Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors

Genome-wide characterization of phospholipase D family genes in allotetraploid peanut and its diploid progenitors revealed their crucial roles in growth and abiotic stress responses

Abiotic stresses such as cold, drought and salinity are the key environmental factors that limit the yield and quality of oil crop peanut. Phospholipase Ds (PLDs) are crucial hydrolyzing enzymes involved in lipid mediated signaling and have valuable functions in plant growth, development and stress tolerance. Here, 22, 22 and 46 PLD genes were identified in Arachis duranensis, Arachis ipaensis and Arachis hypogaea, respectively, and divided into α, β, γ, δ, ε, ζ and φ isoforms. Phylogenetic relationships, structural domains and molecular evolution proved the conservation of PLDs between allotetraploid peanut and its diploid progenitors. Almost each A. hypogaea PLD except for AhPLDα6B had a corresponding homolog in A. duranensis and A. ipaensis genomes. The expansion of Arachis PLD gene families were mainly attributed to segmental and tandem duplications under strong purifying selection. Functionally, the most proteins interacting with AhPLDs were crucial components of lipid metabolic pathways, in which ahy-miR3510, ahy-miR3513-3p and ahy-miR3516 might be hub regulators. Furthermore, plenty of cis-regulatory elements involved in plant growth and development, hormones and stress responses were identified. The tissue-specific transcription profiling revealed the broad and unique expression patterns of AhPLDs in various developmental stages. The qRT-PCR analysis indicated that most AhPLDs could be induced by specific or multiple abiotic stresses. Especially, AhPLDα3A, AhPLDα5A, AhPLDβ1A, AhPLDβ2A and AhPLDδ4A were highly up-regulated under all three abiotic stresses, whereas AhPLDα9A was neither expressed in 22 peanut tissues nor induced by any abiotic stresses. This genome-wide study provides a systematic analysis of the Arachis PLD gene families and valuable information for further functional study of candidate AhPLDs in peanut growth and abiotic stress responses.

Characterization and Expression of Phospholipase D Putatively Involved in Colletotrichummusae Disease Development of Postharvest Banana Fruit

Phospholipase D (PLD) in plants plays an important role in growth, development, and stress response. The effect of hexanal on PLD in banana fruit responding to Colletotrichum musae infection remains poorly understood. In this study, four putative PLD genes, named as MaPLD1, MaPLD2, MaPLD3, and MaPLD4 were identified from banana fruit. The four MaPLDs can be classified into three of the seven known PLD families according to sequence characterization. Their deduced amino acid sequences displayed homology of PLDs from other plant species. Furthermore, the specific expression analysis of PLD genes in banana fruit in response to infection in C. musae was studied and the response relationship between PLD family members and banana fruit under anthracnose stress was clarified. Changes in both the activity of PLD and PLC, and the connection between hexanal and phospholipases in the banana fruit C. musae infection were compared. The results showed that the incidence of disease in banana inoculated with C. musae was dramatically increased after 6 days of storage, the activation of PLD and PLC in infected anthracnose fruit before disease development, and that this activation was inhibited by hexanal treatment, which suggested that both enzymes play a protective role in banana fruit to cope with C. musae infection and the participation of hexanal in their regulation. Of the four MaPLD genes, the anthracnose had a stronger effect on MaPLD1 and MaPLD4. These data demonstrated that hexanal treatment could enhance fruit disease resistance to C. musae, and that PLD could take part in the disease defensive system of harvested banana fruit to C. musae by modulating the metabolism of cell membrane lipids, and thus suppress disease development in C. musae -inoculated banana during storage.

Genome-wide in silico identification of phospholipase D (PLD) gene family from Corchorus capsularis and Corchorus olitorius: reveals their responses to plant stress

Background

Plant grows in nature facing various types of abiotic stresses for their normal growth and development. During abiotic stress, plants evolve different types of mechanisms to survive in a hostile environment. Phospholipase D (PLD) plays important role in the regulation of diverse cellular processes including stress responses in plants. Member of PLD genes are well studied in different model plants; however, their functions in the jute are not clear yet.

