Molecular traits and functional analysis of Rapid Alkalinization Factors (RALFs) in four Gossypium species

Genome-wide exploration and characterization of the RALFs and analysis of its role in peanut (Arachis hypogaea L.)

BACKGROUND

Rapid alkalinization factors (RALFs) are small peptides hormones that regulate plant growth and stress responses. Although RALFs have been identified in a broad range of land plant species, their roles in peanuts (Arachis hypogaea L.) remain largely unexplored.

RESULT

A total of 24 AhRALF genes we identified in the peanut genome and classified them into three clades through phylogenetic analysis. Whole genome duplication (WGD) or segmental duplication primarily drives the expansion of AhRALFs. Gene transcription analysis revealed that two genes from clade II (AhRALF1 and AhRALF12) and three from clade III (AhRALF8, AhRALF10, and AhRALF21) are highly expressed across 18 different tissues. Notably, AhRALF11 and AhRALF24, paralogous genes from clade II, are specifically expressed in immature buds and flowers. Additionally, AhRALF1, AhRALF12, AhRALF8, and AhRALF21 exhibited elevated expression under aluminum (Al) stress. Functional analysis of AhRALF1 confirmed its secretory function and inhibitory effect on root growth in Arabidopsis. Moreover, AhRALF1-silenced plants displayed reduced tolerance to Al stress, with altered antioxidant enzyme activities and increased oxidative damage.

CONCLUSION

This study provides a comprehensive analysis of the AhRALF gene family in peanut, highlighting their roles in growth regulation and stress responses. The function of AhRALF1 in enhancing peanut tolerance to Al stress was preliminary revealed. Our findings provide valuable insights into the roles of AhRALFs in peanuts and lay the groundwork for future functional studies and breeding programs.

Analysis of NRAMP genes in the Triticeae reveals that TaNRAMP5 positively regulates cadmium (Cd) tolerance in wheat (Triticum aestivum)

Natural Resistance-Associated Macrophage Protein (NRAMP), a class of metal transporter proteins widely distributed in plants, is mainly involved in the uptake and transport by plants of metal ions, such as iron, manganese and cadmium. The current study is the first to fully investigate the Triticum aestivum (T. aestivum) NRAMP gene family. 33 NRAMP members were identified from the entire T. aestivum genome and classified into three main groups based on related genes found in five other species. Among the TaNRAMP genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch of the phylogenetic tree. Based on RNA-seq and qRT-PCR analyses, we identified the expression patterns of the TaNRAMP genes in different tissues and under various stress conditions. TaNRAMP genes expression were responsive to induction by cadmium (Cd). Overexpression of the TaNRAMP5 gene enhanced wheat and tobacco tolerance to Cd toxicity. Additionally, the TaNRAMP5 protein physically interacted with protein phosphatase 2A (PP2A) in yeast cells. This study provides a valuable reference point for further investigations into the functional and molecular mechanisms of the NRAMP gene family.

Peptide hormones in plants

Peptide hormones are defined as small secreted polypeptide-based intercellular communication signal molecules. Such peptide hormones are encoded by nuclear genes, and often go through proteolytic processing of preproproteins and post-translational modifications. Most peptide hormones are secreted out of the cell to interact with membrane-associated receptors in neighboring cells, and subsequently activate signal transductions, leading to changes in gene expression and cellular responses. Since the discovery of the first plant peptide hormone, systemin, in tomato in 1991, putative peptide hormones have continuously been identified in different plant species, showing their importance in both short- and long-range signal transductions. The roles of peptide hormones are implicated in, but not limited to, processes such as self-incompatibility, pollination, fertilization, embryogenesis, endosperm development, stem cell regulation, plant architecture, tissue differentiation, organogenesis, dehiscence, senescence, plant-pathogen and plant-insect interactions, and stress responses. This article, collectively written by researchers in this field, aims to provide a general overview for the discoveries, functions, chemical natures, transcriptional regulations, and post-translational modifications of peptide hormones in plants. We also updated recent discoveries in receptor kinases underlying the peptide hormone sensing and down-stream signal pathways. Future prospective and challenges will also be discussed at the end of the article.

