Genome-wide identification, phylogeny and expression profiling of class III peroxidases gene family in Brachypodium distachyon

Genome-Wide Identification and Expression Analysis of the Class III Peroxidase Gene Family under Abiotic Stresses in Litchi (Litchi chinensis Sonn.)

Class III peroxidases (CIII PRXs) are plant-specific enzymes with high activity that play key roles in the catalysis of oxidation-reduction reactions. In plants, CIII PRXs can reduce hydrogen peroxide to catalyze oxidation-reduction reactions, thereby affecting plant growth, development, and stress responses. To date, no systematic analysis of the CIII PRX gene family in litchi (Litchi chinensis Sonn.) has been documented, although the genome has been reported. In this study, a total of 77 CIII PRX (designated LcPRX) gene family members were predicted in the litchi genome to provide a reference for candidate genes in the responses to abiotic stresses during litchi growth and development. All of these LcPRX genes had different numbers of highly conserved PRX domains and were unevenly distributed across fifteen chromosomes. They were further clustered into eight clades using a phylogenetic tree, and almost every clade had its own unique gene structure and motif distribution. Collinearity analysis confirmed that there were eleven pairs of duplicate genes among the LcPRX members, and segmental duplication (SD) was the main driving force behind the LcPRX gene expansion. Tissue-specific expression profiles indicated that the expression levels of all the LcPRX family members in different tissues of the litchi tree were significantly divergent. After different abiotic stress treatments, quantitative real-time PCR (qRT-PCR) analysis revealed that the LcPRX genes responded to various stresses and displayed differential expression patterns. Physicochemical properties, transmembrane domains, subcellular localization, secondary structures, and cis-acting elements were also analyzed. These findings provide insights into the characteristics of the LcPRX gene family and give valuable information for further elucidating its molecular function and then enhancing abiotic stress tolerance in litchi through molecular breeding.

Identification of cysteine-rich receptor-like kinase gene family in potato: revealed StCRLK9 in response to heat, salt and drought stresses

The investigation into cysteine-rich receptor-like kinases (CRLKs) holds pivotal significance as these conserved, upstream signalling molecules intricately regulate fundamental biological processes such as plant growth, development and stress adaptation. This study undertakes a comprehensive characterisation of CRLKs in Solanum tuberosum (potato), a staple food crop of immense economic importance. Employing comparative genomics and evolutionary analyses, we identified 10 distinct CRLK genes in potato. Further categorisation into three major groups based on sequence similarity was performed. Each CRLK member in potato was systematically named according to its chromosomal position. Multiple sequence alignment and phylogenetic analyses unveiled conserved gene structures and motifs within the same groups. The genomic distribution of CRLKs was observed across Chromosomes 2-5, 8 and 12. Gene duplication analysis highlighted a noteworthy trend, with most gene pairs exhibiting a Ka/Ks ratio greater than one, indicating positive selection of StCRLKs in potato. Salt and drought stresses significantly impacted peroxidase and catalase activities in potato seedlings. The presence of diverse cis -regulatory elements, including hormone-responsive elements, underscored their involvement in myriad biotic and abiotic stress responses. Interestingly, interactions between the phytohormone auxin and CRLK proteins unveiled a potential auxin-mediated regulatory mechanism. A holistic approach combining transcriptomics and quantitative PCR validation identified StCRLK9 as a potential candidate involved in plant response to heat, salt and drought stresses. This study lays a robust foundation for future research on the functional roles of the CRLK gene family in potatoes, offering valuable insights into their diverse regulatory mechanisms and potential applications in stress management.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Class III Peroxidases in the Peach (Prunus persica): Genome-Wide Identification and Functional Analysis

Class III peroxidases are plant-specific and play a key role in the response to biotic and abiotic stresses, as well as in plant growth and development. In this study, we investigated 60 POD genes from Prunus persica based on genomic and transcriptomic data available in NCBI and analysed the expression of individual genes with qPCR. Peroxidase genes were clustered into five subgroups using the phylogenetic analysis. Their exon-intron structure and conserved motifs were analysed. Analysis of the transcriptomic data showed that the expression of PpPOD genes varied significantly in different tissues, at different developmental stages and under different stress treatments. All genes were divided into low- and high-expressed genes, and the most highly expressed genes were identified for individual tissues (PpPOD12 and PpPOD42 in flower buds and PpPOD73, PpPOD12, PpPOD42, and PpPOD31 in fruits). The relationship between cold tolerance and the level of peroxidase expression was revealed. These studies were carried out for the first time in the peach and confirmed that chilling tolerance may be related to the specificity of antioxidant complex gene expression.