Result

In the present study, a total of 12 and 11 PLD genes were identified in the genome of C. capsularis and C. olitorius, respectively. The presence of the two conserved HKD motifs in PLD genes except for CoPLDδ-2 in jute suggests their strong lipase activity. Twenty different motifs were found in the identified PLD genes, and PLD-β1, PLD-γ1, and all members of PLD-δ1 of both jute species contained the highest number of motifs. Phylogenetic analysis showed the close evolutionary relationship among the five groups of jute PLD proteins along with the PLD proteins from Arabidopsis. Tissue-specific expression pattern of PLDα1-2, PLD-α2, PLDβ1, PLDγ1, and PLDδ1 of two jute species suggested their involvement in plant growth and development. However, the expression pattern of PLDα1-2, PLDα1-3, PLD-α4, PLDδ1, and PLDδ3 indicated their association during waterlogging stress. In addition, PLD-α2, PLDβ1, and PLDδ2 seemed to be involved in drought stress as well as salinity stress.

Conclusion

This genome-wide identification of jute PLD genes from C. capsularis and C. olitorius will help to further functional characterization of the PLD genes for developing stress-tolerant jute variety.

Genome-Wide Analysis of the Phospholipase D Family in Five Cotton Species, and Potential Role of GhPLD2 in Fiber Development and Anther Dehiscence

Phospholipase D (PLD) and its hydrolysis product phosphatidic acid play an important role in the regulation of several cellular processes, including root growth, pollen tube elongation, and microtubule reorganization. Here, we systematically identified and analyzed the membership, characterization, and evolutionary relationship of PLDs in five species of cotton. The results of the transcriptomic analysis suggested that the evaluated PLD genes showed high expression levels in anther tissue and during the fiber initiation and elongation periods. Quantitative real-time polymerase chain reaction showed differential expression of GhPLD genes in the anthers of photoperiod sensitive male sterility mutant 5 (psm5). Previous research on multiple stable quantitative trait loci also suggests the role of PLD genes in the fiber development. Further analyses showed that GhPLD2 protein is localized to the plasma membrane. The virus-induced gene silencing of GhPLD2 in cotton seedlings repressed its expression by 40-70%, which led to a reduction in reactive oxygen species (ROS) levels, 22% anther indehiscence, and disrupted fiber initiation and elongation. Thus, we inferred that GhPLD2 may promote ROS production, which, in turn, may regulate anther dehiscence and fiber development.

Genome-Wide Analysis and Expression Profiling of the Phospholipase D Gene Family in Solanum tuberosum

Phospholipase D (PLD) is the most important phospholipid hydrolase in plants, which can hydrolyze phospholipids into phosphatidic acid (PA) and choline. When plants encounter low temperature, drought and high salt stress, phospholipase D and its products play an important role in regulating plant growth and development and coping with stress. In this study, 16 members of StPLD gene family were identified in potato genome, which were distributed in α, β, δ, and ζ subfamilies, and their expression patterns under salt, high temperature, drought, and ABA stress were detected by qRT-PCR method. Gene expression analysis showed that the expression of StPLD genes in potato was upregulated and downregulated to varying degrees under the four stresses, indicating that the PLD gene family is involved in the interaction of potato plant hormones and abiotic stress signals. Chromosome distribution showed that StPLD gene was unevenly distributed on 8 chromosomes, and only one pair of tandem repeat genes was found. All StPLD promoters contain hormone and stress-related cis-regulatory elements to respond to different stresses. Structural analysis showed that StPLD genes in the same subgroup had a similar exon-intron structure. Our study provides a valuable reference for further research of the function and structure of PLD gene.

Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress

Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of TLP gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in Gossypium species has not been reported till date. Here, we systematically identified 105 TLP gene family members in cotton (Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense) genomes and classified them into eight phylogenetic groups. Cotton TLP12 gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton TLP gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton TLPs paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of GhTLPs indicated that GhTLP11A and GhTLP12A.1 genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and cis-regulatory elements of GhTLP11A and GhTLP12A.1 genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of GhTLP11A and GhTLP12A.1 genes in exerting control over salt and drought stress responses in G. hirsutum and also provides a reference for future research, elaborating the biological roles of G. hirsutum TLPs in both stress responses.

Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis)

Phospholipase D (PLD) (EC 3.1.4.4) plays important roles in plants growth, development, and response to environmental stresses. Tea plant (Camellia sinensis) is the most important non-alcoholic beverage in the world with health benefits, but tea production decreases in response to environmental stresses such as cold and drought. Therefore, a genome-wide analysis of the C. sinensis PLD gene family (CsPLDs) was carried out. In the current study, identification, evolutionary relationship, duplication, selection pressure, gene structure, promoter analysis, transcript-targeted miRNA, and simple sequence repeat markers prediction, RNA-seq data analysis, and three-dimensional structure of the CsPLDs have been investigated using bioinformatics tools. 15 PLDs were identified from the tea genome which belongs to five groups, including CsPLDα, CsPLDβ, CsPLDδ, CsPLDε, and CsPLDζ. Both segmental and tandem duplications have occurred in the CsPLD gene family. Ka/Ks ratio for the most duplicated pair genes was less than 1 which implies negative selection to conserve their function during the tea evolution. 68 cis-elements have been found in CsPLDs indicating the contribution of these genes in response to environmental stresses. Likewise, 72 SSR loci and 96 miRNA molecules in 14 and 15 CsPLDs have been detected. According to RNA-seq data, the highest expression in all tissues under various abiotic stresses was related to CsPLDα1. Besides, a three-dimensional structure of the CsPLDα1 was evaluated to better understand its biological activity. This research provides comprehensive information that could be useful in future studies to develop stress-tolerant tea.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01007-0.

Genome-Wide Analysis of Phospholipase D Gene Family and Profiling of Phospholipids under Abiotic Stresses in Brassica napus

Oil crop Brassica napus is subjected to environmental stresses such as drought, cold and salt. Phospholipase Ds (PLDs) have vital roles in regulation of plant growth, development and stress tolerance. In this study, 32 BnaPLD genes were identified and classified into six subgroups depending on the conserved protein structures. High similarity in gene and protein structures exists between BnaPLDs and AtPLDs. Gene expression analysis showed that BnaPLDα1s and BnaPLDδs had higher expression than other PLDs. BnaPLDα1 and BnaPLDδ were significantly induced by abiotic stresses including dehydration, NaCl, abscisic acid (ABA) and 4�C. Lipidomic analysis showed that the content of main membrane phospholipids decreased gradually under stresses, except phosphatidylglycerol increased under the treatment of ABA and phosphatidylethanolamine increased under 4�C. Correspondingly, their product of phosphatidic acid increased often with a transient peak at 8 h. The plant height of mutants of PLDα1 was significantly reduced. Agronomic traits such as yield, seed number, silique number and branches were significantly impaired in PLDα1 mutants. These results indicate that there is a large family of PLD genes in B. napus, especially BnaPLDα1s and BnaPLDδs may play important roles in membrane lipids remodeling and maintaining of the growth and stress tolerance of B. napus.

Phytophthora infestans small phospholipase D-like proteins elicit plant cell death and promote virulence

The successful invasion of host tissue by (hemi-)biotrophic plant pathogens is dependent on modifications of the host plasma membrane to facilitate the two-way transfer of proteins and other compounds. Haustorium formation and the establishment of extrahaustorial membranes are probably dependent on a variety of enzymes that modify membranes in a coordinated fashion. Phospholipases, enzymes that hydrolyse phospholipids, have been implicated as virulence factors in several pathogens. The oomycete Phytophthora infestans is a hemibiotrophic pathogen that causes potato late blight. It possesses different classes of phospholipase D (PLD) proteins, including small PLD-like proteins with and without signal peptide (sPLD-likes and PLD-likes, respectively). Here, we studied the role of sPLD-like-1, sPLD-like-12 and PLD-like-1 in the infection process. They are expressed in expanding lesions on potato leaves and during in vitro growth, with the highest transcript levels in germinating cysts. When expressed in planta in the presence of the silencing suppressor P19, all three elicited a local cell death response that was visible at the microscopic level as autofluorescence and strongly boosted in the presence of calcium. Moreover, inoculation of leaves expressing the small PLD-like genes resulted in increased lesion growth and greater numbers of sporangia, but this was abolished when mutated PLD-like genes were expressed with non-functional PLD catalytic motifs. These results show that the three small PLD-likes are catalytically active and suggest that their enzymatic activity is required for the promotion of virulence, possibly by executing membrane modifications to support the growth of P. infestans in the host.

