Budding yeast as seen under the microscope.
Image Credits: Mogana Das Murtey and Patchamuthu Ramasamy, CC BY 3.0 via Wikimedia Commons

The following article was originally written by Mr. Manjeera Gowravaram and published here.

For generations, a tiny piece of DNA has mastered the art of inheritance by hijacking the yeast cell’s division machinery, despite providing no known benefit to its host, the yeast.

Inside every living cell, DNA holds the instructions for life, and it is stored in its chromosomes. But plasmids— small, circular pieces of DNA, exist independently of an organism’s chromosomes, offering an extra set of genes to be passed between cells. Plasmids are most commonly found in bacteria, providing them with advantages such as antibiotic resistance. However, the plasmid present in many yeast species does not provide any known benefit to yeast cells, but still has mastered the art of survival for many generations, earning the term “selfish” DNA. This plasmid makes up only a tiny fraction (0.25–0.37%) of the yeast’s total DNA and measures approximately 2 micrometres in size—hence, it is known as the 2-micron plasmid.

In a recent article, Deepanshu Kumar and Santanu Kumar Ghosh from the Indian Institute of Technology (IIT) Bombay’s Department of Biosciences and Bioengineering review the strategies the 2-micron plasmid uses to interact with its host cell for survival. They focus on the roles of specific plasmid proteins and their interactions with host proteins and chromosomes. They also explore how the 2-micron plasmid attaches to chromosomes to ensure it is passed on during cell division. Understanding these mechanisms provides insights into how additional genetic elements are maintained and inherited in different organisms, helping develop therapeutics and synthetic biology applications.

Yeast cells reproduce by budding, where a small daughter cell forms and grows out from the parent cell. Before division, the yeast cell duplicates its chromosomes, wherein both the mother and daughter cells receive a complete set of genetic material. Similarly, the 2-micron plasmid also duplicates and gets evenly distributed between mother and daughter cells. The review reports that each yeast cell contains 40-100 copies of the 2-micron plasmid. Instead of dispersing randomly, these multiple copies tend to cluster into 3-4 tightly bound groups.

“The probability of these clusters remaining in the mother cell during division is significantly high. To make sure they are passed on, the 2-micron plasmid needs a system to evenly distribute between the mother and daughter cells,” explains Prof. Ghosh. So, instead of floating freely and risking uneven distribution, the 2-micron plasmid has evolved a clever trick of hitchhiking. It attaches itself to the host cell’s chromosomes, ensuring it gets separated along with them during division. “This hitchhiking mechanism prevents the plasmid from being trapped in the mother cell and guarantees that copies are consistently passed on to the daughter cell,” says Prof. Ghosh.

The plasmid’s hitchhiking process relies on two proteins, called Rep1 and Rep2, which bind to a specific site on the plasmid. Several yeast proteins involved in chromosome segregation form a ‘partitioning complex’ at that site. The complex allows the plasmid copies to stay attached to the duplicated chromosomes, ensuring they get evenly distributed during cell division.

In 2023, using genomics, interaction analyses, and cell biology techniques, Prof. Ghosh’s team showed that plasmids use a cellular protein complex (RSC) to help them stick to chromosomes. The researchers found that of the two similar versions of this complex in yeast, only one (RSC2) plays a key role. RSC2 interacts with both the Rep proteins and the cell’s division machinery, acting as a bridge to attach the plasmid to the chromosomes.

The plasmid attaches to specific parts of the chromosomes. In another earlier research, Prof. Ghosh’s lab and others found that the 2-micron plasmid mostly attaches to inactive regions of the chromosome, such as the ends, the middle regions, and regions that help make ribosomes (rDNA). These regions are compact and are less involved in producing proteins, making them a stable place for the plasmid to attach.

The researchers also found that certain proteins, like cohesins and condensins, that help chromosomes to separate properly during cell division are part of the partitioning complex and thus promote plasmids attaching to chromosomes. However, they only become part of the partitioning complex when Rep proteins are present. In the absence of these Rep proteins or when they were altered, the 2-micron plasmids failed to separate properly, leading to uneven distribution.

“The exact role of cohesins and condensins in plasmid attachment to chromosomes is still unclear, but they may act as cementing agents that help keep plasmids attached,” says Prof. Ghosh.

If the plasmid doesn’t benefit the yeast, why hasn’t evolution wiped it out? The review highlights that the answer lies in the plasmid’s inheritance strategy. By mimicking chromosomes, the plasmid makes the yeast cells incapable of recognising it as a foreign invader. Unlike foreign DNA that gets quickly eliminated, “by hitchhiking along with the host’s chromosomes, the 2-micron plasmid avoids the metabolic cost of developing its own segregation mechanism,” remarks Prof. Ghosh. The plasmid thus becomes a successful parasitic DNA.

According to the review, the plasmid’s hitchhiking strategy isn’t unique. It is similar to plasmid-like DNA present in many viruses. For example, the human papillomavirus (HPV) survives by attaching its plasmid-like DNA to human chromosomes using virus-made proteins, akin to how the 2-micron plasmid does. Both target inactive regions of chromosomes, suggesting a shared evolutionary strategy. By studying the 2-micron plasmid, researchers can better understand how viral genetic materials are maintained within host cells and could aid in developing antiviral strategies.

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The original academic article titled Chromosome Hitchhiking: A Potential Strategy Adopted by the Selfish Yeast Plasmids to Ensure Symmetric Inheritance During Cell Division was written by IIT Bombay’s researchers and published in the journal Biochemical Society Transactions.

The original paper can be found here.