Browsing by Author "Laxmi, Ashverya"

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Arabidopsis RSS1 mediates cross-talk between glucose and light signaling during hypocotyl elongation growth
(Nature Publishing Group, 2017) Singh, Manjul; Gupta, Aditi; Singh, Dhriti; Khurana, Jitendra P.; Laxmi, Ashverya
Plants possess exuberant plasticity that facilitates its ability to adapt and survive under challenging environmental conditions. The developmental plasticity largely depends upon cellular elongation which is governed by a complex network of environmental and phytohormonal signals. Here, we report role of glucose (Glc) and Glc-regulated factors in controlling elongation growth and shade response in Arabidopsis. Glc controls shade induced hypocotyl elongation in a dose dependent manner. We have identified a Glc repressed factor REGULATED BY SUGAR AND SHADE1 (RSS1) encoding for an atypical basic helix-loop-helix (bHLH) protein of unknown biological function that is required for normal Glc actions. Phenotype analysis of mutant and overexpression lines suggested RSS1 to be a negative regulator of elongation growth. RSS1 affects overall auxin homeostasis. RSS1 interacts with the elongation growth-promoting proteins HOMOLOG OF BEE2 INTERACTING WITH IBH 1 (HBI1) and BR ENHANCED EXPRESSION2 (BEE2) and negatively affects the transcription of their downstream targets such as YUCs, INDOLE-3-ACETIC ACID INDUCIBLE (IAAs), LONG HYPOCOTYL IN FAR-RED1 (HFR1), HOMEOBOX PROTEIN 2 (ATHB2), XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASES (XTHs) and EXPANSINS. We propose, Glc signals might maintain optimal hypocotyl elongation under multiple signals such as light, shade and phytohormones through the central growth regulatory bHLH/HLH module.
Arabidopsis target of rapamycin coordinates with transcriptional and epigenetic machinery to regulate thermotolerance
(Frontiers Media S.A., 2021) Sharma, Mohan; Jamsheer, K.M.; Shukla, Brihaspati Narayan; Sharma, Manvi; Awasthi, Prakhar; Mahtha, Sanjeet Kumar; Yadav, Gitanjali; Laxmi, Ashverya
Global warming exhibits profound effects on plant fitness and productivity. To withstand stress, plants sacrifice their growth and activate protective stress responses for ensuring survival. However, the switch between growth and stress is largely elusive. In the past decade, the role of the target of rapamycin (TOR) linking energy and stress signalling is emerging. Here, we have identified an important role of Glucose (Glc)-TOR signalling in plant adaptation to heat stress (HS). Glc via TOR governs the transcriptome reprogramming of a large number of genes involved in heat stress protection. Downstream to Glc-TOR, the E2Fa signalling module regulates the transcription of heat shock factors through direct recruitment of E2Fa onto their promoter regions. Also, Glc epigenetically regulates the transcription of core HS signalling genes in a TOR-dependent manner. TOR acts in concert with p300/CREB HISTONE ACETYLTRANSFERASE1 (HAC1) and dictates the epigenetic landscape of HS loci to regulate thermotolerance. Arabidopsis plants defective in TOR and HAC1 exhibited reduced thermotolerance with a decrease in the expression of core HS signalling genes. Together, our findings reveal a mechanistic framework in which Glc-TOR signalling through different modules integrates stress and energy signalling to regulate thermotolerance.