Study of the Involvement of Phosphatidic Acid Formation in the Expression of Wound-Responsive Genes in Cotton

Plants use phospholipase D (PLD, EC 3.1.4.4)/phosphatidic acid (PtdOH) for the transduction of environmental signals including those coming from wounding. Based on our previous findings suggesting that wound-induced PLDα-derived PtdOH can act as a local signaling molecule in cotton (Gossypium hirsutum), we show that wounding immediately increases local NADPH oxidase (NADPHox) and cellulose synthase A (CeSA) gene expression. After developing a novel fluorimetric assay for the investigation of n-butanol inhibitory effect on PLD activity, we show that only NADPHox gene upregulation is reduced when n-butanol is applied prior to wounding. This suggests that NADPHox is a possible downstream target of PLD function, while a different CeSA-involving response system may exist in cotton. Overall, this study provides new knowledge on signal-transduction mechanisms following wounding of cotton leaves.

Genome-wide comparative and evolutionary analysis of Calmodulin-binding Transcription Activator (CAMTA) family in Gossypium species

The CAMTA gene family is crucial in managing both biotic and abiotic stresses in plants. Our comprehensive analysis of this gene family in cotton resulted in the identification of 6, 7 and 9 CAMTAs in three sequenced cotton species, i.e., Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, respectively. All cotton CAMTAs were localized in the nucleus and possessed calmodulin-binding domain (CaMBD) as identified computationally. Phylogenetically four significant groups of cotton CAMTAs were identified out of which, Group II CAMTAs experienced higher evolutionary pressure, leading to a faster evolution in diploid cotton. The expansion of cotton CAMTAs in the genome was mainly due to segmental duplication. Purifying selection played a significant role in the evolution of cotton CAMTAs. Expression profiles of GhCAMTAs revealed that GhCAMTA2A.2 and GhCAMTA7A express profoundly in different stages of cotton fiber development. Positive correlation between expression of these two CAMTAs and fiber strength confirmed their functional relevance in fiber development. The promoter region of co-expressing genes network of GhCAMTA2A.2 and GhCAMTA7A showed a higher frequency of occurrence of CAMTA binding motifs. Our present study thus contributes to broad probing into the structure and probable function of CAMTA genes in Gossypium species.

Expression Profiling of Mitogen-Activated Protein Kinase Genes Reveals Their Evolutionary and Functional Diversity in Different Rubber Tree (Hevea brasiliensis) Cultivars

Rubber tree (Heveabrasiliensis) is the only commercially cultivated plant for producing natural rubber, one of the most essential industrial raw materials. Knowledge of the evolutionary and functional characteristics of kinases in H. brasiliensis is limited because of the long growth period and lack of well annotated genome information. Here, we reported mitogen-activated protein kinases in H. brasiliensis (HbMPKs) by manually checking and correcting the rubber tree genome. Of the 20 identified HbMPKs, four members were validated by proteomic data. Protein motif and phylogenetic analyses classified these members into four known groups comprising Thr-Glu-Tyr (TEY) and Thr-Asp-Tyr (TDY) domains, respectively. Evolutionary and syntenic analyses suggested four duplication events: HbMPK3/HbMPK6, HbMPK8/HbMPK9/HbMPK15, HbMPK10/HbMPK12 and HbMPK11/HbMPK16/HbMPK19. Expression profiling of the identified HbMPKs in roots, stems, leaves and latex obtained from three cultivars with different latex yield ability revealed tissue- and variety-expression specificity of HbMPK paralogues. Gene expression patterns under osmotic, oxidative, salt and cold stresses, combined with cis-element distribution analyses, indicated different regulation patterns of HbMPK paralogues. Further, Ka/Ks and Tajima analyses suggested an accelerated evolutionary rate in paralogues HbMPK10/12. These results revealed HbMPKs have diverse functions in natural rubber biosynthesis, and highlighted the potential possibility of using MPKs to improve stress tolerance in future rubber tree breeding.

Molecular characterization of GhPLDα1 and its relationship with secondary cell wall thickening in cotton fibers

