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. 2025 Feb 10;26:125. doi: 10.1186/s12864-025-11293-7

Genome-wide analysis of the FKBP gene family and the potential role of GhFKBP 13 in chloroplast biogenesis in upland cotton

Jianguang Liu 1,#, Zhao Geng 1,#, Guiyuan Zhao 1, Mengzhe Li 1, Zetong An 1, Hanshuang Zhang 1,✉, Yongqiang Wang 1,✉
PMCID: PMC11809014  PMID: 39930370

Abstract

Background

In plants, FK506-binding proteins (FKBPs) have been shown to participate in various biological processes such as photosynthetic system reaction, stress response, and growth and development. However, the roles of FKBPs in cotton are less well known.

Results

In this study, we investigated FKBP family genes on a genome-wide scale in four Gossypium species. A total of 147 FKBP genes were identified from these four Gossypium species and placed into three classes based on phylogenetic analysis. Collinearity analysis indicated that whole-genome duplication events and segmental duplication events were the main sources of gene amplification during the evolution of FKBP genes. Conserved motif, expression profiles and cis-acting elements prediction of the GhFKBPs analysis revealed that GhFKBPs were differentially expressed in different tissues and under abiotic stress. qRT-PCR analysis showed that some GhFKBPs were predominantly expressed in leaves. The analysis of cis-acting elements prediction revealed that MYB, MYC and ERE related binding sites in the promoters of GhFKBP genes were the most abundant. Furthermore, the composition and distribution of these cis-acting elements exhibited differences between homologous GhFKBP gene pairs. Silencing of GhFKBP13 in cotton resulted in disruption of chloroplast structure and starch metabolism disorders.

Conclusions

Taken together, 147 FKBP family genes in four Gossypium species are comprehensively characterized, and GhFKBP13 play a critical role in chloroplast biogenesis in upland cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-025-11293-7.

Keywords: Gossypium hirsutum, GhFKBPs, Chloroplast biogenesis, Starch and sucrose metabolism

Background

FK506-binding proteins (FKBPs) are part of the peptidyl-proline isomerase (PPIase, EC5.2.1.8) superfamily, catalyzing protein folding and maturation by converting cis-trans configurations of amino acid residues [1]. FKBPs are highly homologous receptor-binding proteins that are widely distributed in all organisms, including bacteria, fungi, animals and plants [2–5]. FKBPs can be divided into single-domain and multidomain FKBPs based on their sequence structure. Single-domain FKBPs have a single FK506-binding domain (FKBD) which contains approximately 110 amino acids that provide the active site and the receptor site, whereas multidomain FKBPs have an additional FKBD containing a tetrapeptide repeat (TPR) or other functional domains, including a C-terminal calmodulin or helix-binding domain [6, 7].

With the continuous improvement of plant genome sequencing and the advancement of bioinformatics, identification of gene families in plant genome databases has become viable, and gene family analysis facilitates the characterization of gene members, their chromosomal positions, and probable functions. FKBP family genes have been reported in different species [8–16]. These proteins are localized mostly in the chloroplast, cytoplasm, nucleus, mitochondria, peroxisome and endoplasmic reticulum, implying that FKBPs have a variety of biological functions. AtFKBP20-2 is located in the chloroplast thylakoid lumen and is required for the accumulation of the PSII supercomplex in Arabidopsis thaliana (A. thaliana); genetic disruption of AtFKBP20-2 resulted in slower plant development [17]. The AtFKBP15-1/15 − 2, which are localized to the endoplasmic reticulum, are expressed prominently in the vascular bundles of the root basal meristem region, and an AtFKBP15-1/15 − 2 double mutant had more lateral roots than did Col-0 or single mutants [18]. Protein interaction studies indicated that AtFKBP15-1/15 − 2 participate in the control of lateral root number by inhibiting the catalytic activity of vacuolar invertase 2 (VIN2) [18]. In addition, FKBPs were also reported to play an impotant role in plant development [19–21], hormone signaling [22], ribosomal RNA gene expression [23], heat stress responsiveness [24–26] and drought and salt stress [27–28] etc. Consequently, there remains intense interest in understanding their function in plant-related research.

As an oil crop and an important source of natural textile fibers, cotton plays an important role in agriculture and industry around the world. However, its production is mainly limited by various environmental stress conditions. Analysis of gene families could contribute to understanding the diversity of genes and environmental adaptability in plants. Over the past decade, an increasing number of cotton genomes have been assembled and many cotton gene families have been extensively characterized recently [29–37]. FKBPs have been shown to play important functions in plant growth and development. Whereas, the FKBP genes family in cotton has not been fully characterized. In this study, we identified FKBP family genes in four Gossypium species and investigated their phylogeny, chromosomal location, synteny relationships and gene structure. The GhFKBPs expression profiles were analysis by bioinformatics and qRT-PCR methods. According to the GhFKBP genes expression results and previous studies, we performed a preliminary exploration of the function of GhFKBP13 in chloroplast development and its possible regulatory mechanism. The results provide a basis for understanding the biological role of FKBPs in chloroplast development in upland cotton and provide a better opportunity for the utilization of the FKBP genes in enhancing photosynthetic light utilization in elite cotton cultivars.

Materials and methods

Identification of FKBP gene members

The cotton genome sequence data of Gossypium arboreum (G. arboreum, ICR), Gossypium hirsutum (G. hirsutum, WHU) were downloaded from Gossypium Resource and Network Database(GRAND, https://grand.cricaas.com.cn/). Gossypium raimondii (G. raimondii, HAU), Gossypium barbadense (G. barbadense, ZJU) were downloaded from Cotton FGD (Cotton Functional Genomics Database) (http://www.cottonfgd.org/). FKBP protein data of A. thaliana were downloaded from TAIR (http://www.arabidopsis.org/). The Hidden Markov Model (HMM) of FKBP (Pfam ID: PF00254) was downloaded from the Pfam database (http://pfam.xfam.org/). Then, Gene IDs containing conserved FKBP domains with an e-value threshold of 0.01 were extracted from the four Gossypium species using HMMER 3.3.2 software (http://hmmer.org/). Finally, the Batch SMART program of TBtools 1.09 (https://github.com/CJ-Chen/TBtools) was used to confirm whether the candidate protein sequences contained the FKBP core domain.

