Stop helping pathogens: engineering plant susceptibility genes for durable resistance

Abstract

Alternatives to protect crops against diseases are desperately needed to secure world food production and make agriculture more sustainable. Genetic resistance to pathogens utilized so far is mostly based on single dominant resistance genes that mediate specific recognition of invaders and that is often rapidly broken by pathogen variants. Perturbation of plant susceptibility (S) genes offers an alternative providing plants with recessive resistance that is proposed to be more durable. S genes enable the establishment of plant disease, and their inactivation provides opportunities for resistance breeding of crops. However, loss of S gene function can have pleiotropic effects. Developments in genome editing technology promise to provide powerful methods to precisely interfere with crop S gene functions and reduce tradeoffs.

Figure 1

Activities of S genes targeted by TAL effectors. Our in-depth understanding of the molecular mechanisms underlying TAL effectors (TALe) action revolutionized the quest for their targets in planta. Because TALes act as bona fide eukaryotic transcription factors which DNA-binding sites are highly predictable, transcriptomic approaches combined to in silico target promoter search allows for rapid identification of their target gene candidates. To such an extent that nearly 10 classes of S genes have been discovered since the elucidation of the TAL code in 2009 [49,50]. Their function is quite diverse, ranging from sucrose (SWEET) and sulfate transporters, enzymes involved in the biosynthesis pathway of various compounds such as polyamines (arginine decarboxylases), ABA (9-cis-epoxycarotenoid dioxygenase) or even small RNAs (the methyltransferase Hen1), to different types of transcription factors (LOB, bHLH, bZIP, ERF) involved in the control of various phenotypes such as host cell enlargement, pustule formation, watersoaking, and so on…It is expected that other categories of S genes will be discovered as novel TAL effectors with major or even moderate virulence functions are characterized. The potential is high because the majority of Xanthomonas species rely on TALes to infect their host and only the S genes corresponding to 7 pathosystems have been investigated today when there are at least fifty species or pathovars of Xanthomonas with unique features that remain to be investigated. This figure gives an overview of the most relevant S gene categories targeted by TALes and for which a function is described. Text in brown refers to the types of activities conferred by S genes. Primary and secondary targets are shown in purple and green (text, shape), respectively. Abbreviations: SWEET, Sugars Will Eventually Be Exported Transporter; SULTR, sulfate transporter; ADCs, arginine decarboxylases; PA, polyamines; TFs, transcription factors; UPA, upregulated by AvrBs3; LOB1, lateral organ boundaries 1; ABA, abscisic acid; bHLH, basic helix-loop-helix; NCED, 9-cis-epoxycarotenoid dioxygenase. Forms: cylinder, nutrient transporter; hexagon, biosynthetic pathway enzyme; two-ovoid, transcription factor; Pacman-like, cell wall-modifying proteins.

Figure 2

Categories of S genes based on the mechanistic activity. Conservation of S genes across pathogen groups is color coded.

Figure 3

Biotechnological approaches to engineer S genes for pathogen resistance and reduce tradeoff effects. For each approach two methods are illustrated. The goal and challenges are indicated below the diagram. Cylinders indicated open reading frames. Edited areas are marked with a red discharge symbol. (a) Multiplex gene editing allows modifications of multiple genes simultaneously, either redundant genes that are members of a gene family, or a combination of an S gene and a tradeoff gene to reduce pleiotropic effects. (b) Allele editing might be used to generate hypomorphic alleles that reduce susceptibility but have no or reduced pleiotropic effects. This can be achieved using base editors to make single nucleotide changes and resulting amino acid substitutions, or by replacing larger sequences through homologous recombination. (c) Promoters can be engineered to reduce their activity to certain conditions or in specific tissues. Using two guide RNAs the CRISPR/Cas9 system can be used to make precise deletions of selected cis elements in the S gene promoter. Editing of promoter sequences can be achieved using prime editing or homologous recombination.