Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

Abstract

Background : As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya ( Carica papaya L. ) has been reported previously. Results: In this study, a total of 73 CpbHLH genes were found in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis, with one orphans. Almost all of the CpbHLH in the same subfamily shared similar gene structures and protein motifs according to an analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLH genes varied from 1 to 11 with an average of 5. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis -element analysis revealed that most of the CpbHLH genes contained cis -elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that Cp bHLH mainly functions in protein dimerization activity and DNA-binding, and most Cp bHLH proteins were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some predicted CpbHLH genes that might be responsible for abiotic stress responses in papaya. Conclusions : A total of 73 bHLH transcription factors were identified from papaya, and their gene structures, conserved domains, sequence features, phylogenetic relationship, promoter cis -element, GO annotation and gene expression profiles responsible for abiotic stress were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of Cp bHLHs. Keywords : papaya, genome-wide analysis, bHLH transcription factors, abiotic stress

Diverse role of basic Helix-Loop-Helix (bHLH) transcription factor superfamily genes in the fleshy fruit-bearing plant species

“…Some potential CpbHLH genes may also be involved in papaya abiotic stress tolerance. Cpb-HLH027 and CpbHLH062, for example, have been reported to participate under chilling stress (Yang et al 2020). In this fashion, the transcripts of Cpb-HLH027 and CpbHLH062 were elevated during cold stress, showing that CpbHLH027 and CpbHLH062 may also be engaged in the chilling stress response (Yang et al 2020).…”

“…Cpb-HLH027 and CpbHLH062, for example, have been reported to participate under chilling stress (Yang et al 2020). In this fashion, the transcripts of Cpb-HLH027 and CpbHLH062 were elevated during cold stress, showing that CpbHLH027 and CpbHLH062 may also be engaged in the chilling stress response (Yang et al 2020). Dong et al (2021) recognised the bHLH genes in the Chinese white pear for the first time, and demonstrated that PbrbHLH195 is actively engaged in the production of reactive oxygen species in response to cold stress, implying that members of the PbrbHLH family play an important role in pear cold stress tolerance.…”

Transcription Factor CpbHLH3 and CpXYN1 Gene Cooperatively Regulate Fruit Texture and Counteract 1-Methylcyclopropene Inhibition of Softening in Postharvest Papaya (Carica papaya L.)

“…14,15 In recent years, CpbHLH has been suggested to function as a major regulator of ripening and quality in papaya fruit. Yang et al 16 identified and screened CpbHLH genes in papaya fruit and found that most assessed CpbHLHs show responses to different stressrelated events, whereas Zhou et al 17 MaEXP2/21, MaPME4/5, MaPG4, and MaPL1/2, thereby subsequently promoting fruit softening. 18 Nevertheless, some researchers have reported that treatment with 1-MCP can have certain detrimental effects on fruit.…”