Phylogenetic and collinearity analyses of four cotton species

To investigate how the FKBP genes differ among the four cotton species, the protein sequences of G. hirsutum, G. barbadense, G. arboreum, G. raimondii and A. thaliana were compared via the ClustalW function of MEGA-X software (https://www.megasoftware.net/docs). A phylogenetic evolutionary tree was subsequently constructed via maximum likelihood estimation (MLE) with 1000 bootstrap replicates. To study the collinearity between different species in cotton, Tbtools software(One step MCScanX-super Fast) was used to conduct collinearity analysis between different cotton FKBPs, and Advanced circos plot in Tbtools was used to visualize the results.

Conserved protein domains, chromosomal location

For FKBP family genes of G. hirsutum, the MEME website (http://meme-suite.org/) was used to identify conserved protein sequences. Ten motif parameters were selected, and the other parameters were unchanged. The generated MAST file was subsequently used to construct protein domain maps via TBtools. The gff files and gene IDs of G. hirsutum, G. barbadense, G. arboreum, and G. raimondii were also generated via TBtools software to construct a map of the chromosomal locations of the family members.

Cis-acting elements analyses of GhFKBPs

The 2000 bp upstream sequences of the GhFKBP genes’ start codon (ATG) were analyzed to identify the cis-acting elements in the putative promoter regions, and the cis-acting elements were identiffed with the online program PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).

Expression analyses of GhFKBPs

The expression of GhFKBP family members in various tissues/organs and sodium chloride and PEG-induced drought stress was determined through previously published RNA sequencing data from Cotton Omics Database (http://cotton.zju.edu.cn/10.rnasearch.html) and is summarized as heatmaps. The regulation transcription factors of GhFKBPs were predicted using PlantRegMap(http://plantregmap.gao-lab.org/go.php/) with G. raimondii as the target species.

Plant materials and qRT-PCR analysis of gene expression

The G. hirsutum cultivar “Jimian176” was selected for GhFKBP family gene expression analysis. Jimian176 seeds were grown in a greenhouse at 25 °C under a 16-h light/8-h dark cycle. The tissues of the roots, stems and leaves of four-leaf-stage cotton plants were immediately frozen in liquid nitrogen and stored at -70 °C. Total RNA was extracted from the samples by using the EASYspin Plus Plant RNA Kit (Aidlab, Beijing, China) following the manufacturer’s instructions. First-strand cDNA was synthesized from total RNA using the TransScript One-Step gDNA Removal and cDNA Synthesis SuperMix (TransGen, China) according to the manufacturer’s protocol. The primer pairs used were designed with Primer 5 (Table S1). qRT-PCR was performed by a C1000 Touch™ PCR (Bio-Rad, USA), and the reaction conditions were set as follows: 95 °C for 10 min, followed by 95 °C for 15 s and 58 °C for 1 min for thirty-five cycles, after which dissociation curve analysis was performed. Transcription quantitative analysis of gene expression used Histone 3 as reference gene for normalization(Table S1). All reactions for each sample were performed in triplicate with biological replicates. The relative expression levels of the target genes were calculated using the 2−ΔΔCt method.

Virus-induced gene silencing assays

Sequence alignment analysis showed that GhFKBP13 has a high degree of homology in the A and D subgenomes, with a sequence similarity of 97.7%. However, GhFKBP13 has limited homology with other GhFKBP genes, with sequence similarities between 42.5% and 51.9% with its closely related GhFKBP genes. To avoid the potential silencing of other homologues, a specific 300 bp fragment amplified from the GhFKBP13 gene ORF was integrated into the TRV vector from General Biol Co., Ltd. (An Hui, China) to construct TRV-GhFKBP13. TRV-GhFKBP13, TRV-GhCLA1 (indicator vector) and the TRV negative control vector were subsequently transformed into Agrobacterium tumefaciens GV3101. These constructed strains were mixed with the strain harboring pYL192 (a helper vector) (1:1 ratio, OD600 = 0.8) and coinjected into two fully expanded cotyledons of cotton seedlings. When injected TRV-GhCLA plants showed albino symptoms about two weeks later, the expression level of GhFKBP13 in the TRV-GhFKBP13 plants and TRV negative control plants was determined via qRT-PCR, and three biological replicates were used.

Transmission electron microscopy (TEM) observation

For TEM analysis, the leaves of VIGS-silenced GhFKBP13 plants and control cotton plants were cut into 1 mm×1 mm pieces on each side of the main vein of the leaf. Leaf sections were washed with 4% glutaraldehyde in phosphate buffer for 5 min and then fixed with 4% glutaraldehyde in phosphate buffer at 4 °C for 4 h. Then, the leaf sections were rinsed with 0.1 M PBS 3 times and postfixed with 1% osmium acid prepared in PBS buffer at 4 °C for 1 h. The leaf sections were rinsed with 0.1 M PBS 3 times and dehydrated with an acetone series (30-50%-70-80%-90-95%-100%-100%) for 20 min each and then embedded in Spurr’s medium before thin sectioning. The leaf sections were then further stained with uranyl acetate and examined with an H-7650 electron microscope (HITACHI Ltd., Tokyo, Japan).

Chlorophyll content assay

The total chlorophyll content in plants was determined using a spectrophotometric method. After silencing the target gene, we took 0.1 g cotton leaf and cut into slices, immersed it in 15 mL of 95% ethanol for 48 h at 4 °C in the dark. The concentrations of chlorophyll a(Ca) and chlorophyll b(Cb) and carotenoids(Cx + c) were measured at 665, 649 and 470 nm using a UV-1800PC spectrophotometer (Mapada Co., Ltd., China) and calculated according to the formula Ca = 13.95A665-6.88A649, Cb = 24.96A649-7.32A665, and Cx + c=(1000A470-3.27Ca-104Cb)/229.

RNA sequencing(RNA-seq) analysis

Total RNA was extracted from VIGS-silenced GhFKBP13 leaves and control plant leaves and subsequently sent to Personalbio Technology Co., Ltd. (Shanghai, China). Paired-end sequencing was performed on an Illumina NovaSeq 6000 sequencer. Differential expression was calculated using DESeq2 software. Genes with an absolute log2-fold change (VIGS silenced/TRV control) > 1 and a p value < 0.05 were considered to be significantly differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis and KEGG enrichment analysis were performed on the differentially expressed genes (DEGs) using ClusterProfiler (adjusted p value < 0.05).

Results

Identification of the FKBP gene family and characteristics of the FKBP genes in G. Hirsutum

A total of 48, 47, 28 and 24 FKBP genes were ultimately identified from G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, respectively (Table S2). All these genes were named according to their orthology with reported isoforms in A. thaliana(He et al., 2004) and labeled A/D based on their location on the At subgenome or the Dt subgenome(Table S3). For more than two proteins with a sequence orthologous to the same A. thaliana protein, lower-case extension letters were added to the name according to the order on the chromosome.

