20 July 2023

– Ranjini Raghunath

Researchers at the Indian Institute of Science (IISc) have designed a short peptide capable of poisoning a key enzyme in disease-causing bacteria, including some of most deadly and antibiotic-resistant species.

Made from a short stretch of about 24 amino acids, the peptide mimics the action of a natural toxin which inhibits a class of enzymes called topoisomerases. These enzymes play a crucial role in unspooling and re-coiling bacterial DNA during replication and protein synthesis. They are an attractive target for antibiotics because the ones in bacteria are very different from those in humans.

Among the most widely used antibiotics are fluoroquinolones such as ciprofloxacin, which target these topoisomerases. However, overuse of these antibiotics around the world has led to the alarming rise of antibiotic-resistant bacteria, prompting scientists to pursue alternative strategies and molecules.

Topoisomerases form a covalent adduct – an intermediate complex – with the bacterial DNA, to coil or uncoil it. The peptide developed by the IISc team binds to this adduct and “traps” it in place, kicking off a cascade of events that lead to cell death, explains Raghavan Varadarajan, Professor at the Molecular Biophysics Unit (MBU), and one of the corresponding authors of the study published in EMBO Reports. This is similar to how a natural toxin called CcdB, produced by certain other bacteria and plasmids, works.

“The full length CcdB protein is large. It is not feasible to use it as a drug in its entirety,” says first author Jayantika Bhowmick, former PhD student at MBU and currently a postdoctoral researcher at the University of Cambridge. Instead, the team snipped out a small stretch from the tail end of this protein and added a few more amino acids that would allow the new peptide to enter bacterial cells. The peptide design was carried out by the lab of Jayanta Chatterjee, Professor in MBU.

Image: Jayantika Bhowmick

The team then tested the new peptide’s effect on the growth of several disease-causing bacterial species, including E. coli, Salmonella Typhimurium, Staphylococcus aureus and a multidrug resistant strain of Acinetobacter baumanii – both in cell culture as well as animal models, in collaboration with the lab of Dipshikha Chakravortty, Professor at the Department of Microbiology and Cell Biology (MCB). They also compared the effect of their peptide against clinical doses of ciprofloxacin. Depending on the species, the peptide was found to either block or “poison” a specific type of topoisomerase – an enzyme called DNA gyrase in many of them, explains Manish Nag, PhD student at MBU and another author. “It is [also] capable of disrupting most of the strains’ membranes,” he adds.

In animal models, the peptide was found to drastically reduce infection. “In most of the cases, we saw that the decline in the bacterial count in major organs following peptide treatment was higher than in the ciprofloxacin-treated group. That was pretty encouraging to us,” says Bhowmick. For example, in animals infected with antibiotic-resistant Acinetabacter baumannii, the peptide treatment caused an 18-fold reduction in bacterial load in the liver, compared to only a 3-fold reduction by ciprofloxacin. The peptide was also found to be relatively safe and did not cause toxic reactions in the animals.

Since the peptide binds to a different site on the bacterial enzyme than ciprofloxacin, the researchers believe that it provides leads for identification of drugs that can be used as a combination therapy with existing antibiotics. Varadarajan adds that the study also reinforces the importance of targeting topoisomerases as a valid approach to finding new antibiotics.

REFERENCE:

Bhowmick J, Nag M, Ghosh P, Rajmani RS, Chatterjee R, Karmakar K, Chandra K, Chatterjee J, Chakravortty D, Varadarajan R, A CcdB toxin-derived peptide acts as a broad-spectrum antibacterial therapeutic in infected mice, EMBO Reports (2023).

CONTACT:

Jayantika Bhowmick
Postdoctoral researcher, University of Cambridge
Former PhD student, Molecular Biophysics Unit, Indian Institute of Science (IISc)
Email: jay18nov@gmail.com

Manish Nag
PhD student
Molecular Biophysics Unit, Indian Institute of Science (IISc)
Email: manishnag@iisc.ac.in

Raghavan Varadarajan
Professor
Molecular Biophysics Unit, Indian Institute of Science (IISc)
Email: varadar@iisc.ac.in
Phone: +91-80-22932612
Website: http://mbu.iisc.ac.in/~rvgrp/home.html

NOTE TO JOURNALISTS:

a) If any of the text in this release is reproduced verbatim, please credit the IISc press release.
b) For any queries about IISc press releases, please write to news@iisc.ac.in or pro@iisc.ac.in.

