Scientists Discover Fungi That Break The 'One Nucleus, One Genome' Rule

Genomes hold the entire repository of instructions needed to create and sustain a living organism - a metaphorical set of life’s blueprints.

In eukaryotes, genomes sit inside nuclei and are arranged into chromosomes. A eukaryote is any organism whose cells contain a membrane-bound nucleus: plants, animals, fungi and many microbes fall into this group.

The human genome, for instance, is packaged into 23 chromosomes, each carrying part of the full genetic code.

Until quite recently, the prevailing assumption was that every nucleus contains at least one complete set of chromosomes - the so-called "one nucleus, one full genome" rule.

Our research, however, shows that in two fungal species the genome can be distributed between several nuclei, so that each nucleus receives only a subset of the total chromosomes.

A surprising discovery in Sclerotinia sclerotiorum

At the University of British Columbia, our lab investigates the fungus Sclerotinia sclerotiorum. This soil-borne pathogen causes stem rot (white mould) in a range of crop plants, including oilseed rape (canola), soya bean and sunflower.

Even though it damages commercially important crops, the genetics and cell biology of S. sclerotiorum remain poorly characterised.

As we worked to clarify the biology of this fungus, we uncovered an unexpected feature of how S. sclerotiorum’s 16 chromosomes are arranged during cell division and reproduction.

Most eukaryotic cells are diploid, which means their nucleus carries two copies of each chromosome. In many fungi - baker’s yeast is a well-known example - reproduction starts with a diploid parent cell dividing to produce haploid spores, each with a single nucleus containing one copy of every chromosome.

By contrast, S. sclerotiorum spores (ascospores) each hold two distinct nuclei. The standard view had been that each of these nuclei is haploid and contains the full set of 16 chromosomes. On that basis, an ascospore would contain 32 chromosomes in total, much like a diploid cell.

Using fluorescent microscopy, we could count chromosomes directly within an individual ascospore. Strikingly, we repeatedly observed just 16 chromosomes per ascospore, contradicting the 32 expected under the current "one nucleus, one full genome" theory.

We also applied fluorescent probes to tag particular chromosomes. These experiments showed that the two nuclei inside an ascospore do not carry identical chromosome sets. Instead, ascospores contain a single set of 16 chromosomes partitioned between two nuclei, rather than having a complete set in each nucleus.

An irregular manner

Next, we wanted to know whether the 16 chromosomes are split between the two nuclei at random, or whether the genome is divided according to a consistent pattern.

To test this, we isolated single nuclei and used polymerase chain reaction (PCR) analysis to identify which chromosomes were present. The mix of chromosomes differed from nucleus to nucleus, indicating that chromosomes are allocated between nuclei in an irregular manner.

This finding led us to ask whether other fungi show the same behaviour. Botrytis cinerea is another plant-pathogenic fungus in the same family as S. sclerotiorum.

Unlike S. sclerotiorum ascospores, which typically contain two nuclei, B. cinerea produces conidial spores that usually have four to six nuclei. Applying comparable approaches, we discovered that the 18 chromosomes of the B. cinerea genome are also divided among nuclei, with each nucleus generally carrying three to eight chromosomes.

Together, these results indicate that haploid genome “splitting” across nuclei occurs in more than one plant-pathogenic fungus. Whether it is widespread across fungal families - or even present in other eukaryotes - will require further investigation.

An unknown mechanism

Seeing the haploid genomes of S. sclerotiorum and B. cinerea distributed across nuclei raises important questions about how this separation fits into the rest of the fungal life cycle.

To generate the next generation, these fungi must re-create a diploid cell containing the full complement of chromosomes, which can then produce new ascospores. Presumably, this demands the fusion of nuclei carrying complementary chromosomes so that the genome is reunited. That, in turn, prompts a key question: how do these fungi make sure the appropriate nuclei fuse?

One straightforward possibility is viability selection: nuclei might fuse at random, but only fusions that restore a complete genome would go on to produce viable ascospores.

That would be a wasteful process. A more appealing possibility is that some form of organisation or mechanism keeps complementary nuclei associated after the initial separation, enabling the genome to be reassembled efficiently later in the life cycle.

We hope that our future research will resolve these intriguing questions and expand what we know about the basic dynamics of nuclei and their genomes.

A stronger grasp of these processes could, in turn, make possible dramatic revolutions in gene editing, by allowing researchers to manipulate chromosomes and nuclei at will.

Xin Li, Professor, Botany, University of British Columbia; Edan Jackson, PhD Student, Botany, University of British Columbia, and Josh Li, Masters Student, Medicine, University of British Columbia

This article is republished from The Conversation under a Creative Commons licence. Read the original article.