The primary characteristics of the G. hirsutum FKBPs were analyzed, including the number of FKBP_C domains, protein length (aa), molecular weight (MW), isoelectric point (pI) and the subcellular location of the predicted proteins. The number of FKBP_C domains in the G. hirsutum FKBP family ranged from 1 to 3, the protein length ranged from 112 aa to 629 aa, the MWs ranged from 12.06 kDa to 70.95 kDa, and the pI values ranged from 4.84 to 9.57. The subcellular localization of the proteins was predicted by WoLF and TargetP online, and the results showed that GhFKBP proteins were mainly located in nucleus(24.4%), cytoplasm(28.5%) and chloroplast(30.6%)(Table S4).

Phylogenetic analysis of the FKBP genes in four Gossypium species and A. Thaliana

To better elucidate the evolutionary relationships of cotton FKBPs, all FKBP amino acid sequences from the four Gossypium species and A. thaliana were used to construct a phylogenetic tree. As expected, the cotton FKBPs and Arabidopsis homologs were classified into three groups (Fig. 1). Among these branches, group I had the fewest members (23), including FKBP16-3, FKBP13, FKBP16-2 and HEN. In addition to G. arboreum having only one HEN gene, there were clearly no other Gossypium species with an identified HEN gene. In group II, there were 51 members, including FKBP16-1, FKBP19, FKBP20-2, FKBP17-1, FKBP17-2, FKBP16-4, FKBP18, and AtTIG. Group III had 97 members, more than half of the total number of FKBP family members. This group included FKBP15-1, FKBP15-2, FKBP43, FKBP53, FKBP12, FKBP20-1, FKBP42, FKBP62, FKBP72 and FKBP65. Among these genes, Arabidopsis FKBP65 and FKBP62 were less closely related to other homologous FKBP proteins in Gossypium species. Overall, the FKBP proteins are very conserved in Gossypium species and A. thaliana.

Fig. 1.

Fig. 1

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Phylogenetic and evolutionary analysis of the FKBP gene family from G.arboreum, G.raimondii, G.hirsutum, G.barbadense and A. thaliana. Group I, Group II and Group III are distinguished by red, blue and green label respectively

Chromosomal distribution and collinearity analysis of FKBP genes in four Gossypium species

To understand the chromosomal distribution of the FKBP genes, we created a physical map of the chromosomal distribution of the FKBP genes in the four Gossypium species (Fig. 2). The FKBP gene family members were found to be distributed on specific chromosomes, except for GaFKBP13-1, which was mapped to the scaffold (contig00019673), and the number of FKBP genes on each chromosome ranged from 1 to 4. In G. arboreum, the FKBP genes were located on all chromosomes except chr 12, whereas in G. raimondii, they were located on all chromosomes except chr02 and chr13. In the tetraploid cotton species G. hirsutum and G. barbadense, the gene distributions were not uniform. FKBPs genes were not present on chrA04, chrA10, chrA13, chrD03 and chrD13 in G. hirsutum; on the other hand, FKBPs were not present on chrA03, chrA13, chrD03 or chrD13 in G. barbadense.

Fig. 2.

Fig. 2

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Chromosomal locations of FKBP gene family of G.arboreum, G.raimondii, G.hirsutum and G.barbadense. The scale on the left is in mega-bases. The gene name on the left side of each chromosome corresponds to the approximate locations of each FKBP gene

Collinearity analysis can reveal the origin and evolutionary history of gene families, including the duplication, transposition, and rearrangement processes of gene family members, as well as functional changes and adaptive evolution during the evolutionary history. Therefore, we performed a collinearity analysis of FKBPs gene in the four cotton species. The results showed that a total 253 gene pairs were identified by comparing the genomes and subgenomes of Ga-Ga(2 gene pairs), Gr-Gr(7 gene pairs), Ga-Gr(30 gene pairs), GhAt-GhAt(6 gene pairs), GhDt-GhDt(8 gene pairs), GhAt-GhDt(33 gene pairs), GbAt-GbAt(5 gene pairs), GbDt-GbDt(5 gene pairs), GbAt-GbDt(21 gene pairs), GhAt-Ga(31 gene pairs), GbAt-Ga(35 gene pairs), GhDt-Gr(35 gene pairs) and GbDt-Gr(29 gene pairs), and all the gene pairs belonged to whole-genome duplication (WGD) or segmentation (Fig. 3A and K, Table S5). It indicated that WGD/segmental duplication were the main sources of gene amplification during the evolution of the FKBP genes in four Gossypium species. The study revealed notable variations in the number of paralogous genes among different genomes and subgenomes. For instance, G. hirsutum had a higher number of paralogous genes compared to G. barbadense, while G. arboreum had significantly fewer paralogous genes than G. raimondii. It indicated that FKBPs in four Gossyium species experienced different evolutionary pressure.

Fig. 3.

Fig. 3

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The collinearity of FKBP genes within and among the four Gossypium species genomes or subgenomes. (A) Ga-Ga, (B) Gr-Gr, (C) Ga-Gr, (D) GhAt-GhAt, (E) GhDt-GhDt, (F) GhAt-GhDt, (G) GbAt-GbAt, (H) GbDt-GbDt, (I) GbAt-GbDt, (J) GhAt-Ga-GbAt, (K) GhDt-Gr-GbDt. (GhAt: A subgenome of G. hirsutum; GhDt: D subgenome of G. hirsutum; GbAt: A subgenome of G. arbadense; GbDt: D subgenome of G. arbadense; Gr: G. raimondii; Ga: G. arboretum)

Conserved motif analysis, expression profiles and cis-acting elements prediction of the GhFKBPs in G. Hirsutum

To further explore the structure of GhFKBP family members, conserved motifs in the GhFKBPs were analyzed. Ten putative motifs were identified and conserved motif analysis revealed that motifs 1 and 7 were present in all the GhFKBP proteins in G. hirsutum except for GhFKBP65-1D, which lacks motif 7. In addition, despite the lack of some motifs in individual proteins, most members exhibited highly conserved motif structures and arrangements within the same group, whereas gene motifs varied greatly within different groups (Fig. 4A and B).

Fig. 4.

