Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis

Abstract

Ethylene plays a pivotal role in plant stress resistance and 1-aminocyclopropane-1-carboxylic acid synthase (ACS) is the rate-limiting enzyme in ethylene biosynthesis. Upland cotton (Gossypium hirsutum L.) is the most important natural fiber crop, but the function of ACS in response to abiotic stress has rarely been reported in this plant. We identified 18 GaACS, 18 GrACS, and 35 GhACS genes in Gossypium arboreum, Gossypium raimondii and Gossypium hirsutum, respectively, that were classified as types I, II, III, or IV. Collinearity analysis showed that the GhACS genes were expanded from diploid cotton by the whole-genome-duplication. Multiple alignments showed that the C-terminals of the GhACS proteins were conserved, whereas the N-terminals of GhACS10 and GhACS12 were different from the N-terminals of AtACS10 and AtACS12, probably diverging during evolution. Most type II ACS genes were hardly expressed, whereas GhACS10/GhACS12 were expressed in many tissues and in response to abiotic stress; for example, they were highly and hardly expressed at the early stages of cold and heat exposure, respectively. The GhACS genes showed different expression profiles in response to cold, heat, drought, and salt stress by quantitative PCR analysis, which indicate the potential roles of them when encountering the various adverse conditions, and provide insights into GhACS functions in cotton’s adaptation to abiotic stress.

1. Introduction

The growth and development of cotton as well as other plants are regulated by phytohormones, such as jasmonic acid [1,2], ethylene [3,4,5,6,7], indole-3-acetic acid [8,9,10], and gibberellin [11,12,13]. Ethylene is an important and unique gaseous phytohormone that regulates various physiological processes including seed germination, seedling growth, leaf and flower senescence and abscission, photo-morphogenesis, and fruit ripening [14]. In cotton, exogenous ethylene induces leaf abscission in seedlings [15,16], causes alterations of radicle cells [17], and promotes fiber elongation [4]. Gossypium arboreum is known to produce short fiber and Gossypium raimondii has a fiberless phenotype [18]. During fiber development, these two species produce significantly lower and higher levels of ethylene, respectively, than upland cotton (Gossypium hirsutum), the cultivated plant that produces the long and white fiber that is used in the textile industry. Therefore, precise regulation of ethylene biosynthesis is crucial for cotton plant growth and fiber development.

In the Yang cycle, ethylene biosynthesis is completed in two steps: (1) the substrate S-adenosyl methionine is converted to the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and 5′-methylthioadenosine by ACC synthase (ACS); and (2) the substrate ACC is converted to ethylene, CO₂, and cyanide by ACC oxidase [19,20]. Step 1, which involves ACS, is usually regarded as the rate-limiting step in ethylene biosynthesis [21], implying that ACS is the important enzyme in this pathway. The Arabidopsis genome encodes nine ACS enzymes with catalytic activity, two ACS enzymes with aminotransferase activity (AtACS10 and AtACS12), and a pseudogene (AtACS3) [22,23,24]. The nine ACS proteins contain a catalytic domain and were classified as type I, II, or III based on their structure: type I (AtACS1, AtACS2, AtACS6) contains target sites for mitogen-activated protein kinase (MAPK) and calcium-dependent protein kinases (CDPK); type II (AtACS4, 5, 8, 9, 11) contains CDPK and E3 ligase target sites at the C-terminal [23,24]; and type III (AtACS7) has no target site at the C-terminal but can be degraded by the interaction between its N-terminal and E3 ubiquitin-protein ligase XBAT32 [25,26] or protein phosphatases 2C [27]. By contrast, the interaction between ACS and 14-3-3 protein repressed the ubiquitination reaction to maintain the stability of the ACS proteins [28,29]. AtACS2, 6, 7, 8, 11 were shown to participate in pathogen invasion [30]; AtACS7, 9, 11 were reported to maintain homeostasis between ethylene, reactive oxygen species, and the brassinosteroid phytohormones [31]; and AtACS2, 5 were involved in abscisic acid-responsive pathways to regulate plant growth and development [32]. By contrast, AtACS4, 8 were negatively modulated by abscisic acid to reduce ethylene production [33]. ACS5 is stabilized by phosphorylation and ubiquitylation, and these post-translational modifications affected the ethylene biosynthesis pathway, which resulted in the change of ethylene production, thus regulated plant growth and development [26,29,34,35,36]. The ethylene-overproducing mutants eto2 and eto3 of AtACS5 and AtACS9, respectively, result in the missense of the C-terminals of the proteins, and exhibit loss of enzymatic activity, indicating that the conserved C-terminal of the type II AtACSs is critical for AtACS activity and the regulation of ethylene biosynthesis [37,38]. In rice, Os-ACS1, OS-ACS2, and Os-ACS3 could be induced by anaerobiosis and IAA [39] and the Os-ACS5 participated in root-shoot communication during submergence stress and might play a role under low-oxygen stress [40]. In cucumber, the CS-ACS1G is linked to the F locus and plays a pivotal role in the determination of sex in cucumber flowers [41,42]. In pear, the expression PpACS1 was up-regulated under salicylic acid and IAA stress in fruit, indicating that PpACS1 might be involved in fruit ripening and response to SA [43]. In banana, the phosphorylation of serine 476 and 479 residues at the C-terminal region of MA-ACS1 is a key regulatory protein in banana fruit repening [44].