27 July 2023

– Sandeep Menon

High up in the Himalayas, scientists at the Indian Institute of Science (IISc) and Niigata University, Japan, have discovered droplets of water trapped in mineral deposits that were likely left behind from an ancient ocean which existed around 600 million years ago. Analysis of the deposits, which had both calcium and magnesium carbonates, also allowed the team to provide a possible explanation for events that might have led to a major oxygenation event in Earth’s history.

“We have found a time capsule for paleo oceans,” says Prakash Chandra Arya, PhD student at the Centre for Earth Sciences (CEaS), IISc, and first author of the study published in Precambrian Research.

Top: Field exposures of magnesite near Chandak hills, Kumaon. Bottom: Microphotographs of ocean water trapped in magnesite crystals (Photos: Prakash Chandra Arya)

Scientists believe that between 700 and 500 million years ago, thick sheets of ice covered the Earth for an extended period, called the Snowball Earth glaciation (one of the major glacial events in Earth’s history). What followed this was an increase in the amount of oxygen in the Earth’s atmosphere, called the Second Great Oxygenation Event, which eventually led to the evolution of complex life forms. So far, scientists have not fully understood how these events were connected due to the lack of well-preserved fossils and the disappearance of all past oceans that existed in the Earth’s history. Exposures of such marine rocks in the Himalayas can provide some answers.

“We don’t know much about past oceans,” says Prakash. “How different or similar were they compared to present-day oceans? Were they more acidic or basic, nutrient-rich or deficient, warm or cold, and what was their chemical and isotopic composition?” Such insights could also provide clues about the Earth’s past climate, and this information can be useful for climate modelling, he adds.

The deposits found by the team – which date back to around the time of the Snowball Earth glaciation – showed that the sedimentary basins were deprived of calcium for an extended period, probably due to low riverine input. “During this time, there was no flow in the oceans, and hence no calcium input. When there is no flow or calcium input, as more calcium precipitates, the amount of magnesium goes up,” explains Sajeev Krishnan, Professor at CEaS and corresponding author of the study. The magnesium deposits formed at this time were able to trap paleo ocean water in their pore space as they crystallised, the researchers suggest.

The calcium deprivation also likely led to a nutrient deficiency, making it conducive for slow-growing photosynthetic cyanobacteria, which could have started spewing out more oxygen into the atmosphere. “Whenever there is an increase in the oxygen level in the atmosphere, you will have biological radiation (evolution),” says Prakash.

The team hunted for these deposits across a long stretch of the western Kumaon Himalayas, extending from Amritpur to the Milam glacier, and Dehradun to the Gangotri glacier region. Using extensive laboratory analysis, they were able to confirm that the deposits are a product of precipitation from ancient ocean water, and not from other places, such as the Earth’s interior (for example, from submarine volcanic activity).

The researchers believe that these deposits can provide information about ancient oceanic conditions such as pH, chemistry, and isotopic composition, which have so far only been theorised or modelled. Such information can help answer questions related to the evolution of oceans, and even life, in Earth’s history.

REFERENCE:

Arya PC, Nambaje C, Kiran S, Satish-Kumar M, Sajeev K, Himalayan magnesite records abrupt cyanobacterial growth that plausibly triggered the Neoproterozoic Oxygenation Event, Precambrian Research (2023).

CONTACT:

Prakash Chandra Arya
PhD student, Centre for Earth Sciences (CEaS)
Indian Institute of Science (IISc)
Email: prakasha@iisc.ac.in

Sajeev Krishnan
Professor, Centre for Earth Sciences (CEaS)
Indian Institute of Science (IISc)
E-mail: sajeev@iisc.ac.in
Phone: +91-80-2293-3404
Website: https://ceas.iisc.ac.in/author/sajeev-krishnan/
Lab website: https://www.petralab.in

NOTE TO JOURNALISTS:

a) If any of the text in this release is reproduced verbatim, please credit the IISc press release.

b) For any queries about IISc press releases, please write to news@iisc.ac.in or pro@iisc.ac.in.