Fig. 4

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Phylogenetic, conserved motifs and expression patterns of GhFKBP genes in G.hirsutum. (A) The phylogenetic analysis of GhFKBP members were based on the protein sequences and color boxes represent different groups. (B) Ten conserved motifs were analysis using MEME and TBtools software, while scale label represent the length of proteins. (C) The heat map was constructed based on transcriptome data (FPKM values) of root, stem and leaf tissue of G.hirsutum. Different colors represented the different expression levels of GhFKBPs. The scale bar on the right was marked according to the log2(FPKM value), and gene names were also shown on the right.Group I, Group II and Group III are distinguished by blue, yellow and red label respectively. (D) The heat map was constructed based on transcriptome data of sodium chloride and PEG-induced drought stress. Different colors represented the different expression levels of GhFKBPs. The scale bar on the right was marked according to the log2(foldchange)

It is generally believed that gene expression characteristics are closely related to its function. The expression profiles of GhFKBPs was examined and the results showed that the GhFKBPs were differentially expressed in different tissues (Fig. 4C). We noted that most genes in group I were predominantly expressed in leaves. In group II and group III, most genes were predominantly expressed in root and stem tissues. On the whole, the expression pattern of GhFKBPs in group I showed opposite expression patterns with group II and group III. Analysis of induced expression of GhFKBPs by sodium chloride and PEG-induced drought stress showed that there was no obvious patten in group I, but there were more down-regulated genes than up-regulated genes. In group II and group III, most genes were predominantly up-regulated (Fig. 4D). In order to further verify the accuracy of gene expression, we selected 6 genes from group I for qRT-PCR analysis, and the results showed that the expression trend was consistent with the RNA-seq data (Fig. 5).

Fig. 5.

Fig. 5

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qRT-PCR analysis of six selected genes in diferent tissues. Mean and SD values represent three independent replicates (Student’s t test, *P < 0.05; **P < 0.01). (A)-(F) Relative expression levels of GhFKBP13, GhFKBP18, GhFKBP19, GhFKBP16-2, GhFKBP16-3 and GhFKBP16-4 in roots, stems, and leaves respectively.

The cis-acting elements analysis provide a powerful clue for defining stress receptive or tissue-specific expression behavior in different environments. In this paper, the cis-acting elements of 2000 bp upstream of the start codon in the promoter regions of GhFKBP genes were predicted. It can be seen from the results that the most abundant cis-acting elements were MYB, MYC and ERE-related binding sites in GhFKBP promoters (Fig. 6A). In addition, we found that the composition and distribution of cis-acting elements are significantly difference between GhFKBP homologous members. Such as there are 8 G-box and 7 ABRE binding sites in GhFKBP20-2–1 A promoter while only 1 G-box binding site and none ABRE binding site in GhFKBP20-2-1D promoter (Fig. 6A and B). Therefore, we speculate that these GhFKBP homologous genes may have different expression patterns in response to environmental changes.

Fig. 6.

Fig. 6

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Predicted cis-elements in the promoter regions of GhFKBP genes. (A) types and numbers of cis-acting elements in promoter regions 2000 bp from the transcription start site of GhFKBPs. (B) Postion of cis-acting elements in promoter regions. Motif names were shown nearby with different colors

Silencing of GhFKBP13 disrupted the structure of chloroplasts and blocked starch metabolism

We noted that most of GhFKBP genes in group I were predominantly expressed in leaves, and some homologous genes of this group were reported to relate to the chloroplast development [17, 38–39]. Therefore, GhFKBP13 were randomly selected in this group to further explore its function in chloroplast development. To obtain clues on the function of this gene, we performed VIGS analysis. TRV:GhCLA served as the positive control and TRV (empty vector) acted as the negative control. When the true leaves of the positive control plants were albino, the expression of GhFKBP13 was determined via qRT-PCR in both the negative control plants and the GhFKBP13 VIGS plants. The results showed that the leaves of the GhFKBP13 VIGS plants were yellow‒green, while those of the WT and negative control plants were green (Fig. 7A), and the expression level of GhFKBP13 in the VIGS plants was significantly lower than that in the negative control plants (Fig. 7B). Additionally, to investigate whether the loss of leaf color is related to chloroplast changes, we used transmission electron microscopy (TEM) to observe the ultrastructure of chloroplasts in the first leaves of the VIGS and negative control plants (Fig. 7C). Compared with those in the negative control plants, the starch granules in the GhFKBP13 VIGS plants exhibited expansion, and the chloroplasts were damaged. Moreover, in the GhFKBP13 VIGS treatment, the chlorophyll a, chlorophyll b and carotenoid contents were significantly reduced (Fig. 7D). These results indicated that silencing GhFKBP13 probablly interfered with starch metabolism, and led to destruction of the chloroplast structure.

Fig. 7.

Fig. 7

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Phenotypic, physiological and chloroplast structure changes in VIGS-GhFKBP13 leaf of cotton. (A) Phenotype of positive control (TRV: GhCLA), empty control (TRV), VIGS-GhFKBP13 plants (TRV: GhFKBP13), and WT (wild type). (B) The expression level of GhFKBP13 in control and VIGS plants. (C) Transmission electron microscopic observation of the WT and VIGS plants. (a), (b) Ultrastructure of the chloroplast in wild-type leaves at different magnifications. (c), (d) Ultrastructure of the chloroplast in VIGS-GhFKBP13 leaves at different magnifications. bar = 2 microns in (a) and (c), bar = 500 nm in (b) and (d). Cp chloroplast, Thy thylakoid lamellar, Sg starch granule. (D) Analysis of chlorophyll contents. Ca chlorophyll a, Cb chlorophyll b, Cx + c carotenoid. Mean and SD values in (B) and (D) represent three independent replicates (Student’s t test, *P < 0.05; **P < 0.01)

Transcriptome analysis of the mechanism by which GhFKBP13 regulates starch metabolism

