Identification of Phytochrome-Interacting Factor Family Members and Functional Analysis of MdPIF4 in Malus domestica

Abstract

Phytochrome-interacting factors (PIFs), members of the basic helix-loop-helix transcription factor family that have been extensively investigated in Arabidopsis thaliana, play essential roles in plant growth and development. However, PIF members have not been systematically investigated in apples, a worldwide perennial woody crop of economic importance. Here, seven PIF genes were identified from the Malus × domestica reference genome. Chromosomal locations, gene structures, and phylogenetic relationships of these members were analyzed. Analysis of cis-acting elements in promoter regions of MdPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Subsequently, subcellular localization and transcriptional activity analysis revealed that MdPIFs were typical nuclear transcription factors with transcriptional activation ability. Expression analysis demonstrated that MdPIF genes had different gene expression patterns for various abiotic factors. Moreover, overexpressed MdPIF4 reduced the sensitivity of apple calluses to abscisic acid (ABA). Our work lays foundations for further investigation of PIF functions in plant growth and development in apples.

Characterization of Phytochrome-Interacting Factor Genes in Pepper and Functional Analysis of CaPIF8 in Cold and Salt Stress

“…In this work, six PIF genes were identified from the pepper genome, and the number was comparable to that in many other plants, such as P. patens (six genes) (Possart et al, 2017), O. sativa (six genes) (Nakamura et al, 2007), Z. mays (seven genes) (Zhang et al, 2018;Wu et al, 2019), M. domestica (seven genes) (Zheng et al, 2020), A. thaliana (eight genes) (Lee and Choi, 2017), and S. lycopersicum (eight genes) (Rosado et al, 2016). Amino acid sequence alignment revealed that all the six CaPIF proteins harbor a conserved bHLH and an APB domain (Figures 1A,B), which is a typical feature of PIF proteins.…”

“…As a result, the bHLH and APB domains were found in all six CaPIF proteins, with the exception of CaPIF7b, which contained an incomplete Helix2 in the bHLH domain ( Table 1 and Figure 1 ). In addition, CaPIF1 and CaPIF3 contained an additional APA domain, which was also observed in PIF proteins from other plants, such as tomato SlPIF1a, SlPIF1b, and SlPIF3 ( Rosado et al, 2016 ), Arabidopsis AtPIF1 and AtPIF3 ( Lee and Choi, 2017 ), and apple MdPIF1–MdPIF5 ( Zheng et al, 2020 ).…”

“…However, CaPIF7b has an incomplete Helix2 in its bHLH domain, which may affect its function to interact with other proteins. Notably, an amino acid substitution (Q to E) in the APB domain was observed in CaPIF4 ( Figure 1B ), which was also identified in MdPIF8 ( Zheng et al, 2020 ), suggesting that they possibly have similar functions. Similar to tomato SlPIF1s and SlPIF3 ( Rosado et al, 2016 ), maize ZmPIF3s ( Wu et al, 2019 ), Arabidopsis AtPIF1 and AtPIF3 ( Leivar and Quail, 2011 ), CaPIF1 and CaPIF3 also contain the conserved functional APA domain ( Figure 1C ), which was found to play a vital role in modulating the interaction with phyA.…”

“…In Arabidopsis , the APA and APB domains are responsible for the physical interaction of PIFs with phyA and phyB, respectively. PIF proteins are widely distributed from bryophytes to angiosperms, with only one member in Marchantia polymorpha ( Inoue et al, 2016 ), six in Physcomitrella patens ( Possart et al, 2017 ), six in Oryza sativa ( Nakamura et al, 2007 ), seven in Zea mays ( Zhang et al, 2018 ; Wu et al, 2019 ), seven in Malus domestica ( Zheng et al, 2020 ), eight in Arabidopsis thaliana ( Lee and Choi, 2017 ), eight in Solanum lycopersicum ( Rosado et al, 2016 ), 11 in Populus trichocarpa ( Ding et al, 2021 ), and 12, 16, and 30 in Brassica rapa , B. oleracea , and B. napus , respectively ( Li W. et al, 2021 ).…”

Transcriptome and Metabolome Analyses Reveal Molecular Responses of Two Pepper (Capsicum annuum L.) Cultivars to Cold Stress

“… Kim et al (2017) showed that MYB15 could interact with MPK6 to reduce its inhibitory effect on CBF gene expression. Moreover, PIFs (phytochrome-interacting factors), a subfamily of bHLH TFs, mainly participate in the photomorphogenic development, and several members also as thermo-sensors, involved in cold response ( Jiang et al, 2020 ; Zheng et al, 2020 ). Yang et al (2021) found that six PIF members were existed in pepper, including CaPIF1 , CaPIF3 , CaPIF4 , CaPIF7a , CaPIF7b and CaPIF8 , among them, CaPIF8 was induced under cold stress.…”