Molecular traits of MAPK kinases and the regulatory mechanism of GhMAPKK5 alleviating drought/salt stress in cotton

Mitogen-activated protein kinase kinases (MAPKKs) play a critical role in the mitogen-activated protein kinase (MAPK) signaling pathway, transducing external stimuli into intracellular responses and enabling plant adaptation to environmental challenges. Most research has focused on the model plant Arabidopsis (Arabidopsis thaliana). The systematic analysis and characterization of MAPKK genes across different plant species, particularly in cotton (Gossypium hirsutum), are somewhat limited. Here, we identified MAPKK family members from 66 different species, which clustered into five different sub-groups, and MAPKKs from four cotton species clustered together. Through further bioinformatic and expression analyses, GhMAPKK5 was identified as the most responsive MAPKK member to salt and drought stress among the 23 MAPKKs identified in Gossypium hirsutum. Silencing GhMAPKK5 in cotton through virus-induced gene silencing (VIGS) led to quicker wilting under salt and drought conditions, while overexpressing GhMAPKK5 in Arabidopsis enhanced root growth and seed germination under these stresses, demonstrating GhMAPKK5's positive role in stress tolerance. Transcriptomics and Yeast-Two-Hybrid assays revealed a MAPK cascade signal module comprising GhMEKK (mitogen-activated protein kinase kinase kinases)3/8/31-GhMAPKK5-GhMAPK11/23. This signaling cascade may play a role in managing drought and salt stress by regulating transcription factor genes, such as WRKYs, which are involved in the biosynthesis and transport pathways of ABA, proline, and RALF. This study is highly important for further understanding the regulatory mechanism of MAPKK in cotton, contributing to its stress tolerance and offering potential in targets for genetic enhancement.

Identification of the succinate-CoA ligase protein gene family reveals that TaSUCL1-1 positively regulate cadmium resistance in wheat

The Succinate-CoA ligase (SUCL1) gene family is involved in energy metabolism, phytohormone signaling, and plant growth, development, and tolerance to stress. This is the first study to analyze the SUCL1 gene family in wheat (Triticum aestivum). 17 TaSUCL1 genes were identified in the complete genome sequence and classified into five subfamilies based on related genes found in three other species. The 17 TaSUCL1 genes were unevenly distributed across 11 chromosomes, and the collinearity of these genes was further investigated. Through using real-time qPCR (RT-qPCR) analysis, we identified the expression patterns of the TaSUCL1 genes under various tissues and different heavy metal stress conditions. The functions of selected TaSUCL1-1 gene were investigated by RNA interference (RNAi). This study provided a comprehensive analysis of the TaSUCL1 gene family. Within the TaSUCL1 genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch. Homology analysis and phylogenetic comparison of the SUCL1 genes in different plants offered valuable insights for studying the evolutionary characteristics of the SUCL1 genes. The expression levels of the TaSUCL1 genes in different tissues and under various metal stress conditions reveal its important role in plant growth and development. Gene function analysis demonstrated that TaSUCL1-1 silenced wheat plants exhibited a decrease in the total cadmium (Cd) concentrations and gene expression levels compared to the wild type (WT). Additionally, TaSUCL1-1 belonging to class c physically interacts with the β-amylase protein TaBMY1 as verified by yeast two-hybridization. This research provides a useful resource for further study of the function and molecular genetic mechanism of the SUCL1 gene family members.

