Metabolism and signaling of auxins and their roles in regulating seed dormancy and germination

During germination, a quiescent seed is converted to a seedling with high metabolic activity by germination, which is a critical step in the life cycle of seed plants. Seed germination is a complex process co-regulated by genetic and environmental factors, of which phytohormone regulation may be a highly conserved mechanism in seed plants. Auxin is one of the most important signaling molecules in plants, and it controls all aspects of plant growth and development, including morphogenesis and responses to environmental changes. Auxin is biosynthesized, stored and inactivated by many parallel pathways, and it is also perceived and transduced by canonical and non-canonical pathways. The role of auxin is mainly regulated by its biosynthesis and catabolism, as well as by a signaling pathway during seed dormancy and germination. Here, we mainly summarize research progress on metabolism and signaling of auxin and its roles in regulating seed dormancy and germination. Tiyptophan (Tip) is a common precursor of indole-3-acetic acid (IAA) in plants, and IAA is biosynthesized from Tip by the indole-3-pyruvate (IPA), indole-3-acetaldoxime (IAOx), indole-3-acetaldoxime (IAM) and tryptamine (TAM) pathways, of which the IPA pathway is a main one. The IAOx pathway may be species-specific in Brassicaceae, and it plays an auxiliary role in IAA biosynthesis in Arabidopsis. However, present evidence is insufficient to propose the IAM and TAM pathways as major routes to IAA biosynthesis in plants. The majority of cellular IAA is inactivated by conjugation to amino acids, peptides, proteins and sugars to produce the transient storage forms, or by irreversible catabolic degradation. Heretofore, oxidative attenuation of IAA through formation of 2-oxindole-3-acetic acid (oxIAA) and subsequent conjugation to glucose was considered the major pathway for IAA inactivation. IAA signaling pathways include canonical and non-canonical auxin signaling pathways. In the canonical auxin signaling pathway, auxin binds to the F-box proteins of the TRANSPORT INHIBITION RESISTANT1/AUXIN SIGNALING F-BOX (TIR1/AFB) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressor families. Then, the SCFTIR1/AFB E3 ubiquitin ligase complex transfers activated ubiquitin to Aux/IAA. The polyubiquitination of Aux/IAA results in its degradation in 26S proteasome, thereby releasing repression of the AUXIN RESPONSEFACTORs (ARFs) and activating transcription of auxin induced genes. The non-canonical auxin signaling pathway mainly includes pathways mediated by TIRL ETTIN and receptor-like kinases; however, the events downstream from auxin binding remain unknown. Auxin regulates seed dormancy and germination in a dose-dependent manner. During seed germination, auxin positively regulates ABA and negatively regulates GA biosynthesis and signaling pathways. Finally, we propose some scientific issues that need to be investigated in the future. There are multiple pathways for biosynthesis and catabolism of auxin. Do these pathways exist in the same tissue of the same species at the same time, or do species, tissues and developmental stages have specific pathways? How are these pathways activated, operated and coordinated in response to growth and development and environmental changes to control auxin levels in tissues or cells? Auxin signaling includes canonical and non-canonical pathways. Which pathways respond preferentially in integrating physiological conditions or in responding to environmental signals, and what is the relationship between them? In the plant genome, the core components of signaling pathways are composed of multiple homologous members, and each member has its specific biochemical characteristics. Does the combination of different members of these core components produce similar reaction results? Do low concentrations of auxin promote seed germination via the auxin induced acid growth model? This paper provides a basis for further investigation of the molecular mechanism regulating seed dormancy and germination by auxin.