Identification, Expression and IAA-Amide Synthetase Activity Analysis of Gretchen Hagen 3 in Papaya Fruit (Carica papaya L.) during Postharvest Process

Genome-wide identification of MAPK family in papaya (Carica papaya) and their involvement in fruit postharvest ripening

BACKGROUND

Papaya (Carica papaya) is an economically important fruit cultivated in the tropical and subtropical regions of China. However, the rapid softening rate after postharvest leads to a short shelf-life and considerable economic losses. Accordingly, understanding the mechanisms underlying fruit postharvest softening will be a reasonable way to maintain fruit quality and extend its shelf-life.

RESULTS

Mitogen-activated protein kinases (MAPKs) are conserved and play essential roles in response to biotic and abiotic stresses. However, the MAPK family remain poorly studied in papaya. Here, a total of nine putative CpMAPK members were identified within papaya genome, and a comprehensive genome-wide characterization of the CpMAPKs was performed, including evolutionary relationships, conserved domains, gene structures, chromosomal locations, cis-regulatory elements and expression profiles in response to phytohormone and antioxidant organic compound treatments during fruit postharvest ripening. Our findings showed that nearly all CpMAPKs harbored the conserved P-loop, C-loop and activation loop domains. Phylogenetic analysis showed that CpMAPK members could be categorized into four groups (A-D), with the members within the same groups displaying high similarity in protein domains and intron-exon organizations. Moreover, a number of cis-acting elements related to hormone signaling, circadian rhythm, or low-temperature stresses were identified in the promoters of CpMAPKs. Notably, gene expression profiles demonstrated that CpMAPKs exhibited various responses to 2-chloroethylphosphonic acid (ethephon), 1-methylcyclopropene (1-MCP) and the combined ascorbic acid (AsA) and chitosan (CTS) treatments during papaya postharvest ripening. Among them, both CpMAPK9 and CpMAPK20 displayed significant induction in papaya flesh by ethephon treatment, and were pronounced inhibition after AsA and CTS treatments at 16 d compared to those of natural ripening control, suggesting that they potentially involve in fruit postharvest ripening through ethylene signaling pathway or modulating cell wall metabolism.

CONCLUSION

This study will provide some valuable insights into future functional characterization of CpMAPKs, and hold great potential for further understanding the molecular mechanisms underlying papaya fruit postharvest ripening.

AcERF1B and AcERF073 Positively Regulate Indole-3-acetic Acid Degradation by Activating AcGH3.1 Transcription during Postharvest Kiwifruit Ripening

Ethylene can accelerate the postharvest ripening process of kiwifruit, while indole-3-acetic acid (IAA) delays it. However, the molecular mechanism by which ethylene regulates IAA degradation is unclear. Here, we found that ethephon promotes the degradation of free IAA in kiwifruit. Furthermore, ethylene can promote the expression of AcGH3.1 and enhance its promoter activity. Two ethylene response factors (ERFs), AcERF1B and AcERF073, were obtained using an AcGH3.1 promoter as bait for a yeast one-hybrid screening library. Both AcERF1B and AcERF073 bind to the AcGH3.1 promoter to activate it. Also, AcERF1B/073 enhanced AcGH3.1 expression, decreased the free IAA content, and increased the IAA-Asp content in kiwifruit. In addition, we found that the AcERF1B and AcERF073 proteins directly interact, and this interaction enhanced their binding to the AcGH3.1 promoter. In summary, our results suggest that AcERF1B and AcERF073 positively regulate IAA degradation by activating AcGH3.1 transcription, which accelerated postharvest kiwifruit ripening.

Comparative Transcriptomics and Metabolomics Reveal an Intricate Priming Mechanism Involved in PGPR-Mediated Salt Tolerance in Tomato

