The putative phytocyanin genes in Chinese cabbage (Brassica rapa L.): genome-wide identification, classification and expression analysis

Molecular evolution of Phytocyanin gene and analysis of expression at different coloring periods in apple (Malus domestica)

BACKGROUND

PC (phytocyanin) is a class of copper-containing electron transfer proteins closely related to plant photosynthesis, abiotic stress responses growth and development in plants, and regulation of the expression of some flavonoids and phenylpropanoids, etc., however, compared with other plants, the PC gene family has not been systematically characterized in apple.

RESULTS

A total of 59 MdPC gene members unevenly distributed across 12 chromosomes were identified at the genome-wide level. The proteins of the MdPC family were classified into four subfamilies based on differences in copper binding sites and glycosylation sites: Apple Early nodulin-like proteins (MdENODLs), Apple Uclacyanin-like proteins (MdUCLs), Apple Stellacyanin-like proteins (MdSCLs), and Apple Plantacyanin-like proteins (MdPLCLs). Some MdPC members with similar gene structures and conserved motifs belong to the same group or subfamily. The internal collinearity analysis revealed 14 collinearity gene pairs among members of the apple MdPC gene. Interspecific collinearity analysis showed that apple had 31 and 35 homologous gene pairs with strawberry and grape, respectively. Selection pressure analysis indicated that the MdPC gene was under purifying selection. Prediction of protein interactions showed that MdPC family members interacted strongly with the Nad3 protein. GO annotation results indicated that the MdPC gene also regulated the biosynthesis of phenylpropanoids. Chip data analysis showed that (MdSCL3, MdSCL7 and MdENODL27) were highly expressed in mature fruits and peels. Many cis-regulatory elements related to light response, phytohormones, abiotic stresses and flavonoid biosynthetic genes regulation were identified 2000 bp upstream of the promoter of the MdPC gene, and qRT-PCR results showed that gene members in Group IV (MdSCL1/3, MdENODL27) were up-regulated at all five stages of apple coloring, but the highest expression was observed at the DAF13 (day after fruit bag removal) stage. The gene members in Group II (MdUCL9, MdPLCL3) showed down-regulated or lower expression in the first four stages of apple coloring but up-regulated and highest expression in the DAF 21 stage.

CONCLUSION

Herein, one objective of these findings is to provide valuable information for understanding the structure, molecular evolution, and expression pattern of the MdPC gene, another major objective in this study was designed to lay the groundwork for further research on the molecular mechanism of PC gene regulation of apple fruit coloration.

Identification and Characterization of Phytocyanin Family Genes in Cotton Genomes

Phytocyanins (PCs) are a class of plant-specific blue copper proteins that have been demonstrated to play a role in electron transport and plant development. Through analysis of the copper ligand residues, spectroscopic properties, and domain architecture of the protein, PCs have been grouped into four subfamilies: uclacyanins (UCs), stellacyanins (SCs), plantacyanins (PLCs), and early nodulin-like proteins (ENODLs). The present study aimed to identify and characterise the PCs present in three distinct cotton species (Gossypium hirsutum, Gossyium arboreum, and Gossypium raimondii) through the identification of 98, 63, and 69 genes respectively. We grouped PCs into four clades by using bioinformatics analysis and sequence alignment, which exhibit variations in gene structure and motif distribution. PCs are distributed across all chromosomes in each of the three species, with varying numbers of exons per gene and multiple conserved motifs, and with a minimum of 1 and maximum of 11 exons found on one gene. Transcriptomic data and qRT-PCR analysis revealed that two highly differentiated PC genes were expressed at the fibre initiation stage, while three highly differentiated PCs were expressed at the fibre elongation stage. These findings serve as a foundation for further investigations aimed at understanding the contribution of this gene family in cotton fibre production.

The gene LpBCP increased NaHCO3 resistance by enhancing lignin or ROS scavenging in the Nicotiana benthamiana