Members of the ACS multigene family are known to play pivotal roles in regulating ethylene biosynthesis, thereby affecting cotton plant growth, especially fiber development [4,18]. In Arabidopsis, ACS genes have been shown to be involved in the response to phytohormones signaling (e.g., abscisic acid), abiotic stresses, pathogens infection, and reactive oxygen species stimulus; however, few studies have reported the response of ACS genes to abiotic stress in cotton. In this study, we identified ACS genes in upland cotton and analyzed their expression patterns as well as the physicochemical properties and conserved domains of the encoded proteins under different abiotic stresses to discover the functional divergence of the ACS genes in response to different abiotic stresses.

2. Results

2.1. Identification and Phylogeny Analysis of the ACS Gene Family in Cotton

In total, 71 ACS genes were identified in cotton, including 35 in G. hirsutum (GhACS), 18 in G. arboreum (GaACS) and 18 in G. raimondii (GrACS). The lengths of the 35 GhACS genes in the genome ranged from 1512 bp (Gh_DACS7.1) to 3254 bp (Gh_AACS2), and the lengths of the protein-coding sequences ranged from 1290 bp (Gh_AACS11.1) to 1632 bp (Gh_AACS10.2). The number of amino acids in the encoded GhACS proteins ranged from 429 (Gh_AACS11.1) to 543 (Gh_AACS5), the molecular weight ranged from 48.32 kDa (Gh_AACS11.1) to 59.704 kDa (Gh_DACS10.1), and the isoelectric points (pI) ranged from 6.381 (Gh_AACS6.1) to 8.957 (Gh_DACS10.2) (Table S1).

To explore the phylogenetic relationship among the cotton ACS genes, 88 ACS protein sequences from cotton, Arabidopsis, and rice were used to construct a phylogenetic tree. As shown in Figure 1, the 88 ACS proteins clustered into four types. Among the cotton ACS proteins, the type I group contained two GhACS1, two GhACS2, and eight GhACS6 proteins; the type II groups contained two GhACS4, two GhACS5, two GhACS8, two GhACS9, and four GhACS11 proteins; the type III group contained four GhACS7; and the type IV group contained four GhACS10 and three GhACS12 proteins (Figure 1). AtACS10 and AtACS12, which were included in the type IV group, have been reported to have no ACS catalytic activity [23].