Machine learning-based classification of deubiquitinase USP26 and its cell proliferation inhibition through stabilizing KLF6 in cervical cancer

OBJECTIVE

We aim to accurately distinguish ubiquitin-specific proteases (USPs) from other members within the deubiquitinating enzyme families based on protein sequences. Additionally, we seek to elucidate the specific regulatory mechanisms through which USP26 modulates Krüppel-like factor 6 (KLF6) and assess the subsequent effects of this regulation on both the proliferation and migration of cervical cancer cells.

METHODS

All the deubiquitinase (DUB) sequences were classified into USPs and non-USPs. Feature vectors, including 188D, n-gram, and 400D dimensions, were extracted from these sequences and subjected to binary classification via the Weka software. Next, thirty human USPs were also analyzed to identify conserved motifs and ascertained evolutionary relationships. Experimentally, more than 90 unique DUB-encoding plasmids were transfected into HeLa cell lines to assess alterations in KLF6 protein levels and to isolate a specific DUB involved in KLF6 regulation. Subsequent experiments utilized both wild-type (WT) USP26 overexpression and shRNA-mediated USP26 knockdown to examine changes in KLF6 protein levels. The half-life experiment was performed to assess the influence of USP26 on KLF6 protein stability. Immunoprecipitation was applied to confirm the USP26-KLF6 interaction, and ubiquitination assays to explore the role of USP26 in KLF6 deubiquitination. Additional cellular assays were conducted to evaluate the effects of USP26 on HeLa cell proliferation and migration.

RESULTS

1. Among the extracted feature vectors of 188D, 400D, and n-gram, all 12 classifiers demonstrated excellent performance. The RandomForest classifier demonstrated superior performance in this assessment. Phylogenetic analysis of 30 human USPs revealed the presence of nine unique motifs, comprising zinc finger and ubiquitin-specific protease domains. 2. Through a systematic screening of the deubiquitinase library, USP26 was identified as the sole DUB associated with KLF6. 3. USP26 positively regulated the protein level of KLF6, as evidenced by the decrease in KLF6 protein expression upon shUSP26 knockdown in both 293T and Hela cell lines. Additionally, half-life experiments demonstrated that USP26 prolonged the stability of KLF6. 4. Immunoprecipitation experiments revealed a strong interaction between USP26 and KLF6. Notably, the functional interaction domain was mapped to amino acids 285-913 of USP26, as opposed to the 1-295 region. 5. WT USP26 was found to attenuate the ubiquitination levels of KLF6. However, the mutant USP26 abrogated its deubiquitination activity. 6. Functional biological assays demonstrated that overexpression of USP26 inhibited both proliferation and migration of HeLa cells. Conversely, knockdown of USP26 was shown to promote these oncogenic properties.

CONCLUSIONS

1. At the protein sequence level, members of the USP family can be effectively differentiated from non-USP proteins. Furthermore, specific functional motifs have been identified within the sequences of human USPs. 2. The deubiquitinating enzyme USP26 has been shown to target KLF6 for deubiquitination, thereby modulating its stability. Importantly, USP26 plays a pivotal role in the modulation of proliferation and migration in cervical cancer cells.

Regulation of hair cell and stomatal size by a hair cell-specific peroxidase in the grass Brachypodium distachyon