Plant-associated beneficial strains inhabiting plants grown under harsh ecosystems can help them cope with abiotic stress factors by positively influencing plant physiology, development, and environmental adaptation. Previously, we isolated a potential plant growth promoting strain (AXSa06) identified as Pseudomonas oryzihabitans, possessing 1-aminocyclopropane-1-carboxylate deaminase activity, producing indole-3-acetic acid and siderophores, as well as solubilizing inorganic phosphorus. In this study, we aimed to further evaluate the effects of AXSa06 seed inoculation on the growth of tomato seedlings under excess salt (200 mM NaCl) by deciphering their transcriptomic and metabolomic profiles. Differences in transcript levels and metabolites following AXSa06 inoculation seem likely to have contributed to the observed difference in salt adaptation of inoculated plants. In particular, inoculations exerted a positive effect on plant growth and photosynthetic parameters, imposing plants to a primed state, at which they were able to respond more robustly to salt stress probably by efficiently activating antioxidant metabolism, by dampening stress signals, by detoxifying Na⁺, as well as by effectively assimilating carbon and nitrogen. The primed state of AXSa06-inoculated plants is supported by the increased leaf lipid peroxidation, ascorbate content, as well as the enhanced activities of antioxidant enzymes, prior to stress treatment. The identified signatory molecules of AXSa06-mediated salt tolerance included the amino acids aspartate, threonine, serine, and glutamate, as well as key genes related to ethylene or abscisic acid homeostasis and perception, and ion antiporters. Our findings represent a promising sustainable solution to improve agricultural production under the forthcoming climate change conditions.

CpARF2 and CpEIL1 interact to mediate auxin-ethylene interaction and regulate fruit ripening in papaya

Papaya (Carica papaya L.) is a commercially important fruit crop. Various phytohormones, particularly ethylene and auxin, control papaya fruit ripening. However, little is known about the interaction between auxin and ethylene signaling during the fruit ripening process. In the present study, we determined that the interaction between the CpARF2 and CpEIL1 mediates the interaction between auxin and ethylene signaling to regulate fruit ripening in papaya. We identified the ethylene-induced auxin response factor CpARF2 and demonstrated that it is essential for fruit ripening in papaya. CpARF2 interacts with an important ethylene signal transcription factor CpEIL1, thus increasing the CpEIL1-mediated transcription of the fruit ripening-associated genes CpACS1, CpACO1, CpXTH12 and CpPE51. Moreover, CpEIL1 is ubiquitinated by CpEBF1 and is degraded through the 26S proteasome pathway. However, CpARF2 weakens the CpEBF1-CpEIL1 interaction and interferes with CpEBF1-mediated degradation of CpEIL1, promoting fruit ripening. Therefore, CpARF2 functions as an integrator in the auxin-ethylene interaction and regulates fruit ripening by stabilizing CpEIL1 protein and promoting the transcriptional activity of CpEIL1. To our knowledge, we have revealed a novel module of CpARF2/CpEIL1/CpEBF1 that fine-tune fruit ripening in papaya. Manipulating this mechanism could help growers tightly control papaya fruit ripening and prolong shelf life.

Identification and Expression Analysis of Gretchen Hagen 3 (GH3) in Kiwifruit (Actinidia chinensis) During Postharvest Process

In plants, the Gretchen GH3 (GH3) protein is involved in free auxin (IAA) and amino acid conjugation, thus controlling auxin homeostasis. To date, many GH3 gene families have been identified from different plant species. However, the GH3 gene family in kiwifruit (Actinidia chinensis) has not been reported. In this study, 12 AcGH3 genes were identified, phylogenetic analysis of AtGH3 (Arabidopsis), SlGH3 (Solanum lycopersicum), and AcGH3 provided insights into various orthologous relationships among these proteins, which were categorized into three groups. Expression analysis of AcGH3 genes at different postharvest stages suggested limited or no role for most of the AcGH3 genes at the initiation of fruit ripening. AcGH3.1 was the only gene exhibiting ripening-associated expression. Further study showed that the expression of AcGH3.1 gene was induced by NAA (1-naphthylacetic acid, auxin analogue) and inhibited by 1-MCP (1-methylcyclopropene, ethylene receptor inhibitor), respectively. AcGH3.1 gene silencing inhibited gene expression and delayed fruit softening in kiwifruit. The results indicate that AcGH3.1 may play an important role in the softening process of fruits. Analysis of the AcGH3.1 promoter revealed the presence of many cis-elements related to hormones, light, and drought. The determination of GUS (β-Galactosidase) enzyme activity revealed that promoter activity increased strikingly upon abscisic acid (ABA), ethylene, or NAA treatment, and significantly decreased with salicylic acid (SA) treatment. The present study could help in the identification of GH3 genes and revelation of AcGH3.1 gene function during postharvest stages, which pave the way for further functional verification of the AcGH3.1 gene.