Identification of acyl-CoA-binding protein gene in Triticeae species reveals that TaACBP4A-1 and TaACBP4A-2 positively regulate powdery mildew resistance in wheat

Plant acyl-CoA-binding proteins (ACBPs), which contain the conserved ACB domain, participate in multiple biological processes, however, there are few reports on wheat ACBPs. In this study, the ACBP genes from nine different species were identified comprehensively. The expression patterns of TaACBP genes in multiple tissues and under various biotic stresses were determined by qRT-PCR. The function of selected TaACBP genes was studied by virus-induced gene silencing. A total of 67 ACBPs were identified from five monocotyledonous and four dicotyledonous species and divided into four classes. Tandem duplication analysis of the ACBPs suggested that tandem duplication events occurred in Triticum dicoccoides, but there was no tandem duplication event in wheat ACBP genes. Evolutionary analysis suggested that the TdACBPs may have experienced gene introgression during tetraploid evolution, while TaACBP gene loss events occurred during hexaploid wheat evolution. The expression pattern showed that all the TaACBP genes were expressed, and most of them were responsive to induction by Blumeria graminis f. sp. tritici or Fusarium graminearum. Silencing of TaACBP4A-1 and TaACBP4A-2 increased powdery mildew susceptibility in the common wheat BainongAK58. Furthermore, TaACBP4A-1, which belonged to class III, physically interacted with autophagy-related ubiquitin-like protein TaATG8g in yeast cells. This study provided a valuable reference for further investigations into the functional and molecular mechanisms of the ACBP gene family.

Structure and character analysis of cotton response regulator genes family reveals that GhRR7 responses to draught stress

Background

Cytokinin signal transduction is mediated by a two-component system (TCS). Two-component systems are utilized in plant responses to hormones as well as to biotic and abiotic environmental stimuli. In plants, response regulatory genes (RRs) are one of the main members of the two-component system (TCS).

Method

From the aspects of gene structure, evolution mode, expression type, regulatory network and gene function, the evolution process and role of RR genes in the evolution of the cotton genome were analyzed.

Result

A total of 284 RR genes in four cotton species were identified. Including 1049 orthologous/paralogous gene pairs were identified, most of which were whole genome duplication (WGD). The RR genes promoter elements contain phytohormone responses and abiotic or biotic stress-related cis-elements. Expression analysis showed that RR genes family may be negatively regulate and involved in salt stress and drought stress in plants. Protein regulatory network analysis showed that RR family proteins are involved in regulating the DNA-binding transcription factor activity (COG5641) pathway and HP kinase pathways. VIGS analysis showed that the GhRR7 gene may be in the same regulatory pathway as GhAHP5 and GhPHYB, ultimately negatively regulating cotton drought stress by regulating POD, SOD, CAT, H₂O₂ and other reactive oxygen removal systems.

Conclusion

This study is the first to gain insight into RR gene members in cotton. Our research lays the foundation for discovering the genes related to drought and salt tolerance and creating new cotton germplasm materials for drought and salt tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40659-022-00394-2.

Identification of ankyrin-transmembrane-type subfamily genes in Triticeae species reveals TaANKTM2A-5 regulates powdery mildew resistance in wheat

The ankyrin-transmembrane (ANKTM) subfamily is the most abundant subgroup of the ANK superfamily, with critical roles in pathogen defense. However, the function of ANKTM proteins in wheat immunity remains largely unexplored. Here, a total of 381 ANKTMs were identified from five Triticeae species and Arabidopsis, constituting five classes. Among them, class a only contains proteins from Triticeae species and the number of ANKTM in class a of wheat is significantly larger than expected, even after consideration of the ploidy level. Tandem duplication analysis of ANKTM indicates that Triticum urartu, Triticum dicoccoides and wheat all had experienced tandem duplication events which in wheat-produced ANKTM genes all clustered in class a. The above suggests that not only did the genome polyploidization result in the increase of ANKTM gene number, but that tandem duplication is also a mechanism for the expansion of this subfamily. Micro-collinearity analysis of Triticeae ANKTMs indicates that some ANKTM type genes evolved into other types of ANKs in the evolution process. Public RNA-seq data showed that most of the genes in class d and class e are expressed, and some of them show differential responses to biotic stresses. Furthermore, qRT-PCR results showed that some ANKTMs in class d and class e responded to powdery mildew. Silencing of TaANKTM2A-5 by barley stripe mosaic virus-induced gene silencing compromised powdery mildew resistance in common wheat Bainongaikang58. Findings in this study not only help to understand the evolutionary process of ANKTM genes, but also form the basis for exploring disease resistance genes in the ANKTM gene family.