Lilium pumilum is an excellent wildflower germplasm resource with high resistance to salinity stress. The gene LpBCP plays an important role in salinity tolerance of L. pumilum. Studying the molecular mechanism of salinity resistance in L. pumilum will provide insights into multiple aspects, including breeding better varieties, environmental protection, improving soil conditions, etc. Conventional methods were used to determine different physiological indicators of Nicotiana benthamiana after NaHCO₃ treatment, i.e. chlorophyll content, soluble phenol content and lignin content. RT-qPCR was carried out to find expression of LpBCP in different organs and under abiotic stresses. DAB was used to detect H₂ O₂ in leaves in situ. A yeast two-hybrid system was used to screen for LpBCP interacting proteins. LpBCP was cloned from bulbs of L. pumilum. The highest expression of LpBCP was in roots and bulbs of transgenic plants. LpBCP-overexpressed plants showed less wilting, compared to WT plants. LpBCP transgenic plants have higher chlorophyll, soluble phenol and lignin content, and lower relative conductivity under 500 mM NaHCO₃ stress. In addition, H₂ O₂ scavenging in transgenic plants was much improved, indicating increased resistance to NaHCO₃ stress. Thirteen LpBCP-interacting proteins were screened using the yeast two-hybrid method and five were associated with salt stress. Based on our findings, LPBCP could be a key gene that can be used to improve L. pumilum salt tolerance.

GhENODL6 Isoforms from the Phytocyanin Gene Family Regulated Verticillium Wilt Resistance in Cotton

Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae, currently devastates cotton fiber yield and quality seriously, yet few resistance germplasm resources have been discovered in Gossypium hirsutum. The cotton variety Nongda601 with suitable VW resistance and high yield was developed in our lab, which supplied elite resources for discovering resistant genes. Early nodulin-like protein (ENODL) is mainly related to nodule formation, and its role in regulating defense response has been seldom studied. Here, 41 conserved ENODLs in G. hirsutum were identified and characterized, which could divide into four subgroups. We found that GhENODL6 was upregulated under V. dahliae stress and hormonal signal and displayed higher transcript levels in resistant cottons than the susceptible. The GhENODL6 was proved to positively regulate VW resistance via overexpression and gene silencing experiments. Overexpression of GhENODL6 significantly enhanced the expressions of salicylic acid (SA) hormone-related transcription factors and pathogenicity-related (PR) protein genes, as well as hydrogen peroxide (H₂O₂) and SA contents, resulting in improved VW resistance in transgenic Arabidopsis. Correspondingly, in the GhENODL6 silenced cotton, the expression levels of both phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) genes significantly decreased, leading to the reduced SA content mediating by the phenylalanine ammonia lyase pathway. Taken together, GhENODL6 played a crucial role in VW resistance by inducing SA signaling pathway and regulating the production of reactive oxygen species (ROS). These findings broaden our understanding of the biological roles of GhENODL and the molecular mechanisms underlying cotton disease resistance.

A mutation in the promoter of the arabinogalactan protein 7-like gene PcAGP7-1 affects cell morphogenesis and brassinolide content in pear (Pyrus communis L.) stems

Dwarfing rootstocks and dwarf cultivars are urgently needed for modern pear cultivation. However, germplasm resources for dwarfing pear are limited, and the underlying mechanisms remain unclear. We previously showed that dwarfism in pear is controlled by the single dominant gene PcDw (Dwarf). We report here that the expression of PcAGP7-1 (ARABINOGALACTAN PROTEIN 7-1), a key candidate gene for PcDw, is significantly higher in dwarf-type pear plants because of a mutation in an E-box in the promoter. Electrophoretic mobility shift assays and transient infiltration showed that the transcription factors PcBZR1 and PcBZR2 could directly bind to the E-box of the PcAGP7-1 promoter and repress transcription. Moreover, transgenic pear lines overexpressing PcAGP7-1 exhibited obvious dwarf phenotypes, whereas RNA interference pear lines for PcAGP7-1 were taller than controls. PcAGP7-1 overexpression also enhanced cell wall thickness, affected cell morphogenesis, and reduced brassinolide (BL) content, which inhibited BR signaling via a negative feedback loop, resulting in further dwarfing. Overall, we identified a dwarfing mechanism in perennial woody plants involving the BL-BZR/BES-AGP-BL regulatory module. Our findings provide insight into the molecular mechanism of plant dwarfism and suggest strategies for the molecular breeding of dwarf pear cultivars.

Comparative analysis of the stellacyanins (SCs) family and focus on drought resistance of PtSC18 in Populus trichocarpa

Stellacyanin (SC) is a type I (blue) copper protein, which plays a crucial role in plant growth and stress response. However, the comprehensive analysis and functional research of SCs in the woody plant is still lacking. Here, a total of 74 SCs were collected and identified from Arabidopsis, papaya, grape, rice and poplar. Bioinformatics was used to analyze the gene structure, protein structure and evolutionary relationship of 74 genes, especially 19 SCs in Populus trichocarpa. Based on the RNA-seq data, expression pattern of SCs in poplar under cold, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC18 that strongly responded to drought stress was screened. Subcellular localization experiment exhibited that PtSC18 was localized in the nucleus and plasma membrane. Overexpression of PtSC18 enhanced drought tolerance of transgenic Arabidopsis by improving water retention and reducing oxidative damage. Measurements of physiological indicators, including chlorophyll, H₂O₂, malondialdehyde content, peroxidase and catalase enzyme activities and electrical conductivity, all supported this conclusion. More importantly, PtSC18 enhanced the expression of some stress-related genes in transgenic Arabidopsis. Overall, our results lay a foundation for understanding the structure and function of PtSCs and provide useful gene resources for breeding through genetic engineering.

