Evolutionary and functional analysis of two-component system in chickpea reveals CaRR13, a TypeB RR, as positive regulator of symbiosis

Shaping resilience: The critical role of plant response regulators in salinity stress

BACKGROUND

Salinity stress affects plant growth, development, biomass, yield, as well as their survival. A series of signaling cascade is activated to cope the deleterious effect of salinity stress. Cytokinins are known for their regulatory roles from cell growth and expansion to abiotic stress signaling. Two component system (TCS) are important multistep phosphorelay signal transduction machinery converging cytokinin, ethylene and light signal transduction pathways together. Plant TCS comprises of histidine kinases, phosho-transfer proteins and response regulators. Histidine kinases perceive the signal and relay it to response regulator via histidine containing phosphor-transfer proteins.

SCOPE OF REVIEW

Response regulators are one of the major and diverse component of TCS system which have been extensively studied for their role in plant growth, development and circadian rhythm. However, knowledge of their regulatory role in abiotic stress signaling is limited. This mini-review specifically focus on role of response regulators in salinity stress signaling.

MAJOR CONCLUSION

Response regulators is the divergent node of TCS machinery, where cross-talks with other stress-mediated, phytohormone-mediated, as well as, light-mediated signaling pathways ensues. Studies from past few years have established central role of response regulators in salinity stress, however, the detailed mechanism of their actions need to be studied further.

GENERAL SIGNIFICANCE

Response regulators act as both negative as well as positive regulator of salinity and cytokinin signaling, making it an excellent target to increase crop yield as well as stress tolerance capabilities.

Genome-wide identification and expression analysis of two-component system genes in switchgrass (Panicum virgatum L.)

The two-component system (TCS) consists of histidine kinase (HK), histidine phosphate transfer protein (HP), and response regulatory factor (RR). It is one of the most crucial components of signal transduction in plants, playing a significant role in regulating plant growth, development, and responses to various abiotic stresses. Although TCS genes have been extensively identified in a variety of plants, the genome-wide recognition and examination of TCS in switchgrass remain unreported. Accordingly, this study identified a total of 87 TCS members in the genome of switchgrass, comprising 20 HK(L)s, 10 HPs, and 57 RRs. Detailed analyses were also conducted on their gene structures, conserved domains, and phylogenetic relationships. Moreover, this study analysed the gene expression profiles across diverse organs and investigated their response patterns to adverse environmental stresses. Results revealed that 87 TCS genes were distributed across 18 chromosomes, with uneven distribution. Expansion of these genes in switchgrass was achieved through both fragment and tandem duplication. PvTCS members are relatively conservative in the evolutionary process, but the gene structure varies significantly. Various cis-acting elements, varying in types and amounts, are present in the promoter region of PvTCSs, all related to plant growth, development, and abiotic stress, due to the TCS gene structure. Protein-protein interaction and microRNA prediction suggest complex interactions and transcriptional regulation among TCS members. Additionally, most TCS members are expressed in roots and stems, with some genes showing organ-specific expression at different stages of leaf and inflorescence development. Under conditions of abiotic stress such as drought, low temperature, high temperature, and salt stress, as well as exogenous abscisic acid (ABA), the expression of most TCS genes is either stimulated or inhibited. Our systematic analysis could offer insight into the characterization of the TCS genes, and further the growth of functional studies in switchgrass.

Analysis of the histidine kinase gene family and the role of GhHK8 in response to drought tolerance in cotton

As an important member of the two-component system (TCS), histidine kinases (HKs) play important roles in various plant developmental processes and signal transduction in response to a wide range of biotic and abiotic stresses. So far, the HK gene family has not been investigated in Gossypium. In this study, a total of 177 HK gene family members were identified in cotton. They were further divided into seven groups, and the protein characteristics, genetic relationship, gene structure, chromosome location, collinearity, and cis-elements identification were comprehensively analyzed. Whole genome duplication (WGD) / segmental duplication may be the reason why the number of HK genes doubled in tetraploid Gossypium species. Expression analysis revealed that most cotton HK genes were mainly expressed in the reproductive organs and the fiber at initial stage. Gene expression analysis revealed that HK family genes are involved in cotton abiotic stress, especially drought stress and salt stress. In addition, gene interaction networks showed that HKs were involved in the regulation of cotton abiotic stress, especially drought stress. VIGS experiments have shown that GhHK8 is a negative regulatory factor in response to drought stress. Our systematic analysis provided insights into the characteristics of the HK genes in cotton and laid a foundation for further exploring their potential in drought stress resistance in cotton.