Balancing growth and defense: Role of target of rapamycin and SNF1-related protein kinase 1 in stress signaling in plants
(John Wiley & Sons, 2021) Sharma, Mohan; Jamsheer, K. Muhammed; Saksena, Harshita B.; Jindal, Sunita; Sharma, Manvi; Singh, Dhriti; Tiwari, Archna; Awasthi, Prakhar; Laxmi, Ashverya
Plants have to maintain the growth and at the same time need to be vigilant about the imminent threat such as pathogen attack and unfavorable growth conditions. It is been observed that the energy status of the plant is an important determinant of the response to stress factors. The Target Of Rapamycin (TOR) and SNF1-Related Protein Kinase 1 (SnRK1) are serine/threonine kinases that originated early in the eukaryotic evolution, work as energy gauges in all eukaryotic lineages. During favorable growth conditions, the nutrient abundance activates TOR, which promotes growth through activation of general protein translation and cell cycle progression. The stress conditions can severely limit energy production, which can activate SnRK1 signaling. By inhibiting TOR kinase and through other effector proteins, the SnRK1 pathway enables the plants to survive in unfavorable growth conditions. The past decade opened a floodgate of studies regarding TOR and SnRK1 interaction regulating growth-defense trade-offs and stress mitigation. This also opened avenues for the utilization of these pathways for crop improvement. This chapter will succinctly summarize the current knowledge in this field and discuss the future direction of research.
CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plant
(Wiley-Blackwell, 2009) Tripathi, Vineeta; Parasuraman, Boominathan; Laxmi, Ashverya; Chattopadhyay, Debasis
Calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CIPK) mediate plant responses to a variety of external stresses. Here we report that Arabidopsis CIPK6 is also required for the growth and development of plants. Phenotype of tobacco plants ectopically expressing a homologous gene (CaCIPK6) from the leguminous plant chickpea (Cicer arietinum) indicated its functional conservation. A lesion in AtCIPK6 significantly reduced shoot-to-root and root basipetal auxin transport, and the plants exhibited developmental defects such as fused cotyledons, swollen hypocotyls and compromised lateral root formation, in conjunction with reduced expression of a number of genes involved in auxin transport and abiotic stress response. The Arabidopsis mutant was more sensitive to salt stress compared to wild-type, while overexpression of a constitutively active mutant of CaCIPK6 promoted salt tolerance in transgenic tobacco. Furthermore, tobacco seedlings expressing the constitutively active mutant of CaCIPK6 showed a developed root system, increased basipetal auxin transport and hypersensitivity to auxin. Our results provide evidence for involvement of a CIPK in auxin transport and consequently in root development, as well as in the salt-stress response, by regulating the expression of genes.
Complex genetic interaction between glucose sensor HXK1 and E3 SUMO ligase SIZ1 in regulating plant morphogenesis
(Taylor & Francis Group, 2024) Rawat, Sanjay Singh; Sandhya, Shital; Laxmi, Ashverya
Sugar signaling forms the basis of metabolic activities crucial for an organism to perform essential life activities. In plants, sugars like glucose, mediate a wide range of physiological responses ranging from seed germination to cell senescence. This has led to the elucidation of cell signaling pathways involving glucose and its counterparts and the mechanism of how these sugars take control over major hormonal pathways such as auxin, ethylene, abscisic acid and cytokinin in Arabidopsis. Plants use HXK1(Hexokinase) as a glucose sensor to modulate changes in photosynthetic gene expression in response to high glucose levels. Other proteins such as SIZ1, a major SUMO E3 ligase have recently been implicated in controlling sugar responses via transcriptional and translational regulation of a wide array of sugar metabolic genes. Here, we show that these two genes work antagonistically and are epistatic in controlling responsiveness toward high glucose conditions.