Phospholipase D (PLD) hydrolyzes phospholipids to generate a free polar head group (e.g., choline) and a second messenger phosphatidic acid and plays diverse roles in plant growth and development, including seed germination, leaf senescence, root hair growth, and hypocotyl elongation. However, the function of PLD in cotton remains largely unexplored. Here, the comprehensive molecular characterization of GhPLDα1 was explored with its role in upland cotton (Gossypium hirsutum) fiber development. The GhPLDα1 gene was cloned successfully, and a sequence alignment showed that GhPLDα1 contains one C2 domain and two HKD (HxKxxxxD) domains. Quantitative reverse transcriptase-polymerase chain reaction measured the expression of GhPLDα1 in various cotton tissues with the highest level in fibers at 20 days post anthesis (d.p.a.). Fluorescent microscopy and immunoblotting in tobacco epidermis showed the GhPLDα1 distribution in both cell membranes and the cytoplasm. An activity assay indicated changes in PLDα enzyme activity in developing fiber cells with a peak level at 20 d.p.a., coinciding with the onset of cellulose accumulation and the increased H₂O₂ content during fiber development. Furthermore, the inhibition of PLDα activity obviously decreased the cellulose and H₂O₂ contents of in vitro-cultured cotton fibers. These results provide important evidence explaining the relationship of GhPLDα1 with secondary cell wall thickening in cotton fibers in that GhPLDα1 may correlate with the increased H₂O₂ content at the onset of secondary cell wall thickening, ultimately promoting cellulose biosynthesis.

Phospholipases Dα and δ are involved in local and systemic wound responses of cotton (G. hirsutum)

Phospholipases D (PLDs) catabolize structural phospholipids to produce phosphatidic acid (PtdOH), a lipid playing central role in signalling pathways in animal, yeast and plant cells. In animal cells two PLD genes have been studied while in model plant Arabidopsis twelve genes exist, classified in six classes (α-ζ). This underlines the role of these enzymes in plant responses to environmental stresses. However, information concerning the PLD involvement in the widely cultivated and economically important cotton plant responses is very limited. The aim of this report was to study the activity of conventional cotton PLD and its participation in plant responses to mechanical wounding, which resembles both biotic and abiotic stresses. PLDα activity was identified and further characterized by transphosphatidylation reaction. Upon wounding, cotton leaf responses consist of an acute in vitro increase of PLDα activity in both wounded and systemic tissue. However, determination of the in vivo PtdOH levels under the same wounding conditions revealed a rapid PtdOH formation only in wounded leaves and a late response of a PtdOH increase in both tissues. Εxpression analysis of PLDα and PLDδ isoforms showed mRNA accumulation of both isoforms in the wounded tissue, but only PLDδ exerts a high and sustainable expression in systemic leaves, indicating that this isoform is mainly responsible for the systemic wound-induced PtdOH production. Therefore, our data suggest that PLDα and PLDδ isoforms are involved in different steps in cotton wound signalling.

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PLDα activity and PtdOH levels rapidly increase in wounded cotton leaves.

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PLDα is also activated rapidly in systemic tissue.

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Doubling of PtdOH levels occurs as a late response in both wounded and systemic tissue.

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PLDδ (but not PLDα) exerts a high and sustainable expression in systemic leaves.

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PLDα and PLDδ are involved in different steps in cotton wound signalling.

GhMCS1, the Cotton Orthologue of Human GRIM-19, Is a Subunit of Mitochondrial Complex I and Associated with Cotton Fibre Growth

GRIM-19 (Gene associated with Retinoid-Interferon-induced Mortality 19) is a subunit of mitochondrial respiratory complex I in mammalian systems, and it has been demonstrated to be a multifunctional protein involved in the cell cycle, cell motility and innate immunity. However, little is known about the molecular functions of its homologues in plants. Here, we characterised GhMCS1, an orthologue of human GRIM-19 from cotton (Gossypium hirsutum L.), and found that it was essential for maintaining complex integrity and mitochondrial function in cotton. GhMCS1 was detected in various cotton tissues, with high levels expressed in developing fibres and flowers and lower levels in leaves, roots and ovules. In fibres at different developmental stages, GhMCS1 expression peaked at 5-15 days post anthesis (dpa) and then decreased at 20 dpa and diminished at 25 dpa. By Western blot analysis, GhMCS1 was observed to be localised to the mitochondria of cotton leaves and to colocalise with complex I. In Arabidopsis, GhMCS1 overexpression enhanced the assembly of complex I and thus respiratory activity, whereas the GhMCS1 homologue (At1g04630) knockdown mutants showed significantly decreased respiratory activities. Furthermore, the mutants presented with some phenotypic changes, such as smaller whole-plant architecture, poorly developed seeds and fewer trichomes. More importantly, in the cotton fibres, both the GhMCS1 transcript and protein levels were correlated with respiratory activity and fibre developmental phase. Our results suggest that GhMCS1, a functional ortholog of the human GRIM-19, is an essential subunit of mitochondrial complex I and is involved in cotton fibre development. The present data may deepen our knowledge on the potential roles of mitochondria in fibre morphogenesis.