2.2. Analysis of the C-Terminal of the ACS Proteins

In a previous study, the AtACS proteins were classified as types I–III based on the C-terminal sequence, and the key roles of the ACS C-terminal in function differentiation were recognized [23]. Here, the multiple sequence alignment showed that the GhACS proteins were similar to the AtACS proteins within each type of ACS proteins. All the GhACS proteins contained the catalytic domain (amino acids 26–418 in Gh_AACS1), and the conserved BOX7 sequence in the catalytic domain as shown in Figure 2a. The 12 type I GhACS proteins contained the CDPK and MAPK sites, and the type II GhACS proteins contained only the CDPK motif, except for Gh_AACS11.1, which had no CDPK motif suggesting it may have lost its catalytic function during evolution. Among the two type III ACS proteins, GhACS7 contained a short region that could interact with XBAT32 (Figure 2b) that was similar to the AtACS7 region; the slight difference may be the result of evolution. The type III and IV ACS protein alignment showed that there was an additional long region in the N-terminal of the ACS10 proteins, and several serine/threonine sites in GhACS10 and GhACS12 were different from those in AtACS10 and AtACS12, respectively (Figure 2b).

2.3. Analysis of Chromosomal Distribution, Gene Structure, and Motifs

We identified 17 and 16 GhACS genes on the eight chromosomes of At-subgenome and seven chromosomes of Dt-subgenome, respectively (Figure 3); the remaining two GhACS genes (Gh_AACS6.3 and Gh_DACS6.3) were localized to scaffold3404_A12 and scaffold4588_D12 and are not shown in the figure. The GhACS genes were localized on chromosomes A01, A02, A05, A07, A08, A10, A11, A12, D03, D05, D07, D08, D10, D11, and D12.

The similar exon–intron structure of the GhACS genes suggests that they belong to the same sub-branch in the phylogenetic tree (Figure 4). The numbers of exons and introns in the GhACS genes were similar; 88.6% (31 of 35) GhACS genes had four exons and three introns. The exceptions were Gh_AACS7.1/Gh_DACS7.1 and Gh_AACS6.3/Gh_DACS6.3, which contained only three exons. In all the GhACS genes, the exons closest to the 3′ ends were longer than the exons at the 5′ ends, but the lengths of the introns were significantly different. For example, the third intron of Gh_AACS2 (1173 bp) was 1090 bp longer than the third intron of Gh_AACS5 (83 bp).

Conserved motifs were identified in the GhACS protein sequences and analyzed using HMMScan (https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan, accessed on 6 April 2022) (Figure 4, Table S2). Among them, motifs 1, 2, and 4–7 were aminotransferase classes I and II, motif 3 was the BRK domain, and motif 12 was Fanconi anemia-associated. All the GhACS proteins contained motifs 1–11; GhACS5, GhACS8, and GhACS9 contained a unique motif 14; the type I GhACS proteins contained motif 13; and the type IV GhACS proteins contained motif 12. The differences in the motifs may contribute to the divergence in function of the GhACS proteins.

2.4. Collinearity and Ka:Ks Analysis

G. hirsutum originated from a whole-genome duplication event experienced by G. arboreum and G. raimondii approximately 1–2 million years ago [45], which led to the formation of GhACS gene family. The collinearity analysis detected 50 and 49 pairs of orthologous genes between G. hirsutum and G. arboreum and between G. hirsutum and G. raimondii, respectively, and 35 pairs of paralogous genes were also identified in the upland cotton genome (Figure 5, Table S3). The whole-genome duplication analysis showed that the GhACS genes were expanded by segmental duplication. The paralogous gene pairs are linked with different color lines in Figure 3. No tandem duplications were detected between the GhACS genes. The Ka:Ks ratios (ratio of the number of nonsynonymous substitutions per nonsynonymous site to the number of synonymous substitutions per synonymous site) of all gene duplication were also calculated. The Ka:Ks ratios ranged from 0.058 to 0.861 between GhACS and GaACS, 0 to 0.584 between GhACS and GrACS, and 0.016 to 0.442 for the paralogous genes on the G. hirsutum At and Dt chromosomes. Overall, the Ka:Ks ratios were <1.0 (Figure 6, Table S2).