Comprehensive evolutionary and expression analysis of FCS-like zinc finger gene family yields insights into their origin, expansion and divergence
(PLOS, 2015) K, Muhammed Jamsheer; Mannully, Chanchal Thomas; Gopan, Nandu; Laxmi, Ashverya
Plant evolution is characterized by frequent genome duplication events. Expansion of habitat resulted in the origin of many novel genes and genome duplication events which in turn resulted in the expansion of many regulatory gene families. The plant-specific FCS-Like Zinc finger (FLZ) gene family is characterized by the presence of a FCS-Like Zinc finger (FLZ) domain which mediates the protein-protein interaction. In this study, we identified that the expansion of FLZ gene family size in different species is correlated with ancestral and lineage-specific whole genome duplication events. The subsequent gene loss found to have a greater role in determining the size of this gene family in many species. However, genomic block duplications played the significant role in the expansion of FLZ gene family in some species. Comparison of Arabidopsis thaliana and Oryza sativa FLZ gene family revealed monocot and dicot specific evolutionary trends. The FLZ genes were found to be under high purifying selection. The spatiotemporal expression analyses of Arabidopsis thaliana FLZ gene family revealed that majority of the members are highly expressed in reproductive organs. FLZ genes were also found to be highly expressed during vegetative-to-reproductive phase transition which is correlated with the proposed role of this gene family in sugar signaling. The comparison of sequence, structural and expression features of duplicated genes identified lineage-specific redundancy and divergence. This extensive evolutionary analysis and expression analysis of Arabidopsis thaliana FLZ genes will pave the way for further functional analysis of FLZ genes.
The confluence of TOR signaling and plant growth regulators in development and stress responses
(Oxford University Press, 2026) Saksena, Harshita B; Kumar, Mukesh; Samtani, Harsha; Sharma, Aishwarye; Rawat, Sanjay Singh; Awasthi, Prakhar; Botta, Halidev Krishna; Sandhya, Shital; Pande, Anjali; Naaz, Sheeba; Kushwah, Sunita; Shukla, Brihaspati N; Laxmi, Ashverya
The Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that serves as a crucial signaling hub, seamlessly integrating a wide range of internal and external signals to meticulously regulate cellular and organismal physiology. TOR is crucial in regulating the different phases of lifecycle in plants including embryogenesis, seed germination, meristem activation, root and leaf development, flowering and senescence. Beyond its central role in growth and development, emerging research has revealed its significant involvement in the response to environmental stresses. Even though plant growth regulators such as auxin, cytokinin (CK), brassinosteroid (BR), gibberellin (GA), abscisic acid (ABA), ethylene (ET), salicylic acid (SA), jasmonic acid (JA) and nitric oxide (NO) function as pivotal signaling molecules in modulating plant development and stress responses, how they coordinate with the energy status still remains obscure. Here we summarize the current findings on the dynamic interconnection between TOR and these discrete phytoregulators and their potential role in executing diverse biological processes in plants.
Cross-talk between brassinosteroids and other phytohormones: biological functions and molecular mechanism
(Elsevier B.V., 2022) Gupta, Aditi; Singh, Manjul; Singh, Dhriti; Laxmi, Ashverya
To maintain optimal growth and survival, plants balance complex developmental processes while simultaneously sensing and responding to both endogenous physiological factors and changes in their surroundings. Phytohormones are an important class of compounds, which regulate various aspects of plant development and responses to adverse environmental conditions. With the signaling pathways well worked out for most of the hormones, it is evident that these signaling pathways interact in a complex network to coordinate such processes. Besides the five established classical groups of phytohormones, brassinosteroids (BRs) have emerged as prominent phytohormones in recent times. BRs are not only strong modulators of cellular division, cellular elongation, and cellular differentiation across plant tissues but also they make a significant contribution in improving adaptation to various stresses. This chapter summarizes mechanisms regulating production, homeostasis, signaling of BR and their interconnections with different plant hormones to control plant growth and adaptation.