Auxin-cytokinin interplay shapes root functionality under low-temperature stress

Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.

The developmental dynamics in cool season legumes with focus on chickpea

Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.

Omics-assisted characterization of two-component system genes from Gossypium Raimondii in response to salinity and molecular interaction with abscisic acid

The two-component system (TCS) genes are involved in a wide range of physiological processes in prokaryotes and eukaryotes. In plants, the TCS elements help in a variety of functions, including cell proliferation, response to abiotic and biotic stresses, leaf senescence, nutritional signaling, and division of chloroplasts. Three different kinds of proteins make up the TCS system in plants. These are known as HKs (histidine kinases), HPs (histidine phosphotransfer), and RRs (response regulators). We investigated the genome of Gossypium raimondii and discovered a total of 59 GrTCS candidates, which include 23 members of the HK family, 8 members of the HP family, and 28 members of the RR family. RR candidates are further classified as type-A (6 members), type-B (11 members), type-C (2 members), and pseudo-RRs (9 members). The GrTCS genes were analyzed in comparison with the TCS components of other plant species such as Arabidopsis thaliana, Cicer arietinum, Sorghum bicolor, Glycine max, and Oryza sativa. This analysis revealed both conservation and changes in their structures. We identified 5 pairs of GrTCS syntenic homologs in the G. raimondii genome. All 59 TCS genes in G. raimondii are located on all thirteen chromosomes. The GrTCS promoter regions have several cis-regulatory elements, which function as switches and respond to a wide variety of abiotic stresses. RNA-seq and real-time qPCR analysis showed that the majority of GrTCS genes are differentially regulated in response to salt and cold stress. 3D structures of GrTCS proteins were predicted to reveal the specific function. GrTCSs were docked with abscisic acid to assess their binding interactions. This research establishes the groundwork for future functional studies of TCS elements in G. raimondii, which will further focus on stress resistance and overall development.

Phytosulfokine-δ: A Small Peptide, but a Big Player in Symbiosis Gene Regulation

Nitrogen availability is one of the critical determinants of agricultural yield. Biological nitrogen fixation, such as legume–rhizobia symbiotic association, might function as a solution to fix nitrogen. Using phytosulfokine (PSK)-α sequences as a query, Yu et al., 2022 performed a comprehensive genome-wide search of legume species to identify PSK-δ, a divergent pentapeptide differing in single amino acid. Furthermore, PSK-δ exhibited nodule-specific expression with lower expression in the root, substantiating the nodule-specific temporal expression and suggesting its role in nodule development and nitrogen fixation. Additionally, in planta functional characterization in Medicago truncatula using overexpression and Tnt1-insertion mutant analysis indicated the role of PSK-δ in symbiotic nodulation. Interestingly, a similar phenotype of MtPSKδ mutant (mtpskδ) with that of wild-type control led to the hypothesis of its functional redundancy with PSK-α in nodule organogenesis. Further investigation regarding its position in the Nod-factor signaling pathway revealed the downstream function of PSK-δ in association with MtENOD11 in regulating nodule formation.

AtABCG14: A Long-Distance Root-to-Shoot Carrier of Cytokinin

Root-synthesized cytokinins regulate the growth, development, and stress responses of aboveground tissues and follow the transport route via xylem tissue. Arabidopsis ATP-binding cassette (ABC) transporter G family member 14 (AtABCG14) is involved in the xylem loading of root-synthesized cytokinins. However, the phloem unloading of root-synthesized cytokinin and shoot distribution have remained elusive. The recent study by Zhao et al., (2021) proved that the AtABCG14 protein mediates the phloem unloading of cytokinins through the apoplastic pathway indicating the AtABCG14 is a master regulator of shoot cytokinin distribution.

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.