2.5. Analysis of GhACS Expression Patterns in Tissues and in Plants under Stress

To characterize the ACS expression patterns, we downloaded and re-analyzed RNA-Seq data from NCBI’s SRA database. The heatmap showed that the type I and IV GhACS genes were expressed in most of the tested tissues (Figure 7) and that Gh_AACS1/Gh_DACS1 and Gh_AACS8/Gh_DACS8 were specifically expressed in torus and stamen, respectively. Notably, Gh_AACS6.3/Gh_DACS6.3 and Gh_AACS10/Gh_DACS10 were expressed in all the tissues, suggesting that they may play key roles in the cotton plants’ growth and fiber development, even though ACS6 is not considered as fiber preferential [4]. For other ACS genes, such as the type II GhACS4, GhACS5, GhACS8, GhACS9, and GhACS11 and type III GhACS7 genes, very low or no transcription was detected in the tissues (Figure 7).

Because the ACS genes encode enzymes in the ethylene biosynthesis pathway, and because ethylene plays critical roles in abiotic stress [46,47,48], we used RNA-Seq data to analyze the expression patterns of the GhACS genes in response to cold, heat, salt, and drought. Similar to the findings for GhACS genes in tissues, the type I and IV ACS genes responded to all four abiotic stresses (Figure 8). When the seedlings were exposed to high temperature (37 °C) for 1 h, the expression of Gh_AACS6.4/Gh_DACS6.4 and Gh_AACS10.2 was quickly up- and down-regulated, respectively, and then remained stable, suggesting that these ACS genes responded positively and negatively at the early stage (1 h) of heat stress. Gh_AACS6.4/Gh_DACS6.4 also responded to drought when exposed for 1–3 h, and to salt stress when exposed for 12 h. The expression of Gh_AACS10.1/Gh_DACS10.1 was up-regulated when exposed to low temperature (4 °C) for 6–24 h, indicating that they responded to cold stress. These results suggest that the GhACS genes have functional divergence when the plants are exposed to abiotic stress.

2.6. Analysis of GhACS Genes Expression Patterns in Plants under Abiotic Stress by Quantitative PCR (qPCR)

We performed qPCR analysis to validate the expression patterns of ACS genes in plants under cold (4 °C), hot (37 °C), drought (polyethylene glycol, PEG), and salt (NaCl 400 mM) stress for 0, 1, 3, 6, and 12 h. Gh_AACS1/Gh_DACS1 had similar expression patterns and were up-regulated in response to salt stress after 6–12 h exposure and to heat stress after 1 h exposure, whereas Gh_AACS2, Gh_DACS6.1, Gh_AACS6.2, Gh_DACS6.2, Gh_AACS6.4, and Gh_DACS6.4 were down-regulated in response to salt stress after 6–12 h exposure (Figure 9). Most of the GhACS6 genes responded to PEG-induced drought stress at the early stage, the exception was Gh_AACS6.1. The expression of Gh_AACS10.2, Gh_DACS10.2, and Gh_AACS12.1 did not change in response to drought. Gh_AACS6.1/Gh_DACS6.1 and Gh_AACS6.3/Gh_DACS6.3 responded to cold stress after 12 h exposure, and Gh_AACS7.1, Gh_AACS10.1, Gh_DACS10.1, Gh_AACS10.2, Gh_DACS10.2, and Gh_DACS12.2 responded to cold treatment after 1–3 h. Interestingly, Gh_AACS10.2 and Gh_DACS10.2 showed high expression at the early stage of cold exposure and high expression at the early stage of heat stress. Gh_AACS12.2 and Gh_DACS12.2 both responded to cold and heat stress, whereas Gh_AACS12.1 expression did not change in response to cold or heat stress. These results suggested that GhACS genes are involved in the response to a variety of abiotic stress conditions during cotton growth and development.

