Dr. Saikrishnan Kayarat’s team @ IISER Pune Published in Nature Chemical Biology.


       Like many other life forms, bacteria too are prone to viral infections. Many bacteria harbor restriction endonuclease enzymes, which help check the infection by selectively cutting and destroying the viral genomic DNA. The perpetual tussle between bacteria and viruses to gain an upper hand has resulted in a battery of restriction enzymes of different complexities. There are the simple nucleases that cut DNA at target sites – two copies of the nuclease come together, each cutting a strand to slice the double-stranded DNA. And there are motor-driven nucleases that are massive in size and use chemical energy to cut DNA only upon collision with another such nuclease and away from the target sites. A collaborative study between a team of scientists at IISER Pune and the University of Bristol, UK, of these energy-driven nucleases, published this week in Nature Chemical Biology, reveals a new mechanism of DNA break formation involving a compound damage caused by DNA shredding rather than slicing.

Dr. Saikrishnan Kayarat’s team at IISER Pune has solved the first atomic resolution x-ray crystal structure of a motor-driven restriction endonuclease bound to DNA. They found that contrary to the prevalently understood mode of action, the nuclease domain of this class of enzyme is positioned such that when two enzymes collide on a DNA, the nuclease domains are distant from each other. This structure also happens to be of one of the largest single-polypeptide chain bound to nucleic acid determined to date.        

             Guided by the structure, Prof. Mark Szczelkun and colleagues at the University of Bristol used single-molecule biophysical approaches, to find that the nucleases use the energy derived from the cellular fuel, ATP, to run along the DNA. Using biochemical approaches they found that upon collision, the distantly spaced nucleases make multiple nicks on the individual strands, thus shredding the double stranded DNA. This is in contrast to a clean-cut slicing brought about by the action of an enzyme with an apposed pair of nuclease domains. Unlike a sliced-DNA, a shredded DNA cannot be easily repaired.

The paper titled “Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymesand authored by Mahesh K. Chand, Neha Nirwan, Fiona M Diffin, Kara van Aelst, Manasi Kulkarni, Christian Pernstich, Mark D. Szczelkun and Kayarat Saikrishnan has appeared as an advance online publication of Nature Chemical Biology.

This work received funding from Wellcome Trust-DBT India Alliance; Wellcome Trust, UK; DBT India; and CSIR India.

Original News : IISER Pune.


Double Treat for Bird Song lover & Music Lover : Beatboxing

Image : NCBS

By Anusha Krishnan

Beatboxing is the art of vocal percussion, and one could say that birds are the masters of beatboxing.  In a contemporary approach to music and social awareness, a bird ecologist, a photographer and a musician have collaborated to create the unique #SkyislandBeatbox project. The trio – V. V. Robin (the ecologist), Prasenjeet Yadav (the photographer) and Ben Mirin (the musician) – enthralled their audience at the National Centre for Biological Sciences (NCBS) with their Birdsong Beatbox performance.
“The overwhelming response was unexpected and I was not sure what to make of it. It wasn’t just in NCBS – our shows in Cochin, Kodi, Trivandrum and Ooty rocked!” says V. V. Robin.

“The experience was all about portraying the birds as the heroes. We wanted to draw attention to the music, not the musician; the science, not the scientist and the photos, not the photographer”, says Aparna Banerjee, one of the curators of the #SkyislandBeatbox initiative from NCBS.

Ben’s music on a beatbox with bird calls from the Western Ghats coupled with Prasenjeet’s footage of these birds created a smorgasbord of audio-visual excitement. “The NCBS show was a really strong capstone to our team’s tour through the Western Ghats. We ended up modifying our structure to make the pieces more integrated and I think it really paid off. It was obvious that everyone in the room really enjoyed the music but also had a deep interest in our process and the science behind it. I’m really excited to see where this model can go, it’s as much about the team as it is about the message,” says Ben Mirin.

Current research by V.V. Robin in collaboration with Uma Ramakrishnan of NCBS shows that some of the birds featured in the program are very special – they are endemic to (which means they live only on) areas called sky-islands. Sky-islands are essentially the tops of mountains that are separated from each other by a “sea” of valleys. They are unique habitats that are in danger of disappearing due to deforestation and climate change. The presentation takes an innovative approach to spreading awareness about the very real dangers of extinction that loom over the wondrous bird life in the Western Ghats.

The effort has been funded by National Geographic, the Indian Bird Conservation Network (IBCN) and the Shola Trust.

For an example of Ben Mirin’s musical work, please click here.

A Must watch Video : Music Made from Real Bird Songs By Ben.

Original News : NCBS News