Comprehensive Analysis of Arabinogalactan Protein-Encoding Genes Reveals the Involvement of Three BrFLA Genes in Pollen Germination in Brassica rapa

Arabinogalactan proteins (AGPs) are a superfamily of hydroxyproline-rich glycoproteins that are massively glycosylated, widely implicated in plant growth and development. No comprehensive analysis of the AGP gene family has been performed in Chinese cabbage (Brassica rapa ssp. chinensis). Here, we identified a total of 293 putative AGP-encoding genes in B. rapa, including 25 classical AGPs, three lysine-rich AGPs, 30 AG-peptides, 36 fasciclin-like AGPs (FLAs), 59 phytocyanin-like AGPs, 33 xylogen-like AGPs, 102 other chimeric AGPs, two non-classical AGPs and three AGP/extensin hybrids. Their protein structures, phylogenetic relationships, chromosomal location and gene duplication status were comprehensively analyzed. Based on RNA sequencing data, we found that 73 AGP genes were differentially expressed in the floral buds of the sterile and fertile plants at least at one developmental stage in B. rapa, suggesting a potential role of AGPs in male reproductive development. We further characterized BrFLA2, BrFLA28 and BrFLA32, three FLA members especially expressed in anthers, pollen grains and pollen tubes. BrFLA2, BrFLA28 and BrFLA32 are indispensable for the proper timing of pollen germination under high relative humidity. Our study greatly extends the repertoire of AGPs in B. rapa and reveals a role for three members of the FLA subfamily in pollen germination.

Expression of Colorectal Cancer Antigenic Protein Fused to IgM Fc in Chinese Cabbage (Brassica rapa)

The epithelial cell adhesion molecule (EpCAM) is a tumor-associated antigen and a potential target for tumor vaccine. The EpCAM is a cell-surface glycoprotein highly expressed in colorectal carcinomas. The objective of the present study is to develop an edible vaccine system through Agrobacterium-mediated transformation in Chinese cabbage (Brassica rapa). For the transformation, two plant expression vectors containing genes encoding for the EpCAM recombinant protein along with the fragment crystallizable (Fc) region of immunoglobulin M (IgM) and Joining (J)-chain tagged with the KDEL endoplasmic reticulum retention motif (J-chain K) were constructed. The vectors were successfully transformed and expressed in the Chinese cabbage individually using Agrobacterium. The transgenic Chinese cabbages were screened using genomic polymerase chain reaction (PCR) in T₀ transgenic plant lines generated from both transformants. Similarly, the immunoblot analysis revealed the expression of recombinant proteins in the transformants. Further, the T₁ transgenic plants were generated by selfing the transgenic plants (T₀) carrying EpCAM-IgM Fc and J-chain K proteins, respectively. Subsequently, the T₁ plants generated from EpCAM-IgM Fc and J-chain K transformants were crossed to generate F₁ plants carrying both transgenes. The presence of both transgenes was validated using PCR in the F₁ plants. In addition, the expression of Chinese cabbage-derived EpCAM-IgM Fc × J-chain K was evaluated using immunoblot and ELISA analyses in the F₁ plants. The outcomes of the present study can be utilized for the development of a potential anti-cancer vaccine candidate using Chinese cabbage.

Identification of Phytocyanin Gene Family in Legume Plants and their Involvement in Nodulation of Medicago truncatula