To examine the impact of GhFKBP13 inhibition on the global transcriptional profile, three biological replicates of leaves from which GhFKBP13 was silenced and leaves from negative control plants were subjected to RNA-seq analysis. A total of 1892 differential expression genes (DEGs) were obtained by comparing the GhFKBP13-silenced plants and the negative control plants; 871 DEGs were upregulated and 1021 DEGs were downregulated (Table S6, Table S7). The GO enrichment analysis showed that DEGs were most enriched in “response to stimulus”, “response to stress”, “extracellular region” and “response to chemical” (Fig. 8A Table S8). Moreover, DEGs related to chloroplast development and photosynthesis, as well as the starch and sucrose metabolism pathways, were also enriched, including “photosynthesis, light harvesting”, “chloroplast thylakoid membrane protein complex”, “sucrose-induced translational repression”, and “starch catabolic process” related proteins (Table S9). KEGG enrichment analysis showed that 16 pathways were significantly enriched (Fig. 8B, Table S10). Among these pathways, DEGs are most significantly enriched in phenylpropanoid biosynthesis which is an important pathway for lignin biosynthesis and MAPK signaling pathway which plays an important role in the signal transduction processes of plant cells in response to environmental stress. It may be related to the adaptation to the changes in the environment in silencing GhFKBP13 gene plant. In addition, we further analyzed the DEGs in starch and sucrose metabolism pathways, photosynthesis-antenna proteins, protein processing in endoplasmic reticulum pathways, which may related to the chloroplast biogenesis. In photosynthesis-antenna proteins pathway, all 7 DEGs of light-harvesting complex i/ii chlorophyll a/b binding proteins including LHCB1, LHCB2, LHCB3 and LHCB4 were down regulated. In the starch and sucrose metabolism pathway, 11 DEGs including glycosyltransferase, β-amylase, β-fructofuranosidases, sucrose synthase, β-glucosidases and glycogen branching enzyme were down regulated and 7 DEGs including β amylases, glycosyltransferase, trehalose phosphate synthase and α amylase were down regulated. In protein processing in endoplasmic reticulum pathways, 5 DEGs including proteasome inhibitor, small heat shock protein 20, C3HC4 domain gene and disulfide-isomerase were down regulated and 24 DEGs involving small heat shock protein 20, heat shock protein 90, heat shock protein 70, heat shock protein 40, ATPase and ubiquitin fusion degradation protein were up regulated. (Table S11).

Fig. 8.

Fig. 8

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Transcriptome analysis of differentially expressed genes (DEGs) in silencing GhFKBP13 plants. (A) Gene ontology (GO) enrichment analysis of DEGs. (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs. (C) Number of transcription factors (TFs) analysis from the DEGs. The size of the circle represents gene numbers, and the color represents the Pvalue in (A) and (B)

Transcription factors are important regulators that play important roles in plant development. The identification of DEGs related to the transcripts of TF genes was subsequently conducted. A total of 182 TF-encoding genes from 32 different families were identified (Fig. 8C, Table S12). The top six DEGs in the TF-encoding gene family with the largest number of genes were MYB, ERF, NAC, WRKY, bHLH and bZIP TFs. Among the six TF families, the overwhelming majority of the ERF TFs were downregulated, while the majority of the NAC TFs were upregulated. Among the bHLH, MYB and bZIP TFs, more DEGs were downregulated than upregulated. However, for WRKY TFs, the number of upregulated DEGs was equal to the number of downregulated DEGs. In addition, to identify a possible GhFKBP13 transcriptional regulator, we performed the prediction of TFs that regulate GhFKBP13 expression, and 28 TFs were predicted, in which two TFs (zf-Dof and GATA transcription factor) were differentially expressed in GhFKBP13-silenced plants (Table S13). It speculated that these two TFs may play a role in the regulation of GhFKBP13 expression. However, the mechanism underlying the interaction between GhFKBP13 and two TFs (zf-Dof and GATA transcription factor) requires further verification.

Discussion

FKBPs are an important gene family that are widely present in prokaryotes and eukaryotes. In plant, FKBPs have been found to participate in various biological and physiological processes like photosynthetic system reaction, stress response, and growth and development etc [40–44]. However, the identification and analysis of the FKBP gene family in cotton genome have not been reported yet. In this study, FKBP genes were identified from G. hirsutum(48 genes), G. barbadense(47 genes), G. arboreum(28), and G. raimondii(24). It was found that the number of FKBP genes in two tetraploid cotton species (G. hirsutum and G. barbadense) was observed to be almost double that of their progenitors (G. arboretum and G. raimondii) and there is good collinearity between species. These results further support the diploid origin of tetraploid cotton. We noted that FKBP genes in the A subgenome experienced gene loss during the evolution of tetraploid cotton, while the FKBP genes in the D subgenome is relatively conserved, which might be caused by asymmetric subgenome domestication. This speculated that FKBP genes between A and D subgenome might play different roles in the adaptive evolution of cotton. In addition, we found that all the family members arose from WGD or segmental duplication according to synteny block analysis (Table S5), which have shown similar results those some previous studies in cotton [32, 37]. This indicated that WGD or segmental duplication might be a main driver of gene expansion during cotton evolution.

The structure and pattern of protein expression are intricately linked to their function. In the analysis of phylogenetic tree, motif and tissue expression in G. hirsutum, it was found that most of FKBPs in group I had 2–3 conserved motifs and predominant of them were highly expressed in leaves (Fig. 5). Previous reports showed that some homologous FKBPs in group I play roles in chloroplast development. TaFKBP16-1 could interact with the subunit PsaL of PSI(photosystem I), and TaFKBP16-3 was shown to bind to Thf1(Thylakoid formation 1) and APO2(Accumulation of PSI-2), which were involved in the formation of photosynthetic membrane [38]. Peng et al. found that Arabidopsis AtFKBP16-2 plays an important role in the formation of NDH-PS I subcomplexes [39]. Lima et al. showed that AtFKBP20-2 participates specifically in the accumulation of the PSII upercomplex in the chloroplast thylakoid lumen [17]. In this study, we found that GhFKBP13 can also affect chloroplast development. It is generally believed that genes with similar structures and expression patterns have similar biological functions. Therefore, we speculated that these GhFKBPs in group I may play important role in regulating chloroplast biogenesis. In additon, the FKBP genes have also been reported to play an important role in abiotic and biotic stress responses. We noted that most of FKBPs in group II showed ubiquitously expressed across all plant tissues, and many genes in this group were reported to be involved in abiotic stress responses. For example, overexpressing polar moss PaFKBP12 in Arabidopsis showed enhanced resistances to salt, heat, and drought treatments [27]. In Arabidopsis, Overexpressing of maize FKBP gene ZmFKBP20-1 significantly enhanced the tolerances to drought and salt [28]. AtFKBP62 and AtFKBP65 responded to high temperature stress and affect the accumulation of the heat shock transcription factor HsfA2 [45]. In this study, based on gene expression analysis, it was found that these genes in group II showed an up-regulation trend under salt stress and PEG stress, suggesting that these genes may play an important role in responding to adversity stress.