The leaf epidermis is the outermost cell layer forming the interface between plants and the atmosphere that must both provide a robust barrier against (a)biotic stressors and facilitate carbon dioxide uptake and leaf transpiration.¹ To achieve these opposing requirements, the plant epidermis developed a wide range of specialized cell types such as stomata and hair cells. Although factors forming these individual cell types are known,^2,3,4,5 it is poorly understood how their number and size are coordinated. Here, we identified a role for BdPRX76/BdPOX, a class III peroxidase, in regulating hair cell and stomatal size in the model grass Brachypodium distachyon. In bdpox mutants, prickle hair cells were smaller and stomata were longer. Because stomatal density remained unchanged, the negative correlation between stomatal size and density was disrupted in bdpox and resulted in higher stomatal conductance and lower intrinsic water-use efficiency. BdPOX was exclusively expressed in hair cells, suggesting that BdPOX cell-autonomously promotes hair cell size and indirectly restricts stomatal length. Cell-wall autofluorescence and lignin stainings indicated a role for BdPOX in the lignification or crosslinking of related phenolic compounds at the hair cell base. Ectopic expression of BdPOX in the stomatal lineage increased phenolic autofluorescence in guard cell (GC) walls and restricted stomatal elongation in bdpox. Together, we highlight a developmental interplay between hair cells and stomata that optimizes epidermal functionality. We propose that cell-type-specific changes disrupt this interplay and lead to compensatory developmental defects in other epidermal cell types.

Genome-wide identification of the class III peroxidase gene family of sugarcane and its expression profiles under stresses

INTRODUCTION

Plant-specific Class III peroxidases (PRXs) play a crucial role in lignification, cell elongation, seed germination, and biotic and abiotic stresses.

METHODS

The class III peroxidase gene family in sugarcane were identified by bioinformatics methods and realtime fluorescence quantitative PCR.

RESULTS

Eighty-two PRX proteins were characterized with a conserved PRX domain as members of the class III PRX gene family in R570 STP. The ShPRX family genes were divided into six groups by the phylogenetic analysis of sugarcane, Saccharum spontaneum, sorghum, rice, and Arabidopsis thaliana. The analysis of promoter cis-acting elements revealed that most ShPRX family genes contained cis-acting regulatory elements involved in ABA, MeJA, light responsiveness, anaerobic induction, and drought inducibility. An evolutionary analysis indicated that ShPRXs was formed after Poaceae and Bromeliaceae diverged, and tandem duplication events played a critical role in the expansion of ShPRX genes of sugarcane. Purifying selection maintained the function of ShPRX proteins. SsPRX genes were differentially expressed in stems and leaves at different growth stages in S. spontaneum. However, ShPRX genes were differentially expressed in the SCMV-inoculated sugarcane plants. A qRT-PCR analysis showed that SCMV, Cd, and salt could specifically induce the expression of PRX genes of sugarcane.

DISCUSSION

These results help elucidate the structure, evolution, and functions of the class III PRX gene family in sugarcane and provide ideas for the phytoremediation of Cd-contaminated soil and breeding new sugarcane varieties resistant to sugarcane mosaic disease, salt, and Cd stresses.

Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum

Class III peroxidase (PRX) genes play essential roles in various processes, such as auxin catabolism, removal of H₂O₂, crosslinking cell wall components, and response to biotic and abiotic stresses. In this study, we identified 166, 78 and 89 PRX genes from G. hirsutum, G. arboretum and G. raimondii, respectively. These PRX genes were classified into seven subfamilies based on phylogenetic tree analysis and the classification of PRX genes in Arabidopsis. Segmental duplication and purifying selection were the major factors driving the evolution of GhPRXs. GO and KEGG enrichment analysis revealed that GhPRX genes were mainly associated with responding to oxidative stresses, peroxidase activities and phenylpropanoid biosynthesis pathways. Transcriptome data analysis showed that GhPRX genes expression were significantly different in microspore development between the sterility line-JinA and the maintainer line MB177. We confirmed the up-regulation of GhPRX107 and down-regulation of GhPRX128 in the sterile line compared to its maintainer line using qRT-PCR, suggesting their roles in pollen fertility. In addition, silencing GhPRX107 in cotton showed a significant decrease of the reactive oxygen species (ROS) levels of microsporocyte stage anthers compared to control. Overexpressing GhPRX107 in Arabidopsis significantly increased the ROS levels of anthers compared to wild type. In conclusion, we identified GhPRX107 as a determinant of ROS levels in anther. This work sets a foundation for PRX studies in pollen development.

