Fungal systems biology articles from across Nature Portfolio

In this Review, Snyder et al. discuss the global impacts of food spoilage, mechanisms and causative agents, and strategies and emerging tools to control microbial food spoilage.

In vivo triple RNA-seq analysis reveals that a biocontrol yeast consumes host nutrients to outcompete a fungal pathogen on apple, while pattern-triggered immunity and effector-triggered immunity are triggered in the host in response to the fungal pathogen only.

Long-read sequencing and chromatin capture methods reveal that two nuclear genomes segregate among thousands of co-existing nuclei in arbuscular mycorrhizal fungi.

Here, the authors generate strain-specific genome-scale metabolic models of Aspergillus fumigatus and analyze fungal metabolism of infection of the lung of cystic fibrosis patients, finding that the fungus shapes the lung microbiome to promote its own growth.

Takhaveev et al. use single-cell methods and mathematical modeling to reveal distinct waves in the synthesis rates of proteins, lipids and polysaccharides during the budding yeast cell cycle and relate them to flux changes in primary metabolism.

Protein abundance is controlled at the transcriptional, translational and posttranslational levels. Here, Öztürk et al. determine proteome changes resulting from individual knockout of 3308 nonessential genes in the yeast S. pombe, infer gene functionality, and show that protein upregulation under stable transcript expression utilizes optimal codons.

We present evidence that lignin, a recalcitrant and partially aromatic polymer found in plant cell walls, can be modified by anaerobic microorganisms. This finding overturns a long-standing paradigm that all biological processes of lignin degradation require oxygen and motivates further exploration of understudied biology to inform biotechnological innovation.

A systems biology approach to analyse yeast auxotrophs shows that, even when supplemented, they have profoundly altered transcriptomic, proteomic and metabolic profiles.

Fungal taxonomy has recently undergone its biggest shake-up and embraced the modernization of its nomenclatural rules. Here, Hibbett and Taylor describe these changes and what their implications might be for fungal researchers.