Chloroplasts are important organelles for plant energy conversion and photosynthesis. Within chloroplasts, starch is the primary compound for storing energy in the form of grains and serves as the primary storage for excess carbohydrates produced during photosynthesis. Previous reports have indicated that various genes could interfere with starch metabolism and lead to chloroplasts destruction. For instance, silencing the Nicotiana benthamiana chloroplast thylakoid membrane protein TMP14 (NbTMP14) results in the destruction of most chloroplasts and an enlargement of starch granules [46]. In Arabidopsis thaliana, maltose-excess mutant mex1, which lacks the chloroplast envelope maltose transporter, could accumulate large amounts of starch in chloroplasts, leading to degradation of chloroplasts [47]. Rice mutant lses1 (leaf starch excess and senescence 1) has an obvious excess starch phenotype in leaves, which may lead to chloroplast damage [48]. In this study, a similar phenomenon occured in the GhFKBP13-silenced cotton plants through transmission electron microscope observation. It implied that GhFKBP13 is essential for maintaining chloroplast integrity and starch granule morphology in cotton. In addition, KEGG pathway enrichment analysis showed that starch and sucrose metabolism pathway was enriched in GhFKBP13-silenced plants, including β-fructofuranosidases, sucrose synthase, amylase, β-glucosidases and glycogen branching enzyme. Some of these genes have been previously reported to be associated with starch metabolism. For example, overexpression of Arabidopsis sucrose synthase in tobacco results in increased leaf starch [49]. β-Amylases (BAMs) are key enzymes of transitory starch degradation in chloroplasts, the loss of BAM3 leads to starch-excess phenotype, which is further exacerbated by the loss of BAM1 [50, 51], and bam4 mutants have a starch-excess phenotype [52, 53]. Therefore, It is hypothesized that GhFKBP13 may play an important role in chloroplast development and starch metabolism by regulating the genes involved in this pathway. However, the exact role of the GhFKBP13 gene is still unclear, and further experiments will be conducted to investigate its function and regulatory network.

Conclusions

In this study, a total of 48, 47, 28 and 24 FKBP genes were identified from G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, respectively. Phylogenetic analysis showed that these FKBP family members can be divided into three groups and that FKBP family members were conserved in the evolution of cotton. The WGD/segmental duplication events played a vital role in the expansion of GhFKBPs. When the GhFKBP13 gene was silenced using VIGS, the plant leaves turned yellow-green, and the contents of chlorophyll a, chlorophyll b and carotenoid were significantly reduced. Furthermore, electron microscopy observations revealed damage to the chloroplasts and packing with large starch granules in chloroplasts, indicating that GhFKBP13 may play a critical role in chloroplast biogenesis. This study is the first to systematically analyze the cotton GhFKBP gene family and provides a new understanding the function of GhFKBPs in chloroplast biogenesis in upland cotton.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1 (1.1MB, xlsx)

Acknowledgements

Not applicable.

Author contributions

HZ and YW conceived and designed the project. JL and ZG designed and performed the experiments and wrote the manuscript. GZ prepared materials. ML and ZA contributed bioinformatic analysis.

Funding

This study was funded by Three-three-three talent Project of Hebei Province. (C20221135), Basic Research Funds of Hebei Academy of Agriculture and Forestry Sciences (2024070203), Biological Breeding of Stress tolerant and High Yield Cotton Varieties (NO.2023ZD04040), Cotton Research Institute, Hebei Academy of Agriculture and Forestry Sciences Established project (MHS-2022-04).

Data availability

Data will be made available on request. The data presented in the study are deposited in the GSA, accession number CRA015118. Access it from the following link: https://bigd.big.ac.cn/gsa/browse/CRA015118.

Declarations

Ethics approval and consent to participate

Not applicable. The sampling of plant material was performed in compliance with institutional guidelines. The research conducted in this study required neither approval from an ethics committee, nor involved any human or animal subjects.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Jianguang Liu and Zhao Geng contributed equally to this work.

Contributor Information

Hanshuang Zhang, Email: hanshuangzhang@126.com.

Yongqiang Wang, Email: wangyongqiang502@126.com.

