Noble rot, the alchemist of wines, is setting fungal biology abuzz

In wine-making circles, ‘noble rot’ is an exalted name for the botrytis fungus (Botrytis cinerea). It infects grapes, penetrates the skin, causes the berries to lose water by evaporation and shrivel up, and thus concentrates the sugars and flavours in them. Since only a small percentage of grapes in a vineyard are infected, they must be picked by hand.

This makes the picking process labour-intensive and drives up the cost. The crushed grape juice from rotted grapes is used to make high-quality sweet wines like the Sauternes of Bordeaux, the Trockenbeerenauslese of Germany and Austria, and the Tokaji Aszús of Hungary. They are also very expensive.

Befitting its exalted status, the botrytis fungus was also found recently to exhibit an unusual idiosyncrasy. In all animals, plants, and fungi, the nucleus of a cell contains one or more sets of all of the chromosomes of the organism. This property of nuclei allows us to clone animals. Scientists can transfer such a nucleus, which contains all the DNA instructions, into an egg cell whose own nucleus has been removed and, in the right conditions, prompt it to develop into a new organism.

But because of the idiosyncrasy, botrytis fungus cannot be cloned — nor can another fungus called Sclerotinia sclerotiorum.

A team of researchers from Sichuan University in China and the University of British Columbia in Canada have made a startling discovery: in these fungi, no single nucleus contains a complete set of chromosomes. Instead, the chromosome set is distributed across two or more nuclei, and any one nucleus contains only a subset.

These unexpected findings were reported in Science.

Ascomycetes, asci, ascospores

Botrytis and Sclerotinia are ascomycetes fungi. The first cell of a baby fungus born following a mating between two ascomycetes fungi is called the ascospore. All the subsequent other cells of the individual are derived from it. This is the defining feature of ascomycetes fungi. The ascospores are produced in a sac-like cell called the ascus (plural asci). An ascus, produced when two parental strains mate, contains two complete sets of chromosomes.

In many well-studied ascomycetes fungi, eight ascospores are made in each ascus. All the nuclei of an individual ascospore are genetically identical. That is, they all have the same set of chromosomes. B. cinerea and S. sclerotiorum also make asci with eight spores. The researchers had no reason to suspect them to be any different.

How are discoveries made?

People are often curious to know how scientists make their discoveries.  Most discoveries originate in experiments that did not work in the way they were meant to. Sadly, the converse is not true.

The most common explanation for experiments that don’t work the way were meant to is some kind of ‘operator error’ — i.e. a silly mistake of some kind: a growth medium was not properly made, the incubator was not set to the right temperature, the wrong strain was used, etc. Silly mistakes are more common than serendipitous leads.

Not surprisingly, scientists get mad with experiments that don’t work. But once in a while, this type of experiment is a harbinger of an unexpected discovery. This is the scientist’s dilemma.

Improbable versus true

The research team set out to obtain mutants of S. sclerotiorum.  For this they exposed the ascospores to ultraviolet light. Each S. sclerotiorum ascospore contains two nuclei. Both nuclei were assumed to carry the same set of chromosomes. UV-induced mutations occur at random.  Therefore, it was highly unlikely the same gene would become inactivated in both nuclei of an ascospore.

Consequently, a colony containing mutant cells was also expected to include a sector with non-mutant cells. The non-mutant cells would have nuclei descended from the ascospore nucleus with the non-mutant gene.

But in the experiment, of the more than 100 mutant colonies the researchers examined, all contained only mutant cells. None of them had a non-mutant sector. This was most unexpected. Why weren’t any non-mutant cells seen in these colonies?

This observation set the researchers up for their Sherlock Holmes moment: “When you have eliminated all which is impossible, then whatever remains, however improbable, must be the truth.”

Could the two nuclei between them contain only one set of chromosomes?

Closer examination

The researchers wrote in their paper: “Because this prediction challenges established principles of chromosome biology, we conducted a closer examination of the ascospores’ nuclei and chromosomes.”

They used molecular probes that bind specifically to individual chromosomes, allowing them to say whether or not a nucleus contains the chromosome. When the probes were used individually, they lit up exclusively one nucleus per ascospore.  The probe never lit up both nuclei.

This meant the two nuclei harboured distinct chromosome sets. When both probes were used together, in some ascospores the signals showed up in only one nucleus and in other ascospores the signals were seen in both nuclei. This meant the distribution of chromosomes in the nuclei differed between ascospores.

Further tests revealed that each nucleus of a S. sclerotiorum or B. cinerea ascospore contained only three to eight chromosomes.

New questions

The findings have already spawned many questions in the research community. What is the mechanism by which chromosomes are allocated to the different nuclei? How is genetic integrity preserved during cell division? What restores a complete set of chromosomes when the fungus mates, and with its mating partner forms new asci? Which genes and mechanisms are involved in chromosome sorting and regulation? What advantage does chromosome distribution confer to Botrytis and Sclerotinia?

The questions have generated a new buzz in fungal biology. Right now, scientists doing research with fruit flies, nematodes, zebrafish, mice, and other model organisms might be envying those working with rot fungi — noble or otherwise.

D.P. Kasbekar is a retired scientist.

Published – June 30, 2025 05:30 am IST