Cytokinin interplay with ethylene, auxin and glucose signaling controls Arabidopsis seedling root directional growth
(Am. Soc. of Plant Biologists, 2011) Kushwah, Sunita; Jones, Alan M.; Laxmi, Ashverya
Optimal root architecture is established by multiple intrinsic (e.g. hormones) and extrinsic (e.g. gravity and touch) signals and is established, in part, by directed root growth. We show that asymmetrical exposure of cytokinin (CK) at the root tip in Arabidopsis (Arabidopsis thaliana) promotes cell elongation that is potentiated by glucose in a hexokinase-influenced, G protein-independent manner. This mode of CK signaling requires the CK receptor, ARABIDOPSIS HISTIDINE KINASE4 and, at a minimum, its cognate type B ARABIDOPSIS RESPONSE REGULATORS ARR1, ARR10, and ARR11 for full responsiveness, while type A response regulators act redundantly to attenuate this CK response. Ethylene signaling through the ethylene receptor ETHYLENE RESISTANT1 and its downstream signaling element ETHYLENE INSENSITIVE2 are required for CK-induced root cell elongation. Negative and positive feedback loops are reinforced by CK regulation of the expression of the genes encoding these elements in both the CK and ethylene signaling pathways. Auxin transport facilitated by PIN-FORMED2 as well as auxin signaling through control of the steady-state level of transcriptional repressors INDOLE-3-ACETIC ACID7 (IAA7), IAA14, and IAA17 via TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN are involved in CK-induced root cell elongation. This action lies downstream of ethylene and CK induction. Intrinsic signaling in this response operates independently of the extrinsic signal touch, although actin filament organization, which is important in the touch response, may be important for this response, since latrunculin B can induce similar growth. This root growth response may have adaptive significance, since CK responsiveness is inversely related to root coiling and waving, two root behaviors known to be important for fitness.
Cytokinin-induced root growth involves actin filament reorganization
(Landes Bioscience, 2011) Kushwah, Sunita; Jones, Alan M.; Laxmi, Ashverya
Root architecture is developmentally plastic and affected by many intrinsic factors (e.g. plant hormones) and extrinsic factors (e.g. touch, gravity) in order to maximize nutrient and water acquisition. We have recently shown that asymmetrical exposure of cytokinin (CK) at the root tip causes root growth directional changes that is dependent on ethylene signaling and is potentiated by glucose signaling. Auxin homeostasis as maintained by auxin signaling and transport is also involved in CK-induced root cell elongation and differential growth. The signaling pathways eventually converge at actin filament organization since actin filament organization inhibitor latrunculin B (Lat B) can also induce similar growth. We, show that CK can actually alter actin filament organization as seen in actin binding protein 35S::GFP-ABD2-GFP transgenic lines as is also altered by auxin polar transport inhibitor 1-N-naphthylphthalamic acid (NPA) and Lat B in different manners.
Cytokinin-mediated repression of anthocyanin biosynthesis in banana fruits
(John Wiley & Sons, 2025) Rajput, Ruchika; Tyagi, Shivi; Anchal, Kumar; Singh, Samar; Laxmi, Ashverya; Misra, Prashant; Pandey, Ashutosh
Anthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. This study compares two banana cultivars, Grand Naine (GN) and Red Banana (RB), which exhibit significant differences in anthocyanin pigmentation. Transcriptomic profiling of peel (PL) and pulp (PP) tissues revealed cytokinin-responsive type-B response regulators (RRs), MaRR_B9 and MaRR_B12, as key modulators of anthocyanin biosynthesis. Cytokinin treatment of PP tissues increased the expression of MaRR_B9 and MaRR_B12, while significantly reducing the expression of dihydroflavanol reductase (MaDFR1, MaDFR2) and anthocyanidin synthase (MaANS) genes along with anthocyanin content. Through a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, MaDFRs and MaANS. Additionally, a type B-RRs motif (AGATT) was identified in the promoter regions of MaDFR2 and MaANS, suggesting that MaRRs might directly regulate the transcription of MaDFR2 and MaANS. MaRR_B9 and MaRR_B12 interact with the promoters of MaDFR2 and MaANS, repressing these genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, notably the cyanidin derivative, accompanied by altered expression patterns of MaDFRs and MaANS. Thus, the present study identifies MaRR_B9 and MaRR_B12 as novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs, for the genetic optimization aimed at enhancing anthocyanin content, stress resilience, and nutritional value in crop plants.