3. Discussion

ACSs are recognized as the rate-limiting enzymes in ethylene biosynthesis that determine ethylene accumulation and signal transduction in plant development and abiotic stress tolerance. The different roles of ACSs in response to different abiotic stress and diverse regulatory mechanisms have been widely reported [27,29,46,47,48,49]. Here, we identified 35 ACS genes from cultivated cotton G. hirsutum. The numbers of ACS genes in tetraploid cotton are approximately double the numbers in diploid cotton, indicating that the ACS genes were expanded only through whole-genome-duplication [18]. However, the numbers of ACS genes in a monocot (six in rice) and in a dicot (nine in Arabidopsis) imply that ACS genes may have undergone gene division from angiosperms [50]. In Arabidopsis, AtACS10 and AtACS12 were reported to have no catalytic activity [23], and their function is largely unknown. However, GhACS10/GhACS12, the homologous genes of AtACS10/AtACS12, seem to play roles in cotton plant growth and response to abiotic stress because they were expressed in many tissues, including ovules, stamen, and calycle, and their expression levels changed in response to abiotic stress. The multiple sequence alignment showed several possible phosphorylation sites on serine and threonine residues, which were different from those in the N-terminal of Arabidopsis ACSs, suggesting that GhACS10 and GhACS12 are type IV proteins that may have divergent functions. These findings suggest that the unique ethylene signaling controlled by ACSs seems to occur at different developmental stages or under different environmental conditions and may play essential roles in plant evolution.

Ethylene is a fruit-ripening phytohormone that has multifaceted roles in plants. Ethylene that is synthesized in response to environmental stresses can either exacerbate the symptoms of stress or enhance plant survival depending on the species, age, and the type of stress (VanLoon and Glick 2004). The different effects of ethylene have been explained by the two-phase model proposed by Glick et al. (2007a), in which the ACS-mediated synthesis of additional ACC may be harmful to the plant by causing a second ethylene peak that could result in senescence, chlorosis, and abscission of the plant (Ciardi et al. 2000; VanLoon and Glick 2004). Ethylene usually participates in plants’ abiotic stress responses by regulating the accumulation of reactive oxygen species. In cotton, ethylene production plays key roles in fiber development [4] and the abiotic stress response [12,49,51]. In apple (Malus domestica), the ADP-ribosylation factor MdARF5 bound to the promoter of MdACS1 and MdACS3 to activate ethylene biosynthesis in apple fruit ripening [52]. In Arabidopsis, the type II ACS5 protein acts as a scaffold that links SINAT2 and EOL2 to form a functional complex and increase the stability of ACS5, which is critical for the autophagy stress response triggered by ethylene biosynthesis and brassinosteroid signaling [53]. These findings suggest that ACS may be a central molecular component that can transduce environmental signals into cells via crosstalk with phytohormone pathways. The expression pattern of the GhACS genes in RNA-Seq analysis is not consistent with those in QPCR, which might be attributed to the different genotypes of materials and the sampling methods. In detail, TM-1 and the leaf tissues were planted and sampled in the RNA-Seq experiments; however, the cultivar ZM24 was used in our study and the whole seedlings were sampled for the QPCR. Nevertheless, we found that the transcription of only a few of the GhACS genes changed in response to heat, cold, and osmotic (PEG and NaCl treatment) stresses. GhACS1 was significantly up-regulated after exposure to NaCl for a long time, and GhACS6.3, GhACS7.1, and GhACS10/12 showed different induction patterns in response to cold stress. These results indicate that the type I, III, and IV ACSs, but not the type II ACSs, may be involved in the tolerance of cotton to various abiotic stresses, which is different from the results reported for Arabidopsis ACSs. Serine and threonine are common phosphorylation sites and their phosphorylation can regulate protein activity and stability and is critical for protein function [54,55]. In the type IV ACS proteins, serine/threonine phosphorylation sites were identified in cotton but not in Arabidopsis, indicating that GhACS10 and GhASC12 may have different functions and regulatory mechanisms than the corresponding genes in Arabidopsis. Therefore, the different ACSs may mediate abiotic stresses in different plant species, indicating the functional diversity of ACSs in adapting to external conditions. However, how the cotton ACSs are regulated at both the transcriptional and translational levels is largely unknown, and therefore much effort is needed to explore this.

The ACS enzymes played pivotal roles in plant growth and response to abiotic stress. In this study, we identified GhACS genes in cotton that encoded proteins with diverse motif patterns that function in fiber development and abiotic stress tolerance. The results imply the complexity of ethylene synthesis and signaling in the cotton development and growth. Furthermore, the GhACSs that were found to be involved in different stress conditions may provide clues for further studies of ethylene function in abiotic stress tolerance of cotton.