Auxin Metabolism Controls Developmental Decisions in Land Plants

Unlike animals, whose body plans are set during embryo development, plants maintain the ability to initiate new organs throughout their life cycle. Auxin is a key regulator of almost all aspects of plant development, including morphogenesis and adaptive responses. Cellular auxin concentrations influence whether a cell will divide, grow, or differentiate, thereby contributing to organ formation, growth, and ultimately plant shape. Auxin gradients are established and maintained by a tightly regulated interplay between metabolism, signalling, and transport. Auxin is synthesised, stored, and inactivated by a multitude of parallel pathways that are all tightly regulated. Here we summarise the remarkable progress that has been achieved in identifying some key components of these pathways and the genetic complexity underlying their precise regulation.

Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

BACKGROUND

Papaya (Carica papaya L.) is a popular climacteric fruit, undergoing various physico-chemical changes during ripening. Although papaya is widely cultivated and consumed, few studies on the changes in metabolism during its ripening process at the proteasome level have been performed. Using a newly developed TMT-LCMS analysis, proteomes of papaya fruit at different ripening stages were investigated.

RESULTS

In total, 3220 proteins were identified, of which 2818 proteins were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. The KEGG enrichment analysis showed that various metabolic pathways were significantly altered, particularly in flavonoid and fatty acid metabolisms. The up-regulation of several flavonoid biosynthesis-related proteins may provide more raw materials for pigment biosynthesis, accelerating the color variation of papaya fruit. Variations in the fatty acid metabolism- and cell wall degradation-related proteins were investigated during the ripening process. Furthermore, the contents of several important fatty acids were determined, and increased unsaturated fatty acids may be associated with papaya fruit volatile formation.

CONCLUSIONS

Our data may give an intrinsic explanation of the variations in metabolism during the ripening process of papaya fruit.

The Gene Structure and Expression Level Changes of the GH3 Gene Family in Brassica napus Relative to Its Diploid Ancestors

The GH3 gene family plays a vital role in the phytohormone-related growth and developmental processes. The effects of allopolyploidization on GH3 gene structures and expression levels have not been reported. In this study, a total of 38, 25, and 66 GH3 genes were identified in Brassica rapa (A_rA_r), Brassica oleracea (C_oC_o), and Brassica napus (A_nAC_nC_n), respectively. BnaGH3 genes were unevenly distributed on chromosomes with 39 on A_n and 27 on C_n, in which six BnaGH3 genes may appear as new genes. The whole genome triplication allowed the GH3 gene family to expand in diploid ancestors, and allopolyploidization made the GH3 gene family re-expand in B. napus. For most BnaGH3 genes, the exon-intron compositions were similar to diploid ancestors, while the cis-element distributions were obviously different from its ancestors. After allopolyploidization, the expression patterns of GH3 genes from ancestor species changed greatly in B. napus, and the orthologous gene pairs between A_n/A_r and C_n/C_o had diverged expression patterns across four tissues. Our study provides a comprehensive analysis of the GH3 gene family in B. napus, and these results could contribute to identifying genes with vital roles in phytohormone-related growth and developmental processes.

Comparative Genomic and Transcriptomic Analysis Suggests the Evolutionary Dynamic of GH3 Genes in Gramineae Crops

Glycoside hydrolase 3 (GH3) gene family belongs to auxin-responsive gene families and is tightly linked with hormone homeostasis and signaling pathways. However, our knowledge about the evolutionary dynamic of GH3 genes in Gramineae crops is limited. In this study, a comparative genomic and transcriptomic analysis was conducted to study evolutionary patterns and the driving selective forces of GH3 gene family in six representative Gramineae crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa ssp. japonica (Os). A total of 17, 13, 11, 9, 8, and 11 GH3 proteins (GH3s) were identified in Si, Zm, Sb, Hv, Bd, and Os, respectively. Phylogenetic, conserved motif, and gene structural analyses could divide all GH3s into two groups (I and II), and all GH3s consisted of seven orthogroups (Ors) on the basis of Or identification result. We further found that genes in the same Or showed similar sequence and structural features, whereas genes in the same groups exhibited intrinsic differences in exon numbers and intron lengths. These results revealed GH3 genes in the same groups have been differentiated. Obvious differences in total numbers of GH3 genes, Ors, and duplication events among these six tested Gramineae crops reflected lineage-specific expansions and homologous gene loss/gain of GH3 gene family during the evolutionary process. In addition, selective force and expression analyses indicated that all GH3 genes were constrained by strong purifying selection, and GH3 genes in conserved Ors showed higher expression levels than that in unconserved Ors. The current study highlighted different evolutionary patterns of GH3 genes in Gramineae crops resulted from different evolutionary rates and duplication events and provided a vital insight into the functional divergence of GH3 genes.

Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon

Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B. distachyon was performed. A comprehensive overview of the characterization of the BdARFs was obtained by multiple bioinformatics analyses, including the gene and protein structure, chromosome locations, conserved motifs of proteins, phylogenetic analysis, and cis-elements in promoters of BdARF. Results showed that all BdARFs contained conserved DBD, MR, and CTD could be divided into four classes, Ia, IIa, IIb, and III. Expression profiles of BdARF genes indicated that they were expressed across various tissues and organs, which could be clustered into three main expression groups, and most of BdARF genes were involved in phytohormone signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. And predicted regulatory network between B. distachyon ARFs and IAAs was also discussed. Our genomics analysis of BdARFs could yield new insights into the complexity of the control of BdARF genes and lead to potential applications in the investigation of the accurate regulatory mechanisms of ARFs in herbaceous plants.

A qualitative proteome-wide lysine crotonylation profiling of papaya (Carica papaya L.)

Lysine crotonylation of histone proteins is a recently-identified post-translational modification with multiple cellular functions. However, no information about lysine crotonylation of non-histone proteins in fruit cells is available. Using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity antibody analysis, a global crotonylation proteome analysis of papaya fruit (Carica papaya L.) was performed. In total, 2,120 proteins with 5,995 lysine crotonylation sites were discovered, among which eight conserved motifs were identified. Bioinformatic analysis linked crotonylated proteins to multiple metabolic pathways, including biosynthesis of antibiotics, carbon metabolism, biosynthesis of amino acids, and glycolysis. particularly, 40 crotonylated enzymes involved in various pathways of amino acid metabolism were identified, suggesting a potential conserved function for crotonylation in the regulation of amino acid metabolism. Numerous crotonylation sites were identified in proteins involved in the hormone signaling and cell wall-related pathways. Our comprehensive crotonylation proteome indicated diverse functions for lysine crotonylation in papaya.

A qualitative proteome-wide lysine crotonylation profiling of papaya (Carica papaya L.)

Lysine crotonylation of histone proteins is a recently-identified post-translational modification with multiple cellular functions. However, no information about lysine crotonylation of non-histone proteins in fruit cells is available. Using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity antibody analysis, a global crotonylation proteome analysis of papaya fruit (Carica papaya L.) was performed. In total, 2,120 proteins with 5,995 lysine crotonylation sites were discovered, among which eight conserved motifs were identified. Bioinformatic analysis linked crotonylated proteins to multiple metabolic pathways, including biosynthesis of antibiotics, carbon metabolism, biosynthesis of amino acids, and glycolysis. particularly, 40 crotonylated enzymes involved in various pathways of amino acid metabolism were identified, suggesting a potential conserved function for crotonylation in the regulation of amino acid metabolism. Numerous crotonylation sites were identified in proteins involved in the hormone signaling and cell wall-related pathways. Our comprehensive crotonylation proteome indicated diverse functions for lysine crotonylation in papaya.

Genome-wide analysis and characterization of Aux/IAA family genes related to fruit ripening in papaya (Carica papaya L.)

Background

Auxin/indole-3-acetic acid (Aux/IAA) family genes encode short-lived nuclear proteins that mediate the responses of auxin-related genes and are involved in several plant developmental and growth processes. However, how Aux/IAA genes function in the fruit development and ripening of papaya (Carica papaya L.) is largely unknown.

Results

In this study, a comprehensive identification and a distinctive expression analysis of 18 C. papaya Aux/IAA (CpIAA) genes were performed using newly updated papaya reference genome data. The Aux/IAA gene family in papaya is slightly smaller than that in Arabidopsis, but all of the phylogenetic subfamilies are represented. Most of the CpIAA genes are responsive to various phytohormones and expressed in a tissues-specific manner. To understand the putative biological functions of the CpIAA genes involved in fruit development and ripening, quantitative real-time PCR was used to test the expression profiling of CpIAA genes at different stages. Furthermore, an IAA treatment significantly delayed the ripening process in papaya fruit at the early stages. The expression changes of CpIAA genes in ACC and 1-MCP treatments suggested a crosstalk between auxin and ethylene during the fruit ripening process of papaya.

Conclusions

Our study provided comprehensive information on the Aux/IAA family in papaya, including gene structures, phylogenetic relationships and expression profiles. The involvement of CpIAA gene expression changes in fruit development and ripening gives us an opportunity to understand the roles of auxin signaling in the maturation of papaya reproductive organs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3722-6) contains supplementary material, which is available to authorized users.