Deciphering the physiological and molecular functions of phytohormones
(Elsevier B.V., 2023) Sharma, Manvi; Laxmi, Ashverya
Plants rely on a diverse set of small molecules called phytohormones for growth, development, and adaptability. Since the discovery of auxin, hormones have been at the frontier of plant biology. Classically, hormone functions and responses were studied using synthetic hormones and analogs. However, the advent of technology, multidisciplinary approaches, and the genome sequencing of the model system of Arabidopsis and rice has dramatically increased our understanding of physiological and molecular mechanisms driving plant hormone actions. In this chapter, we talk about how independent or combined molecular action of phytohormones such as with their signaling components and regulators leads to changes in plant physiology to regulate multiple aspects of plant development, defense, and adaptation. We envisage that such detailed knowledge will allow a far greater understanding of the complex dynamics underlying plant hormone action.
DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction
(PLOS, 2014) K, Muhammed Jamsheer; Laxmi, Ashverya
Zinc fingers are a ubiquitous class of protein domain with considerable variation in structure and function. Zf-FCS is a highly diverged group of C2-C2 zinc finger which is present in animals, prokaryotes and viruses, but not in plants. In this study we identified that a plant specific domain of unknown function, DUF581 is a zf-FCS type zinc finger. Based on HMM-HMM comparison and signature motif similarity we named this domain as FCS-Like Zinc finger (FLZ) domain. A genome wide survey identified that FLZ domain containing genes are bryophytic in origin and this gene family is expanded in spermatophytes. Expression analysis of selected FLZ gene family members of A. thaliana identified an overlapping expression pattern suggesting a possible redundancy in their function. Unlike the zf-FCS domain, the FLZ domain found to be highly conserved in sequence and structure. Using a combination of bioinformatic and protein-protein interaction tools, we identified that FLZ domain is involved in protein-protein interaction.
Ethylene acts as a negative regulator of glucose induced lateral root emergence in Arabidopsis
(Taylor & Francis Group, 2015) Singh, Manjul; Gupta, Aditi; Laxmi, Ashverya
Plants, being sessile organisms, are more exposed to the hazards of constantly changing environmental conditions globally. During the lifetime of a plant, the root system encounters various challenges such as obstacles, pathogens, high salinity, water logging, nutrient scarcity etc. The developmental plasticity of the root system provides brilliant adaptability to plants to counter the changes exerted by both external as well as internal cues and achieve an optimized growth status. Phytohormones are one of the major intrinsic factors regulating all aspects of plant growth and development both independently as well as through complex signal integrations at multiple levels. We have previously shown that glucose (Glc) and brassinosteroid (BR) signalings interact extensively to regulate lateral root (LR) development in Arabidopsis. (1) Auxin efflux as well as influx and downstream signaling components are also involved in Glc-BR regulation of LR emergence. Here, we provide evidence for involvement of ethylene signaling machinery downstream to Glc and BR in regulation of LR emergence.
Evolution of TOR-SnRK dynamics in green plants and its integration with phytohormone signaling networks
(Oxford University Press, 2019) Jamsheer, K Muhammed; Jindal, Sunita; Laxmi, Ashverya
The Target Of Rapamycin-SNF1-Related Protein Kinase 1 (TOR-SnRK1) arms race is an ancient regulatory mechanism evolved in eukaryotes to regulate nutrient-dependent growth. The autotrophic nature makes plants a distinct class in the eukaryotic lineage. Although TOR-SnRK1 signaling cascade shows highly conserved functions, studies in the past two decades identified many important plant-specific innovations in this pathway. Plants also possess SnRK2 and SnRK3 kinases which are originated from the ancient SnRK1-related kinases and do specialized functions in controlling growth, stress responses and nutrient homeostasis in plants. Recently, an integrative picture has started to emerge where different SnRKs and TOR kinase are highly interconnected to control nutrient and stress responses of plants. Further, these kinases are intimately involved with phytohormone signaling networks which originated at different stages of plant evolution. In this review, we are highlighting the evolution and divergence of TOR-SnRKs signaling components in plants and their communication between each other and phytohormone signaling to fine-tune growth and stress responses in plants.