4. Material and Methods

4.1. Identification of ACS Genes in Cotton

The protein sequences of G. hirsutum, G. arboreum, and G. raimondii were obtained from the CottonGen database (https://www.cottongen.org/, accessed on 3 March 2022), and the protein sequences of rice (Oryza sativa) were obtained from the Phytozome database (https://phytozome-next.jgi.doe.gov/, accessed on 3 March 2022). The sequences of the 12 Arabidopsis ACS proteins were downloaded from The Arabidopsis Information Resource v10 (TAIR10; https://www.arabidopsis.org, accessed on 3 March 2022) and used as the query sequences in BLAST searches (e-value of 1 × 10⁻⁵) against the cotton and rice protein sequences. The domain structure of all the protein sequences was determined using the HMMScan program in the HMMER 3.0 package [56]. Only sequences that contained an aminotransferase class I and II “Aminotran_1_2” (PF00155) domain were considered to be ACS proteins [56]. The taxa labels and gene IDs of the identified ACS proteins are listed in Table S1.

4.2. Phylogenetic Tree Construction

The amino acid sequences of the ACS proteins of A. thaliana, Gossypium, and O. sativa were aligned using the ClustalW program integrated in MEGA 6.06 (v 6.06) software [28]. A neighbor-joining phylogenetic tree was constructed based on the multiple sequence alignment, with the model of p-distance and the bootstrap as 1000 replicates.

4.3. Chromosomal Location, Gene Structure, and Motif Analysis

The physical positions of the upland cotton ACS genes on the chromosomes were obtained from the GFF3 file that we downloaded from the CottonGen database (https://www.cottongen.org/, accessed on 18 April 2022) [57] and visualized usingTBtools [58]. The exon–intron structure of the GhACS genes was visualized using the Gene Structure Display Server v2.0 [59]. The conserved motifs of the GhACS proteins were analyzed using the MEME suite (https://meme-suite.org/meme/, accessed on 6 March 2022) [60] with the following parameters: maximum number of motifs, 15; minimum motif width, 6; and maximum motif width, 50.

4.4. Plant Growth and Tissue Sampling

G. hirsutum cv. ZM24 seedlings were grown in Hoagland nutrient solution for 2 weeks [61]. Then, the seedlings were exposed to PEG-induced drought (20% PEG 6000) [62], cold (4 °C), heat (37 °C), or high salt (400 mM NaCl) conditions [49]. In detail, for the drought and salt treatment, PEG 6000 and NaCl were added into Hoagland nutrient solution with a final concentration of 20% (w/v) and 400 mM, respectively. For the cold and hot stress, the plants were put into 4 °C and 37 °C conditions. The seedlings were sampled at 0, 1, 3, 6, and 12 h, after the abiotic stress treatment, there were three biological replicates.

4.5. Expression Patterns Analysis

For the RNA-Seq data analysis, the raw transcriptome data were downloaded from NCBI’s SRA database (PRJNA490626) [63], and analyzed using the HISAT2-StringTie software [64,65,66]. The expression patterns were visualized using TBtools with a homogenize method of log₂(FPKM+1) [58].

For the qPCR analysis, total RNA was extracted using the RNAprep Pure Kit (for polysaccharides and polyphenolics-rich plants) (Tiangen, Beijing, China). The RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and the quality was determined by 1% agarose gel electrophoresis. The absorbance ratio A260/280 was 1.8–2.1. Approximately 1 μg RNA was used as the template to synthesize cDNA using TransScript II All-in-One First-Strand cDNA Synthesis SuperMix for qPCR (AT301-02, TransGen) according to the manufacturer’s instructions. The qPCR experiments were performed using a LightCycler 480 system with a SYBR-Green Real-time PCR SuperMix (AQ101-01, TransGen), with three biological and three technical replicates for each sample. The cotton histone 3 gene (GhHistone3; AF024716) was used as the internal gene. The 2^−∆ Ct method was used to calculate the relative expression of each gene, with three technical repetitions and three biological repetitions [67]. Data are shown as mean ± SD. The Student’s t-test was used for the significance statistic. The primer sequences were designated using NCBI Primer-BLAST (https://blast.ncbi.nlm.nih.gov/, accessed on 10 March 2022) and are listed in Table S4.