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

Nikhat Imam; Aftab Alam; Rafat Ali; Mohd Faizan Siddiqui; Sher Ali; Md Zubbair Malik; Romana Ishrat

doi:10.1016/j.heliyon.2019.e02734

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

Heliyon. 2019 Nov 1;5(10):e02734. doi: 10.1016/j.heliyon.2019.e02734. eCollection 2019 Oct.

Authors

Nikhat Imam^{1

2}, Aftab Alam², Rafat Ali², Mohd Faizan Siddiqui³, Sher Ali², Md Zubbair Malik⁴, Romana Ishrat²

Affiliations

¹ Institute of Computer Science and Information Technology, Magadh University, Bodhgaya, India.
² Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India.
³ International Medical Faculty, Osh State University, Osh City, 723500, Kyrgyz Republic (Kyrgyzstan).
⁴ School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, Delhi, 110067, India.

Abstract

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.

Keywords: Biochemistry; Bioinformatics; Functional annotation; Genetics; Hypothetical proteins (HPs); Microbiology; ROC analysis; Scrub typhus; Virulence.