Cryo-EM structure of a lethal pore-forming toxin- γ-hemolysin from the superbug S. aureus

Work done in the lab of Prof. Somnath Dutta at Molecular Biophysics Unit, Indian Institute of Science, Bengaluru

About author

Suman Mishra hails from Madhubani, Bihar. He was born to Raj Kumar Mishra- a banker and a prolific writer in Maithili, and Rupa Mishra- tireless homemaker, and doting mother of two. He completed his B. Tech degree in Biotechnology from Padmashri Dr. D. Y. Patil University, Navi Mumbai with his thesis titled “Understanding genetic variations in TOLLIP gene and its association with malaria susceptibility/ resistance in west coast Indian population” under Dr. K. Thangaraj, CSIR- CCMB, Hyderabad. He further joined as a doctoral student at Molecular Biophysics Unit, Indian Institute of Science, Bengaluru in the laboratory of Prof. Somnath Dutta. He currently works on cryo-EM structural characterization of bacterial pore-forming toxins and virulence factors.

Interview

How would you explain your research outcomes to the non-scientific community?

Staphylococcus aureus (S. aureus) is typically associated with hospital-acquired infections, with an annual killing rate of over 1 lakh people worldwide. It has been a global concern owing to the emergence of resistance to the latest generations of antibiotics, thus labeled a “superbug”. In the wake of antibiotic resistance, it is important to identify alternative potential targets in these life-threatening pathogens to mitigate their pathogenesis. S. aureus secretes over half a dozen different pore-forming toxins, including γ-hemolysin, to puncture holes into host cellular membranes causing osmotic imbalance, rupturing and cell death. γ-hemolysin plays a vital role in lysis of human erythrocytes (red blood cells) to snatch free iron from hemoglobin which is essential for bacterial growth. In our laboratory, we have characterized the atomic structure of this protein complex in a near-physiological membrane environment using cryo-electron microscopy (cryo-EM). Through our study, we gained several novel insights on how the soluble pore-forming toxin monomers interact with the host cellular membrane and oligomerize into an octamer, thus forming a functional pore spanning across the lipid membrane.

How do these findings contribute to your research area?

We provide the first structure of γ-hemolysin in a lipid environment that closely resembles the infection model. This has directly led to structural understanding of lipid-binding clefts in the atomic structure, which can now be targeted via drug/antibody design. In addition, our structure adds to the current knowledge of the pore-formation mechanism for the bi-component pore-forming toxins of S. aureus. These bi-component toxins have high sequence and structural similarities, and thus, it will be interesting to see if the new insights our study provides on γ-hemolysin also helps us unravel potential targets for the other bi-component pore-forming toxins.

“We provide the first structure of γ-hemolysin in a lipid environment that closely resembles the infection model. “

What was the exciting moment during your research?

For cryo-EM studies, protein samples in general should be highly monodispersed and homogeneous. This was a difficult part of our study since the toxins were constituted in liposomes. Unexpectedly, I could also observe the formation of an octahedral super assembly of these protein-lipid complexes upon membrane rupturing, that turned out to be instrumental for the three-dimensional cryo-EM reconstruction of γ-hemolysin. Moments like these- where we get to think out of the box, kept me on my toes throughout the course of this research project.

What do you hope to do next?

I am currently working on other structural aspects of γ-hemolysin as continuation of this study and am excited to see how things unfold! In the long run, I am particularly interested in taking my research further into structural understanding of host-pathogen interactions and neurodegenerative diseases.

Where do you seek scientific inspiration from?

I will remain indebted to my Ph.D. mentor, Prof. Somnath Dutta, for honing the art of observation and critical thinking in me. I also seek scientific inspiration from my department- Molecular Biophysics Unit, which I am grateful to be a part of.

How do you intend to help Indian science improve?

Given the challenges of being the second largest country population-wise, research work at several laboratories in India are at par with the international science community. The difficulty lies in providing equal opportunities to everyone interested in science at college-level and also bringing basic and applied research into the undergraduate curriculum. I envision all research and educational institute campuses ensuring equal opportunities are provided to all genders and celebrating ethnic diversity. That has always been my plan all along.

Reference

Mishra, S., Roy, A., & Dutta, S. (2023). Cryo-EM-based structural insights into supramolecular assemblies of γ-hemolysin from S. aureus reveal the pore formation mechanism. Structure (London, England : 1993), S0969-2126(23)00085-0. https://www.cell.com/structure/fulltext/S0969-2126(23)00085-0

Copy Editor

Anjali Mahilkar

Postdoctoral Fellow at University of Michigan

Anjali is an evolutionary biologist working as a postdoctoral researcher in the department of Ecology and Evolutionary Biology at University of Michigan, Ann Arbor. Her research interests mainly lie in understanding the relationship between natural selection, adaptation and drift in deciding the evolutionary fates of biological functions as well as of whole organisms. She has a PhD from IIT Bombay where her research focused on understanding the process of speciation. Anjali also has her Masters from IIT Kanpur and Bachelor’s from NIT Raipur. She also had short work stints at Dr. Reddy’s Institute of Life Science and at a Central University in Chhattisgarh. She is interested in science communication and volunteers for several organizations towards the same. Although not an avid reader, she likes to read fiction in her free time.

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