Overexpression of DfRaf from Fragrant Woodfern (Dryopteris fragrans) Enhances High-Temperature Tolerance in Tobacco (Nicotiana tabacum)

Heat stress seriously affects medicinal herbs’ growth and yield. Rubisco accumulation factor (Raf) is a key mediator regulating the activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which plays important roles in carbon assimilation and the Calvin cycle in plants. Raf has been studied in many plants, but has rarely been studied in the important medicinal plant fragrant woodfern (Dryopteris fragrans). The aim of this study was to analyze the effects of Raf on carbohydrate metabolism and the response to heat stress in medicinal plants. In this study, high temperature treatment upregulated the expression of DfRaf, which was significantly higher than that of phosphoribokinase (DfPRK), Rubisco small subunits (DfRbcS), Rubisco large subunits (DfRbcL) and Rubisco activase (DfRCA). The subcellular localization showed that the DfRaf proteins were primarily located in the nucleus; DfPRK, DfRbcS, DfRbcL and DfRCA proteins were primarily located in the chloroplast. We found that overexpression of DfRaf led to increased activity of Rubisco, RCA and PRK under high-temperature stress. The H₂O₂, O₂⁻ and MDA content of the DfRaf-OV-L2 and DfRaf-OV-L6 transgenic lines were significantly lower than those of WT and VC plants under high-temperature stress. The photosynthetic pigments, proline, soluble sugar content and ROS-scavenging ability of the DfRaf-OV-L2 and DfRaf-OV-L6 transgenic lines were higher than those of WT and VC plants under high-temperature stress. The results showed that overexpression of the DfRaf gene increased the Rubisco activity, which enhanced the high-temperature tolerance of plants.

The introduced strain Mesorhizobium ciceri USDA3378 is more competitive than an indigenous strain in nodulation of chickpea in newly introduced areas of China

The present study aimed to compare the competitive advantage of two chickpea nodulating rhizobia strains (an indigenous strain Mesorhizobium muleiense CCBAU 83963^T and an introduced strain Mesorhizobium ciceri USDA 3378) in different soils originated from new chickpea cultivation areas of China. The results showed that USDA 3378 had a significant competitive advantage in nodulation, with nodulation occupation rates ranging from 84.6% to 100% in all the sampled soils. According to the efficiency of symbiosis under single inoculation, chickpea plants inoculated with USDA 3378 showed better symbiotic performance based on the plant dry weight, leaf chlorophyll content and nodule numbers. The chickpea plants inoculated with USDA 3378 formed nodules about 2 days earlier than those inoculated with CCBAU 83963^T . The higher growth in media and the stronger adsorption on chickpea roots of USDA 3378 when mixed with CCBAU 83963^T may explain why USDA3378 shows a competitive advantage. The results from this study will contribute towards the development of effective chickpea rhizobial inoculants for soil conditioning and more environmentally friendly production of chickpeas in China.

Genetic and molecular mechanisms underlying root architecture and function under heat stress-A hidden story

Heat stress events are resulting in a significant negative impact on global food production. The dynamics of cellular, molecular and physiological homoeostasis in aboveground parts under heat stress are extensively deciphered. However, root responses to higher soil/air temperature or stress signalling from shoot to root are limited. Therefore, this review presents a holistic view of root physio-morphological and molecular responses to adapt under hotter environments. Heat stress reprogrammes root cellular machinery, including crosstalk between genes, phytohormones, reactive oxygen species (ROS) and antioxidants. Spatio-temporal regulation and long-distance transport of phytohormones, such as auxin, cytokinin and abscisic acid (ABA) determine the root growth and development under heat stress. ABA cardinally integrates a signalling pathway involving heat shock factors, heat shock proteins and ROS to govern heat stress responses. Additionally, epigenetic modifications by transposable elements, DNA methylation and acetylation also regulate root growth under heat stress. Exogenous application of chemical compounds or biological agents such as ascorbic acid, metal ion chelators, fungi and bacteria can alleviate heat stress-induced reduction in root biomass. Future research should focus on the systemic effect of heat stress from shoot to root with more detailed investigations to decipher the molecular cues underlying the roots architecture and function.