References

  • 1.Schreiber SL. Chemistry and biology of the immunophilins and their immunosuppressive ligands. Science. 1991;251(4991):283–7. [DOI] [PubMed] [Google Scholar]
  • 2.Standaert RF, Galat A, Verdine GL, Schreiber SL. Molecular cloning and overexpression of the human FK506-binding protein FKBP. Nature. 1990;346(6285):671–4. [DOI] [PubMed] [Google Scholar]
  • 3.Nielsen JB, Foor F, Siekierka JJ, Hsu MJ, Ramadan N, Morin N, Shafiee A, Dahl AM, Brizuela L, Chrebet G. Yeast FKBP-13 is a membrane-associated FK506-binding protein encoded by the nonessential gene FKB2. Mol Genet Genomics. 1992;89(16):7471–5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Vallon O. Chlamydomonas immunophilins and parvulins: survey and critical assessment of gene models. Eukaryot Cell. 2005;4(2):230–41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Tomašić Paić A, Fulgosi H. Chloroplast immunophilins. Protoplasma. 2016;253(2):249–58. [DOI] [PubMed] [Google Scholar]
  • 6.Gollan PJ, Bhave M, Aro E. The FKBP families of higher plants: exploring the structures and functions of protein interaction specialists. Febs Lett. 2012;586(20):3539–47. [DOI] [PubMed] [Google Scholar]
  • 7.Ghartey-Kwansah G, Li Z, Feng R, Wang L, Zhou X, Chen FZ, Xu MM, Jones O, Mu Y, Chen S, Bryant J, Isaacs WB, Ma JJ, Xu XH. Comparative analysis of FKBP family protein: evaluation, structure, and function in mammals and Drosophila melanogaster. BMC Dev Biol. 2018;18(1):7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.He Z, Li L, Luan S. Immunophilins and parvulins. Superfamily of Peptidyl Prolyl Isomerases in Arabidopsis. Plant Physiol. 2004;134(4):1248–67. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Nigam N, Singh A, Sahi C, Chandramouli A, Grover A. SUMO-conjugating enzyme (sce) and FK506-binding protein (FKBP) encoding rice (Oryza sativa L.) genes: genome-wide analysis, expression studies and evidence for their involvement in abiotic stress response. Mol Genet Genomics. 2008;279(4):371–83. [DOI] [PubMed] [Google Scholar]
  • 10.Wang WW, Ma Q, Xiang Y, Zhu SW, Cheng BJ. Genome-wide analysis of immunophilin FKBP genes and expression patterns in Zea mays. Genet Mol Res. 2012;11(2):1690–700. [DOI] [PubMed] [Google Scholar]
  • 11.Shangguan L, Kayesh E, Leng X, Sun X, Korir NK, Mu Q, Fang J. Whole genome identification and analysis of FK506-binding protein family genes in grapevine (Vitis vinifera L). Mol Biol Rep. 2013;40(6):4015–31. [DOI] [PubMed] [Google Scholar]
  • 12.Leng X, Liu D, Zhao M, Sun X, Li Y, Mu Q, Zhu X, Li P, Fang J. Genome-wide identification and analysis of FK506-binding protein family gene family in strawberry (Fragaria×ananassa). Gene. 2014;534(2):390–9. [DOI] [PubMed] [Google Scholar]
  • 13.Zhang Y, Han J, Liu D, Wen X, Li Y, Tao R, Peng Y, Fang J, Wang C. Genome-wide identification and analysis of FK506-binding protein gene family in peach (Prunus persica). Gene. 2014;536(2):416–24. [DOI] [PubMed] [Google Scholar]
  • 14.Waseem M, Ahmad F, Habib S, Gao Y, Li Z. Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L). Gene. 2018;678:143–54. [DOI] [PubMed] [Google Scholar]
  • 15.Ge Q, Peng P, Cheng M, Meng Y, Cao Y, Zhang S, Long Y, Li G, Kang G. Genome-wide identification and analysis of FKBP gene family in wheat (Triticum Asetivum). Int J Mol Sci. 2022;23(23):14501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Dong Q, Mao K, Duan D, Zhao S, Wang Y, Wang Q, Huang D, Li C, Liu C, Gong X, Ma FW. Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple. BMC Genomics. 2018;19(1):707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Lima A, Lima S, Wong JH, Phillips RS, Buchanan BB, Luan S. A redox-active FKBP-type immunophilin functions in accumulation of the photosystem II supercomplex in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2006;103(33):12631–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Wang J, Sun W, Kong X, Zhao C, Li J, Chen Y, Gao Z, Zuo K. The peptidyl-prolyl isomerases FKBP15-1 and FKBP15-2 negatively affect lateral root development by repressing the vacuolar invertase VIN2 in Arabidopsis. Planta. 2020;252(4):52. [DOI] [PubMed] [Google Scholar]
  • 19.Vittorioso P, Cowling R, Faure J, Caboche M, Bellini C. Mutation in the Arabidopsis PASTICCINO1 gene, which encodes a new FK506-Binding protein-like protein, has a dramatic effect on plant development. Mol Cell Biol. 1998;18(5):3034–43. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Carol RJ, Breiman A, Erel N, Vittorioso P, Bellini C. PASTICCINO1 (AtFKBP70) is a nuclear-localised immunophilin required during Arabidopsis thaliana embryogenesis. Plant Sci. 2001;161(3):527–35. [Google Scholar]
  • 21.Smyczynski C, Roudier F, Gissot L, Vaillant E, Grandjean O, Morin H, Masson T, Bellec Y, Geelen D, Faure J. The C terminus of the immunophilin PASTICCINO1 is required for plant development and for interaction with a NAC-like transcription factor. J Biol Chem. 2006;281(35):25475–84. [DOI] [PubMed] [Google Scholar]
  • 22.Jääskeläinen T, Makkonen H, Palvimo JJ. Steroid up-regulation of FKBP51 and its role in hormone signaling. Curr Opin Pharmacol. 2011;11(4):326–31. [DOI] [PubMed] [Google Scholar]
  • 23.Li H, Luan S. AtFKBP53 is a histone chaperone required for repression of ribosomal RNA gene expression in Arabidopsis. Cell Res. 2010;20(3):357–66. [DOI] [PubMed] [Google Scholar]
  • 24.Kurek I, Aviezer K, Erel N, Herman E, Breiman A. The wheat peptidyl prolyl cis-trans-isomerase FKBP77 is heat induced and developmentally regulated. Plant Physiol. 1999;119(2):693–704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Magiri EN, Farchi-Pisanty O, Avni A, Breiman A. The expression of the large rice FK506 binding proteins (FKBPs) demonstrate tissue specificity and heat stress responsiveness. Plant Sci. 2006;170(4):695–704. [Google Scholar]
  • 26.Meiri D, Breiman A. Arabidopsis ROF1 (FKBP62) modulates thermotolerance by interacting with HSP90.1 and affecting the accumulation of HsfA2-regulated sHSPs. Plant J. 2009;59(3):387–99. [DOI] [PubMed] [Google Scholar]
  • 27.Alavilli H, Lee H, Park M, Yun DJ, Lee BH. Enhanced multiple stress tolerance in Arabidopsis by overexpression of the polar moss peptidyl prolyl isomerase FKBP12 gene. Plant Cell Rep. 2018;37(3):453–65. [DOI] [PubMed] [Google Scholar]
  • 28.Yu Y, Zhang H, Li W, Mu C, Zhang F, Wang L, Meng Z. Genome-wide analysis and environmental response profifiling of the FK506-binding protein gene family in maize (Zea mays L). Gene. 2012;498(2):212–22. [DOI] [PubMed] [Google Scholar]
