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Amoeba-attacking Giant Viruses Found in Mumbai's Lakes

Researchers report numerous giant viruses in water bodies of Mumbai and identify a unique protein that these viruses make.

Viruses, the minutest and the most primitive beings, live almost everywhere on earth—in soil, plants, water and animals. One can find them even inside other microbial forms like bacteria and fungi. Although several viruses cause diseases, many, like the one discovered in England, are harmless to us. In a recent study, Prof Kiran Kondabagil and his group from the Indian  Institute of Technology Bombay (IIT Bombay) have reported the presence of giant viruses in water samples of Mumbai.  

Like all living beings, viruses also contain genes, which include the instructions required to make proteins and sustain life. Typically, genome sizes of viruses range from just a few thousands to about 200,000 base pairs. However, giant viruses have a genome size as massive as a few million base pairs. Some giant viruses are bigger than bacteria. Scientists have found giant  viruses in various environments such as oceans, lakes, forest soils and the human gut. They speculate that these viruses contribute towards maintaining the ecosystem.  

“When the first giant virus was discovered, it was thought of as an isolated case. But, further studies showed that these viruses are present everywhere and in large numbers,” says Prof Kondabagil. “Our findings from India and those from other studies suggest that they are present in almost all types of environment. They can be found in places where one can find living creatures like protozoa and plankton, similar to the amoeba,” he adds.  

The current study, published in the journal Scientific Reports, is the first report of numerous giant viruses from India. It found viruses belonging to the families Pandoraviridae, Phycodnaviridae,  Mimiviridae, Iridoviridae and Megaviridae. The study was funded by the Department of Biotechnology (DBT), Department of Science and Technology (DST), and the Novozymes and Holck- Larsen Foundation.  

The researchers analysed genome sequence information present in samples collected from the pre-filter of a water purifier, moist soil (sludge), and the drying bed of a wastewater treatment plant in Mumbai. Five families of giant viruses were found in these samples, all of which infect amoeba. The researchers further sequenced the genome of four giant viruses  belonging to the families Mimiviridae, Megaviridae and Marseilleviridae. Interestingly, some genes of the giant viruses from Mumbai were similar to those of giant viruses discovered in other continents. “This might indicate that such genes play important roles in these viruses,” say the authors.  

Unlike most other viruses, giant viruses prepare several proteins of their own without relying on the proteins from their hosts. However, scientists do not yet understand the functions of a lot of these proteins. In another study, Prof Kondabagil and his team studied the role of one such protein known as gp577. This protein is synthesised by a giant virus named Acanthamoeba polyphaga mimivirus, belonging to the family Mimiviridae.  

“While looking for replication related proteins to understand the mechanism of genome replication and its packaging into the virus, we stumbled upon this protein,” says Prof Kondabagil on this accidental discovery. There are no previous studies that describe the exact function of gp577 in giant viruses.  

The researchers found that this protein has essential enzymatic activities that help in the survival of the virus. Identified as PrimPol—a type of protein involved in DNA repair—it has the ability to play multiple roles in almost all the steps beginning from making of DNA and RNA to their final processing. This is the first time such an enzyme is identified in any giant virus. This enzyme helps in the synthesis of both kinds of nucleic acids, DNA and RNA, which is a quality rarely found in viruses. Further, it helps in mitigating DNA damage.  

The functions of gp577 correspond to similar proteins in other taxa such as protozoa and humans. “Mimiviral gp577, a multifunctional and versatile PrimPol, shares sequence and functional similarities with PrimPols of other organisms,” mention the authors. This finding has opened up an avenue for understanding the seemingly mysterious evolutionary origin of the giant viruses.

The newly identified protein in the giant virus adds towards our understanding of its biology and the role different proteins play in the survival of the virus. Further studies can highlight the different hosts infected by giant viruses, the habitats where they exist, and the relationship they hold with the other occupants that live alongside the viruses. Addressing these questions  would guide us towards a clearer understanding of the role of giant viruses in the environment.  

Article written by

Kiran Gurung

Image credits

Ramya Badrinath, Gubbi Labs

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