Fungal pathogen loses “jumping genes” to gain stability and virulence

In the disease world of fungal pathogens, Cryptococcus neoformans is known to cause havoc among the immunocompromised individuals. Recently another sister fungal pathogen Cryptococcus deuterogattii has sickened hundreds of otherwise healthy people. Researchers around the world proposed that loss or gain of a whole bunch of genes could have been the key behind acquired virulence attributes. In a recent paper published in PNAS, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India in collaboration with Duke University established a link between the loss of RNA interference ((RNAi) genes, reduction in the centromere length and gaining virulence attributes in Cryptococcus deuterogattii.

Sitting at the waistline of chromosomes, the centromere is an essential stretch of DNA that is required for accurate chromosome segregation, and to maintain genome stability. The researchers at JNCASR have been working on understanding the evolution of centromeres in human fungal pathogens for over a decade. In the current study published in PNAS, a team led by Prof. Kaustuv Sanyal identified centromeres in three closely related Cryptococcus species, assembled the genome at the chromosome level and scrutinized the centromeres. Remarkably, the team found a correlation between the centromere length and the presence of RNAi genes that are known to play a vital role in regulating genome and their stability. The two RNAi-proficient Cryptococcus species have large and complex centromeres with full-length DNA sequences called retrotransposons. These segments of DNA can jump around to different positions in the genome and cause mutations or increase (or decrease) amount of DNA. On the other hand, the RNAi-deficient Cryptococcus deuterogattii harbours smaller centromeres without full length or inactive retrotransposons. “We believe that shortening of centromeres in Cryptococcus deuterogattii led to its genome shrinkage that provided a replicative advantage in terms of faster growth rate, possibly contributing towards enhanced virulence of this species” said Prof. Sanyal, lead author and Professor at JNCASR.

RNAi is known to suppress transcription at the centromere. One would imagine that due to the loss of RNAi, transposons present at the centromere would have run wild in the genome! “In contrast, we see that they are in essence gone. The model is that the only way to survive the loss of RNAi may have been to get rid of the transposons from the genome or inactivate them so they cannot transpose anymore” says Vikas Yadav, first author of the study. To understand this, the team experimentally recreated the evolution in the lab by growing RNAi- proficient and RNAi-deficient strains for 1000 generations. Upon sequencing the genomes of these strains, it was seen that in the RNAi deficient strains, the retrotransposons at the centromere had undergone recombination causing shortening of centromeres. This is contrary to earlier studies from elsewhere that reported the suppression of recombination at centromere loci. Results of the current study suggest a role of RNAi in the evolution of centromeres. The team aims to extend the study to understand the impact of genomic changes on pathogenesis and virulence.

This work is a result of a long-term collaboration between the team JNCASR, Joseph Heitman’s group at Duke University Medical Center, USA, Christina Cuomo at Broad Institute of MIT & Harvard (USA) and Guus Bakkeren at Summerland Research and Development Centre, BC, Canada.

This research is funded by JNCASR, National Institutes of Health/National Institute of Allergy and Infectious Diseases, USA, and Tata Innovation Fellowship of Department of Biotechnology, Govt of India.

This article is authored by Kripa V. Jalapathy, Technical Research Centre (TRC), JNCASR.

Journal reference:

  1. Vikas Yadav, Sheng Sun, R. Blake Billmyre, Bhagya C. Thimmappa, Terrance Shea, Robert Lintner, Guus Bakkeren, Christina A. Cuomo, Joseph Heitman, Kaustuv Sanyal. RNAi is a critical determinant of centromere evolution in closely related fungi. Proceedings of the National Academy of Science USA. Mar 2018, 201713725; DOI: 1073/pnas.1713725115

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