TY - JOUR

T1 - PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

AU - Thieffry, Axel

AU - López-Márquez, Diego

AU - Bornholdt, Jette

AU - Gholami Malekroudi, Mojgan

AU - Bressendorff, Simon

AU - Barghetti, Andrea

AU - Sandelin, Albin

AU - Brodersen, Peter

N1 - © The Author(s) 2022. Published by Oxford University Press on behalf of American Society of Plant Biologists.

PY - 2022

Y1 - 2022

N2 - Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression (CAGE). We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames (uORFs) in mRNA leader sequences. We also find that 60% of PAMP-response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct MAP kinase control, support the notion that the rapidly induced transcription factors could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.

AB - Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression (CAGE). We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames (uORFs) in mRNA leader sequences. We also find that 60% of PAMP-response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct MAP kinase control, support the notion that the rapidly induced transcription factors could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.

U2 - 10.1093/plcell/koac108

DO - 10.1093/plcell/koac108

M3 - Journal article

C2 - 35404429

VL - 34

JO - The Plant Cell

JF - The Plant Cell

SN - 1040-4651

IS - 7

ER -