Characterisation of the class III peroxidase gene family in carrot taproots and its role in anthocyanin and lignin accumulation

Plant class III peroxidases (CIII Prxs) are involved in numerous essential plant life processes, such as plant development and differentiation, lignification and seed germination, and defence against pathogens. However, there is limited information about the structure-function relationships of Prxs in carrots. This study identified 75 carrot peroxidases (DcPrxs) and classified them into seven subgroups based on phylogenetic analysis. Gene structure analysis revealed that these DcPrxs had between one and eight introns, while conserved motif analysis showed a typical motif composition and arrangement for CIII Prx. In addition, eighteen tandem duplication events, but only eight segmental duplications, were identified among these DcPrxs, indicating that tandem duplication was the main contributor to the expansion of this gene family. Histochemical analyses showed that lignin was mainly localised in the cell walls of xylem, and Prx activity was determined in the epidermal region of taproots. The xylem always showed higher lignin concentration and lower Prx activity compared to the phloem in the taproots of both carrot cultivars. Combining these observations with RNA sequencing, some Prx genes were identified as candidate genes related to lignification and pigmentation. Three peroxidases (DcPrx30, DcPrx32, DcPrx62) were upregulated in the phloem of both genotypes. Carrot taproots are an attractive resource for natural food colourants and this study elucidated genome-wide insights of Prx for the first time, developing hypotheses concerning their involvement with lignin and anthocyanin in purple carrots. The findings provide an essential foundation for further studies of Prx genes in carrot, especially on pigmentation and lignification mechanisms.

Screening and identification of salt-tolerance genes in Sophora alopecuroides and functional verification of SaAQP

Overexpression of SaAQP can improve the salt tolerance of transgenic soybean hairy roots and A. thaliana. Salt stress severely affects crop yield and food security. There is a need to improve the salt tolerance of crops, but the discovery and utilization of salt-tolerance genes remains limited. Owing to its strong stress tolerance, Sophora alopecuroides is ideal for the identification of salt-tolerance genes. Therefore, we aimed to screen and identify the salt-tolerance genes in S. alopecuroides. With a yeast expression library of seedlings, salt-tolerant genes were screened using a salt-containing medium to simulate salt stress. By combining salt-treatment screening and transcriptome sequencing, 11 candidate genes related to salt tolerance were identified, including genes for peroxidase, inositol methyltransferase, aquaporin, cysteine synthase, pectinesterase, and WRKY. The expression dynamics of candidate genes were analyzed after salt treatment of S. alopecuroides, and salt tolerance was verified in yeast BY4743. The candidate genes participated in the salt-stress response in S. alopecuroides, and their overexpression significantly improved the salt tolerance of yeast. Salt tolerance mediated by SaAQP was further verified in soybean hairy roots and Arabidopsis thaliana, and it was found that SaAQP might enhance the salt tolerance of A. thaliana by participating in a reactive oxygen species scavenging mechanism. This result provides new genetic resources in plant breeding for salt resistance.

Genome-wide identification, phylogenetic analysis and expression profiling of the late embryogenesis-abundant (LEA) gene family in Brachypodium distachyon

Late embryogenesis-abundant (LEA) proteins are the products of an important gene family in plants that play vital roles in regulating growth and development as well as a variety of stress responses. In our study, 67 members of LEA (BdLEA) were identified in the genome of Brachypodium distachyon L. Analyses of gene structure, evolutionary relationships and protein motifs showed that the BdLEAs belonged to six subfamilies. Analyses of chromosomal locations and duplication events revealed that the 67 BdLEAs were distributed over all five chromosomes and 26 BdLEAs were identified as products of duplication events. Gene Ontology (GO) annotation results suggested that nearly 60% of BdLEAs could be involved in stress response. Furthermore, transcriptomic analysis showed that the BdLEAs were differentially expressed in nine organs and responded to low stringency of exogenous phytohormones. Subsequently, 18 BdLEAs from six subfamilies were randomly selected for quantitative real-time PCR (qRT-PCR) analysis, which showed that they were mainly expressed in the spikelets and they may preferentially respond to salt, drought and abscisic acid (ABA) stress. This study is the first to report the characteristics of the BdLEA family, providing valuable information for understanding the evolution of LEAs in the model plant B. distachyon and supporting future functional research on these proteins.

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

BACKGROUND

Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat.

RESULTS

In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR).

CONCLUSIONS

The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)

BACKGROUND

The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

RESULTS

We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

CONCLUSIONS

In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.