The establishment of symbiosis between legume and rhizobium results in the formation of nodule. Phytocyanins (PCs) are a class of plant-specific blue copper proteins, playing critical roles in plant development including nodule formation. Although a few PC genes have been isolated from nodules, their functions are still unclear. Here, we performed a genome-wide identification of PC family in seven sequenced legume species (Medicago truncatula, Glycine max, Cicer arietinum, Cajanus cajan, Lotus japonicus, Vigna angularis and Phaseolus vulgaris) and found PCs experienced a remarkable expansion in M. truncatula and G. max. Further, we conducted an in-depth analysis of PC family in the model legume M. truncatula. Briefly, 82 MtPCs were divided into four subfamilies and clustered into seven clades, with a large proportion of tandem duplications and various cross-tissues expression patterns. Importantly, some PCs, such as MtPLC1, MtENODL27 and MtENODL28 were preferentially expressed in nodules. Further, RNA interference (RNAi) experiment revealed the knockdown of MtENDOL27 and MtENDOL28 impaired rhizobia infection, nodule numbers and nitrogenase activity. Moreover, in the MtENODL27-RNAi nodules, the infected cells were reduced and the symbiosomes did not reach the elongated stage, indicating MtENDOL27 is required for rhizobia infection and nodule development. In addition, co-expression analysis showed MtPLC1, MtENODL27 and MtENODL28 were grouped into two different functional modules and co-expressed with the known symbiotic nitrogen fixation-related genes, suggesting that they might participate in nodulation via different ways. In summary, this study provides a useful resource for future researches on the structure and function of PCs in nodulation.

Genome-wide identification, classification, and expression of phytocyanins in Populus trichocarpa

74 phytocyanin genes were identified in the Populus trichocarpa genome. Phylogenetic analysis grouped the PC proteins into four subfamilies (UCs, PLCs, SCs, and ENODLs). Closely related PC proteins share similar motifs, implying similar functions. Expression profiles of PtPC genes were analyzed in response to drought and salt-stress. Phytocyanins (PCs) are blue copper proteins associated with electron carrier activity that have a large influence on plant growth and resistance. The majority of PCs are chimeric arabinogalactan proteins (AGPs). In this work, we identified 74 PC genes in Populus trichocarpa and analyzed them comprehensively. Based on the ligands composition of copper-binding sites, glycosylation state, the domain structure and spectral characteristics of PC genes, PCs were divided into four subfamilies [uclacyanins (UCs), plantacyanins (PLCs), stellacyanins (SCs) and early nodulin-like proteins (ENODLs)], and phylogenetic relationship analysis classified them into seven groups. All PtPCs are randomly distributed on 17 of the 19 poplar chromosomes, and they appear to have undergone expansion via segmental duplication. Eight PtPCs do not contain introns, and each group has a similar conserved motif structure. Promoter analysis revealed cis-elements related to growth, development and stress responses, and established orthology relationships of PCs between Arabidopsis and poplar by synteny analysis. Expression profile analysis and qRT-PCR analysis showed that PtPCs were expressed widely in various tissues. Quantitative real-time RT-PCR analysis of PC genes expression in response to salt and drought stress revealed their stress-responses profiles. This work provides a theoretical basis for a further study of stress resistance mechanisms and the function of PC genes in poplar growth and development.

The distinct functions of two classical arabinogalactan proteins BcMF8 and BcMF18 during pollen wall development in Brassica campestris

Arabinogalactan proteins (AGPs) are extensively glycosylated hydroxyproline-rich glycoproteins ubiquitous in all plant tissues and cells. AtAGP6 and AtAGP11, the only two functionally known pollen-specific classical AGP encoding genes in Arabidopsis, are reported to have redundant functions in microspore development. BcMF18 and BcMF8 isolated from Brassica campestris are the orthologues of AtAGP6 and AtAGP11, respectively. In contrast to the functional redundancy of AtAGP6 and AtAGP11, single-gene disruption of BcMF8 led to deformed pollen grains with abnormal intine development and ectopic aperture formation in B. campestris. Here, we further explored the action of BcMF18 and its relationship with BcMF8. BcMF18 was specifically expressed in pollen during the late stages of microspore development. Antisense RNA transgenic lines with BcMF18 reduction resulted in aberrant pollen grains with abnormal cellulose distribution, lacking intine, cytoplasm and nuclei. Transgenic plants with repressive expression of both BcMF8 and BcMF18 showed a hybrid phenotype, expressing a mixture of the phenotypes of the single gene knockdown plant lines. In addition, we identified functional diversity between BcMF18/BcMF8 and AtAGP6/AtAGP11, mainly reflected by the specific contribution of BcMF18 and BcMF8 to pollen wall formation. These results suggest that, unlike the orthologous genes AtAGP6 and AtAGP11 in Arabidopsis, BcMF18 and BcMF8 are both integral to pollen biogenesis in B. campestris, acting through independent pathways during microspore development.