  • 29.Huang H, He Y, Cui A, Sun L, Han M, Wang J, Rui C, Lei Y, Liu X, Xu N, Zhang H, Zhang Y, Fan Y, Feng X, Ni K, Jiang J, Zhang X, Chen C, Wang S, Chen X, Lu X, Wang D, Wang J, Yin Z, Qaraevna BZ, Guo L, Zhao L, Ye W. Genome-wide identification of GAD family genes suggests GhGAD6 functionally respond to Cd2+ stress in cotton. Front Genet. 2022;13:13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Li Y, Zhu S, Yao J, Fang S, Li T, Li B, Wang X, Wang M, Wu L, Pan J, Feng X, Chen W, Zhang Y. Genome-wide characterization of the JmjC domain-containing histone demethylase gene family reveals GhJMJ24 and GhJMJ49 involving in somatic embryogenesis process in cotton. Front Mol Biosci. 2022;9:888983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Cheng K, Lei C, Zhang S, Zheng Q, Wei C, Huang W, Xing M, Zhang J, Zhang X, Zhang X. Genome-wide identification and characterization of polycomb repressive complex 2 core components in upland cotton (Gossypium hirsutum L). BMC Plant Biol. 2023;23:166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Jian H, Wei F, Chen P, Hu T, Lv X, Wang B, Wang H, Guo X, Ma L, Lu J, Fu X, Wei H, Yu S. Genome-wide analysis of SET domain genes and the function of GhSDG51 during salt stress in upland cotton (Gossypium hirsutum L). BMC Plant Biol. 2023;23:1653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Yang Y, Sun F, Wang P, Yusuyin M, Kuerban W, Lai C, Li C, Ma J, Xiao F. Genome-wide identification and preliminary functional analysis of BAM (β-Amylase) gene family in upland cotton. Genes. 2023;14(11):2077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Tian M, Wu A, Zhang M, Zhang J, Wei H, Yang X, Ma L, Lu J, Fu X, Wang H, Yu S. Genome-wide identification of the early flowering 4 (ELF4) Gene Family in cotton and silent GhELF4-1 and GhEFL3-6 decreased cotton stress resistance. Front Genet. 2021;6:12686852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Han J, Jawad Umer M, Yang M, Hou Y, Gereziher Mehari T, Zheng J, Wang H, Liu J, Dong W, Xu Y, Wang Y, Liu F, Zhou Z, Cai X. Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi GthICE2 is responsible for cold and drought stress tolerance. Plant Physiol Bioch. 2023;199:107708. [DOI] [PubMed] [Google Scholar]
  • 36.Wang J, Tu Z, Wang M, Zhang Y, Hu Q, Li H. Genome-wide identification of GROWTH-REGULATING FACTORs in Liriodendron chinense and functional characterization of LcGRF2 in leaf size regulation. Plant Physiol Bioch. 2024;206:108204. [DOI] [PubMed] [Google Scholar]
  • 37.Wu C, Xiao S, Zuo D, Cheng H, Zhang Y, Wang Q, Lv L, Song G. Genome-wide analysis elucidates the roles of GhHMA genes in different abiotic stresses and fiber development in upland cotton. Plant Physiol Bioch. 2023;194:281–301. [DOI] [PubMed] [Google Scholar]
  • 38.Gollan PJ, Ziemann M, Bhave M. PPIase activities and interaction partners of FK506-binding proteins in the wheat thylakoid. Physiol Plant. 2011;143(4):385–95. [DOI] [PubMed] [Google Scholar]
  • 39.Peng L, Fukao Y, Fujiwara M, Takami T, Shikanai T. Efficient operation of NAD(P)H dehydrogenase requires supercomplex formation with Photosystem I via minor LHCI in Arabidopsis. Plant Cell. 2009;21(11):3623–40. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Aviezer-Hagai K, Skovorodnikova J, Galigniana M, Farchi-Pisanty O, Maayan E, Bocovza S, Efrat Y, von Koskull-Döring P, Ohad N, Breiman A. Arabidopsis immunophilins ROF1 (AtFKBP62) and ROF2 (AtFKBP65) exhibit tissue specificity, are heat-stress induced, and bind HSP90. Plant Mol Biol. 2007;63(2):237–55. [DOI] [PubMed] [Google Scholar]
  • 41.Bissoli G, Niñoles R, Fresquet S, Palombieri S, Bueso E, Rubio L, García Sánchez MJ, Fernández JA, Mulet JM, Serrano R. Peptidyl-prolyl cis-trans isomerase ROF2 modulates intracellular pH homeostasis in Arabidopsis. Plant J. 2012;70(4):704–16. [DOI] [PubMed] [Google Scholar]
  • 42.Kamphausen T, Fanghänel J, Neumann D, Schulz B, Rahfeld JU. Characterization of Arabidopsis thaliana AtFKBP42 that is membrane-bound and interacts with Hsp90. Plant J. 2002;32(3):263–76. [DOI] [PubMed] [Google Scholar]
  • 43.Luan S, Albers MW, Schreiber SL. Light-regulated, tissue-specific immunophilins in a higher plant. Proc Natl Acad Sci USA. 1994;91(3):984–8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 44.Yu Y, Li Y, Huang G, Meng Z, Zhang D, Wei J, Yan K, Zheng C, Zhang L. PwHAP5, a CCAAT-binding transcription factor, interacts with PwFKBP12 and plays a role in pollen tube growth orientation in Picea Wilsonii. J Exp Bot. 2011;62(14):4805–17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 45.Thirumalaikumar VP, Gorka M, Schulz K, Masclaux-Daubresse C, Sampathkumar A, Skirycz A, Vierstra RD, Balazadeh S. Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1. Autophagy. 2021;17(9):2184–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Zhan J, Shi H, Li W, Zhang C, Zhang Y. NbTMP14 is involved in tomato spotted wilt virus infection and symptom development by interaction with the viral NSm protein. Viruses. 2021;13(3):427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Stettler M, Eicke S, Mettler T, Messerli G, Hörtensteiner S, Zeeman SC. Blocking the metabolism of starch breakdown products in Arabidopsis leaves triggers chloroplast degradation. Mol Plant. 2009;2(6):1233–46. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Chen Z, Wang Y, Huang R, Zhang Z, Huang J, Yu F, Lin Y, Guo Y, Liang K, Zhou Y, Chen F. Integration of transcriptomic and proteomic analyses reveals several levels of metabolic regulation in the excess starch and early senescent leaf mutant lses1 in rice. BMC Plant Biol. 2022;22(1):137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Nguyen QA, Luan S, Wi SG, Bae H, Lee D, Bae H. Pronounced phenotypic changes in transgenic tobacco plants overexpressing sucrose synthase may reveal a novel sugar signaling pathway. Front Plant Sci. 2016;6:1216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 50.Sparla F, Costa A, Lo Schiavo F, Pupillo P, Trost P. Redox regulation of a novel plastid-targeted. Plant Physiol. 2006;141(3):840–50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Monroe JD. Involvement of five catalytically active Arabidopsis β-amylases in leaf starch metabolism and plant growth. Plant Direct. 2020;4(2):e00199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 52.Li J, Francisco P, Zhou W, Edner C, Steup M, Ritte G, Bond CS, Smith SM. Catalytically-inactive β-amylase BAM4 required for starch breakdown in Arabidopsis leaves is a starch-binding-protein. Arch Biochem Biophys. 2009;489(1–2):92–8. [DOI] [PubMed] [Google Scholar]
  • 53.Fulton DC, Stettler M, Mettler T, Vaughan CK, Li J, Francisco P, Gil M, Reinhold H, Eicke S, Messerli G, Dorken G, Halliday K, Smith AM, Smith SM, Zeeman SC. Beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in Arabidopsis chloroplasts. Plant Cell. 2008;20(4):1040–58. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Material 1 (1.1MB, xlsx)

Data Availability Statement

Data will be made available on request. The data presented in the study are deposited in the GSA, accession number CRA015118. Access it from the following link: https://bigd.big.ac.cn/gsa/browse/CRA015118.

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