Effective Use of Water in Crop Plants in Dryland Agriculture: Implications of Reactive Oxygen Species and Antioxidative System

Under dryland conditions, annual and perennial food crops are exposed to dry spells, severely affecting crop productivity by limiting available soil moisture at critical and sensitive growth stages. Climate variability continues to be the primary cause of uncertainty, often making timing rather than quantity of precipitation the foremost concern. Therefore, mitigation and management of stress experienced by plants due to limited soil moisture are crucial for sustaining crop productivity under current and future harsher environments. Hence, the information generated so far through multiple investigations on mechanisms inducing drought tolerance in plants needs to be translated into tools and techniques for stress management. Scope to accomplish this exists in the inherent capacity of plants to manage stress at the cellular level through various mechanisms. One of the most extensively studied but not conclusive physiological phenomena is the balance between reactive oxygen species (ROS) production and scavenging them through an antioxidative system (AOS), which determines a wide range of damage to the cell, organ, and the plant. In this context, this review aims to examine the possible roles of the ROS-AOS balance in enhancing the effective use of water (EUW) by crops under water-limited dryland conditions. We refer to EUW as biomass produced by plants with available water under soil moisture stress rather than per unit of water (WUE). We hypothesize that EUW can be enhanced by an appropriate balance between water-saving and growth promotion at the whole-plant level during stress and post-stress recovery periods. The ROS-AOS interactions play a crucial role in water-saving mechanisms and biomass accumulation, resulting from growth processes that include cell division, cell expansion, photosynthesis, and translocation of assimilates. Hence, appropriate strategies for manipulating these processes through genetic improvement and/or application of exogenous compounds can provide practical solutions for improving EUW through the optimized ROS-AOS balance under water-limited dryland conditions. This review deals with the role of ROS-AOS in two major EUW determining processes, namely water use and plant growth. It describes implications of the ROS level or content, ROS-producing, and ROS-scavenging enzymes based on plant water status, which ultimately affects photosynthetic efficiency and growth of plants.

Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study

Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.

Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses

The two-component signal transduction system (TCS) acts in a variety of physiological processes in lower organisms and has emerged as a key signaling system in both prokaryotes and eukaryotes, including plants. TCS genes assist plants in processes such as stress resistance, cell division, nutrition signaling, leaf senescence, and chloroplast division. In plants, this system is composed of three types of proteins: response regulators (RRs), histidine kinases (HKs), and histidine phosphotransfer proteins (HPs). We aimed to study the Sorghum bicolor genome and identified 37 SbTCS genes consisting of 13 HKs, 5 HPs, and 19 RRs (3 type-A RRs, 7 type-B RRs, 2 type-C RRs, and 7 pseudo-RRs). The structural and phylogenetic comparison of the SbTCS members with their counterparts in Arabidopsis thaliana, Oryza sativa, Cicer arietinum, and Glycine max showed group-specific conservations and variations. Expansion of the gene family members is mostly a result of gene duplication, of both the tandem and segmental types. HKs and RRs were observed to be originated from segmental duplication, while some HPs originated from tandem duplication. The nuclear genome of S. bicolor contain 10 chromosomes and these SbTCS genes are randomly distributed on all the chromosomes. The promoter sequences of the SbTCS genes contain several abiotic stress-related cis-elements. RNA-seq and qRT-PCR-based expression analysis demonstrated most of the TCS genes were responsive to drought and salt stresses in leaves, which suggest their role in leaf development. This study lays a foundation for further functional study of TCS genes for stress tolerance and developmental improvement in S. bicolor.

Evolutionary and expression dynamics of LRR-RLKs and functional establishment of KLAVIER homolog in shoot mediated regulation of AON in chickpea symbiosis

Chickpea shoot exogenously treated with cytokinin showed stunted phenotype of root, shoot and significantly reduced nodule numbers. Genome-wide identification of LRR-RLKs in chickpea and Medicago resulted in 200 and 371 genes respectively. Gene duplication analysis revealed that LRR-RLKs family expanded through segmental duplications in chickpea and tandem duplications in Medicago. Expression profiling of LRR-RLKs revealed their involvement in cytokinin signaling and plant organ development. Overexpression of KLAVIER ortholog of chickpea, Ca_LRR-RLK147, in roots revealed its localization in the membrane but showed no effect on root nodulation despite increased cle peptide levels. Two findings (i) drastic effect on nodule number by exogenous cytokinin treatment to only shoot and restoration to normal nodulation by treatment to both root and shoot tissue and (ii) no effect on nodule number by overexpression of Ca_LRR-RLK147 establishes the fact that despite presence of cle peptides in root, the function of Ca_LRR-RLK147 was shoot mediated during AON.