Genomic, Molecular Evolution, and Expression Analysis of Genes Encoding Putative Classical AGPs, Lysine-Rich AGPs, and AG Peptides in Brassica rapa

Arabinogalactan proteins (AGPs) belong to a class of Pro/Hyp-rich glycoproteins and are some of the most complex types of macromolecules found in plants. In the economically important plant species, Brassica rapa, only chimeric AGPs have been identified to date. This has significantly limited our understanding of the functional roles of AGPs in this plant. In this study, 64 AGPs were identified in the genome of B. rapa, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between B. rapa and A. thaliana suggested that the whole genome triplication event dominated the expansion of the AGP gene family in B. rapa. This resulted in a high retained proportion of the AGP family in the B. rapa genome, especially in the least fractionated subgenome. Phylogenetic and motif analysis classified the classical AGPs into six clades and three orphan genes, and the AG peptides into three clades and five orphan genes. Classical AGPs has a faster rate of molecular evolution than AG peptides revealed by estimation of molecular evolution rates. However, no significant differences were observed between classical AGPs and lys-rich AGPs. Under control conditions and in response to phytohormones treatment, a complete expression profiling experiment has identified five anther-specific AGPs and quite a number of AGPs responding to abscisic acid, methyl jasmonate and/or gibberellin. In this study, we presented a bioinformatics approach to identify important types of AGPs. Moreover, the association between their function and their protein structure, as well as the evolution and the expression of AGP genes were investigated, which might provide fundamental information for revealing the roles of AGPs in B. rapa.

Bioinformatics Prediction and Evolution Analysis of Arabinogalactan Proteins in the Plant Kingdom

Arabinogalactan proteins (AGPs) are a family of extracellular glycoproteins implicated in plant growth and development. With a rapid growth in the number of genomes sequenced in many plant species, the family members of AGPs can now be predicted to facilitate functional investigation. Building upon previous advances in identifying Arabidopsis AGPs, an integrated strategy of systematical AGP screening for "classical" and "chimeric" family members is proposed in this study. A Python script named Finding-AGP is compiled to find AGP-like sequences and filter AGP candidates under the given thresholds. The primary screening of classical AGPs, Lys-rich classical AGPs, AGP-extensin hybrids, and non-classical AGPs was performed using the existence of signal peptides as a necessary requirement, and BLAST searches were conducted mainly for fasciclin-like, phytocyanin-like and xylogen-like AGPs. Then glycomodule index and partial PAST (Pro, Ala, Ser, and Thr) percentage are adopted to identify AGP candidates. The integrated strategy successfully discovered AGP gene families in 47 plant species and the main results are summarized as follows: (i) AGPs are abundant in angiosperms and many "ancient" AGPs with Ser-Pro repeats are found in Chlamydomonas reinhardtii; (ii) Classical AGPs, AG-peptides, and Lys-rich classical AGPs first emerged in Physcomitrella patens, Selaginella moellendorffii, and Picea abies, respectively; (iii) Nine subfamilies of chimeric AGPs are introduced as newly identified chimeric subfamilies similar to fasciclin-like, phytocyanin-like, and xylogen-like AGPs; (iv) The length and amino acid composition of Lys-rich domains are largely variable, indicating an insertion/deletion model during evolution. Our findings provide not only a powerful means to identify AGP gene families but also probable explanations of AGPs in maintaining the plant cell wall and transducing extracellular signals into the cytoplasm.

Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays

Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.

Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage

The Hsf gene family, one of the most important transcription factor families, plays crucial roles in regulating heat resistance. However, a systematic and comprehensive analysis of this gene family has not been reported in Chinese cabbage. Therefore, systematic analysis of the Hsf gene family in Chinese cabbage has profound significance. In this study, 35 BrHsf genes were identified from Chinese cabbage, which could be classified into three groups according to their structural characteristics and phylogenetic comparisons with Arabidopsis and rice. Thirty-three BrHsf genes mapped on chromosomes were further assigned to three subgenomes and eight ancestral karyotypes. Distribution mapping showed that BrHsf genes were non-randomly localized on chromosomes. Chinese cabbage and Arabidopsis shared 22 orthologous gene pairs. The expansion of BrHsf genes mainly resulted from genome triplication. Comparative analysis showed that the most Hsf genes were in Chinese cabbage among the five species analyzed. Interestingly, the number of Hsf genes of heat-resistant plants (Theobroma cacao and Musa acuminata) was fewer than that in Chinese cabbage. The expression patterns of BrHsf genes were different in six tissues, based on RNA-seq. Quantitative real-time-PCR analysis showed that the expression level of BrHsf genes varied under various abiotic stresses. In conclusion, this comprehensive analysis of BrHsf genes will provide rich resources, aiding the determination of Hsfs functions in plant heat resistance. Furthermore, the comparative genomics analysis deepened our understanding of Hsf genes' evolution accompanied by the polyploidy event of Chinese cabbage.