes of Ott strains was performed using CD-HIT at 80 % identity. A total of 1429 protein clusters were obtained having 80 % identity, i.e., the pan-proteome of Ott has 1429 total protein clusters. Further, the manual analysis of these clusters listed 694 core (shared by all eight
Conclusions
In the current study, the bioinformatics investigation of the pan-proteome of Ott was done to find best possible therapeutic targets. The pan-proteome of Ott was found extensive or open in nature and was rich in core proteins followed by accessory and unique proteins. The evaluation of specific attributes, i.e., essentiality, virulent, resistant, and similarity search with host proteins, further, helped in the prioritization of therapeutic targets. The functionality and interactome analysis of
Funding
Not applicable.
Authors’ contributions
Dixit Sharma: Conceptualization, Methodology; Dixit Sharma, Ankita Sharma: Data curation, Analyses, Validation; Dixit Sharma: Writing-Original draft preparation, Birbal Singh, Ankita Sharma: Writing-Reviewing; Birbal Singh, Shailender Kumar Verma: Editing and suggestions.
Declaration of competing interest
The authors declare that there is no conflict of interest.
Acknowledgements
DS and AS acknowledge the Indian Council of Medical Research, Government of India, New Delhi, India for Senior Research Fellowship and Research Associate respectively. Authors duly acknowledge to Central University of Himachal Pradesh for providing computational facilities.
References (113)
- et al.
Scrub typhus: no longer restricted to the Tsutsugamushi Triangle
Trav. Med. Infect. Dis.
(2018) - et al.
Scrub typhus infections poorly responsive to antibiotics in northern Thailand
Lancet
(1996) - et al.
Ten years of pan-genome analyses
Curr. Opin. Microbiol.
(2015) - et al.
The bacterial pangenome as a new tool for analysing pathogenic bacteria
New Microbes New Infect
(2015) - et al.
Comparative genomics: the bacterial pan-genome
Curr. Opin. Microbiol.
(2008) - et al.
Using bacterial genomes and essential genes for the development of new antibiotics
Biochem. Pharmacol.
(2017) - et al.
Pan-proteomics: technologies, applications, and challenges
- et al.
Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and Protein-Protein interaction network
Comput. Biol. Chem.
(2018) - et al.
In silico identification of copper-binding proteins of Xanthomonas translucens pv. undulosa for their probable role in plant-pathogen interactions
Physiol. Mol. Plant Pathol.
(2019) - et al.
Basic local alignment search tool
J. Mol. Biol.
(1990)
Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins
J. Theor. Biol.
Antibiotic targeting of the bacterial secretory pathway
Biochim. Biophys. Acta Mol. Cell Res.
Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development
Tuberculosis
The bacterial lipid II flippase MurJ functions by an alternating-access mechanism
J. Biol. Chem.
Interdependence of bacterial cell division and genome segregation and its potential in drug development
Microbiol. Res.
Penicillin-binding proteins: evergreen drug targets
Curr. Opin. Pharmacol.
Cytochrome c biogenesis: the Ccm system
Trends Microbiol.
Scrub typhus: the geographic distribution of phenotypic and genotypic variants of Orientia tsutsugamushi
Clin. Infect. Dis.
Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus
J. Mol. Recogn.
Approaches to vaccines against Orientia tsutsugamushi
Front. Cell. Infect. Microbiol.
Unresolved problems related to scrub typhus: a seriously neglected life-threatening disease
Am. J. Trop. Med. Hyg.
Endemic scrub typhus in South America
N. Engl. J. Med.
A review of the global epidemiology of scrub typhus
PLoS Neglected Trop. Dis.
Scrub typhus: an emerging threat
Indian J. Dermatol.
Clinical manifestations of scrub typhus
Trans. R. Soc. Trop. Med. Hyg.
Scrub typhus as a cause of acute encephalitis syndrome, Gorakhpur, Uttar Pradesh, India, Emerg
Inf. Disp.
The historical case for and the future study of antibiotic-resistant scrub typhus
Trav. Med. Infect. Dis.
Antibiotics for treating scrub typhus
Cochrane Database Syst. Rev.
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome
Proc. Natl. Acad. Sci. Unit. States Am.
The bacterial pan-genome: a new paradigm in microbiology
Int. Microbiol.
Pan-genomics in the human genome era
Nat. Rev. Genet.
Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains
Expert Rev. Proteomics
Label-free quantitative proteomics analysis of antibiotic response in Staphylococcus aureus to oxacillin
J. Proteome Res.
Proteomics uncovers extreme heterogeneity in the Staphylococcus aureus exoproteome due to genomic plasticity and variant gene regulation
Proteomics
Antibacterial resistance worldwide: causes, challenges and responses
Nat. Med.
Defining the core essential genome of Pseudomonas aeruginosa
Proc. Natl. Acad. Sci. Unit. States Am.
Comparative genomic analyses reveal core-genome-wide genes under positive selection and major regulatory hubs in outlier strains of Pseudomonas aeruginosa
Front. Microbiol.
Bioinformatic exploration of metal-binding proteome of zoonotic pathogen Orientia tsutsugamushi
Front. Genet.
Zinc binding proteome of a phytopathogen Xanthomonas translucens pv
undulosa, R. Soc. Open Sci.
Proteome wide identification of iron binding proteins of Xanthomonas translucens pv. undulosa: focus on secretory virulent proteins
Biometals
In silico study of iron, zinc and copper binding proteins of Pseudomonas syringae pv. lapsa: emphasis on secreted metalloproteins
Front. Microbiol.
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Nucleic Acids Res.
Accelerated for clustering the next-generation sequencing data
Bioinformatics
PanGP: a tool for quickly analyzing bacterial pan-genome profile
Bioinformatics
DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements
Nucleic Acids Res.
VFDB 2019: a comparative pathogenomic platform with an interactive web interface
Nucleic Acids Res.
Exploitation of antibiotic resistance as a novel drug target: development of a β-lactamase-activated antibacterial prodrug
J. Med. Chem.
A new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
Antimicrob. Agents Chemother.
Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions
Protein Sci.
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
Bioinformatics
Cited by (6)
Editorial: Special issue: Advances in microbial pathogenesis
2023, Microbial PathogenesisDifferential analysis of Orientia tsutsugamushi genomes for therapeutic target identification and possible intervention through natural product inhibitor screening
2022, Computers in Biology and MedicineCitation Excerpt :Therefore, the current study aimed to prioritize the potential drug targets in Ott. Previously, scientific community had to rely on a single reference genome for the drug target identification, which was not sufficient for extracting information regarding pathogenesis, and conservancy of drug against various strains of the pathogen [53]. Thus, pan-genomic analysis is one of the appropriate approaches to encompass functional diversity among the bacterial species.
Neglected scrub typhus: An updated review with a focus on omics technologies
2022, Asian Pacific Journal of Tropical MedicineGenetic variation of chigger mites in the Republic of Korea
2022, Entomological Research