Expression of Arabidopsis FCS-like zinc finger genes is differentially regulated by sugars, cellular energy level, and abiotic stress
(Frontiers Media S.A., 2015) K, Muhammed Jamsheer; Laxmi, Ashverya
Cellular energy status is an important regulator of plant growth, development, and stress mitigation. Environmental stresses ultimately lead to energy deficit in the cell which activates the SNF1-RELATED KINASE 1 (SnRK1) signaling cascade which eventually triggering a massive reprogramming of transcription to enable the plant to survive under low-energy conditions. The role of Arabidopsis thaliana FCS-Like Zinc finger (FLZ) gene family in energy and stress signaling is recently come to highlight after their interaction with kinase subunits of SnRK1 were identified. In a detailed expression analysis in different sugars, energy starvation, and replenishment series, we identified that the expression of most of the FLZ genes is differentially modulated by cellular energy level. It was found that FLZ gene family contains genes which are both positively and negatively regulated by energy deficit as well as energy-rich conditions. Genetic and pharmacological studies identified the role of HEXOKINASE 1- dependent and energy signaling pathways in the sugar-induced expression of FLZ genes. Further, these genes were also found to be highly responsive to different stresses as well as abscisic acid. In over-expression of kinase subunit of SnRK1, FLZ genes were found to be differentially regulated in accordance with their response toward energy fluctuation suggesting that these genes may work downstream to the established SnRK1 signaling under low-energy stress. Taken together, the present study provides a conceptual framework for further studies related to SnRK1-FLZ interaction in relation to sugar and energy signaling and stress response
The FCS-LIKE ZINC FINGER 6 and 10 are involved in regulating osmotic stress responses in Arabidopsis
(Taylor & Francis Group, 2019) Jamsheer, K Muhammed; Singh, Dhriti; Sharma, Mohan; Sharma, Manvi; Jindal, Sunita; Mannully, Chanchal T.; Shukla, Brihaspati N.; Laxmi, Ashverya
The TARGET OF RAPAMYCIN-SNF1-RELATED PROTEIN KINASE 1 (TOR-SnRK1) arms race is a key regulator of plant growth in response to energy fluctuations and stress. Recently, we have identified that two members of the FCS-LIKE ZINC FINGER (FLZ) protein family, FLZ6 and 10, repress SnRK1 signaling and thereby involved in the activation of the TARGET OF RAPAMYCIN (TOR) signaling. In this study, we demonstrate that FLZ6 and 10 are also involved in the regulation of osmotic stress responses. Downregulation of FLZ6 and 10 results in enhanced expression of stress-responsive genes and better resilience towards osmotic stress at the seedling stage. These results indicate that FLZ6 and 10 are involved in the regulation of stress mitigation in plants through directly affecting SnRK1 signaling.
FCS-like zinc finger 6 and 10 repress SnRK1 signalling in Arabidopsis
(John Wiley & Sons, 2018) Jamsheer, Muhammed K.; Sharma, Manvi; Singh, Dhriti; Mannully, Chanchal Thomas; Jindal, Sunita; Shukla, Brihaspati Narayan; Laxmi, Ashverya
SNF1-Related Protein Kinase 1 (SnRK1) is a central regulator of plant growth during energy starvation. The FCS-Like Zinc finger (FLZ) proteins are recently identified adaptor proteins which facilitate the interaction of SnRK1 with other proteins. In this study, we identified that two starvation-induced FLZ genes, FLZ6 and FLZ10, work as repressors of SnRK1 signalling. The reduced expression of these genes resulted in an increase in the level of SnRK1α1, which is the major catalytic subunit of SnRK1. This resulted in a concomitant increase in the phosphorylated protein and SnRK1 activity in the flz6 and flz10 mutants. FLZ6 and FLZ10 specifically interact with SnRK1α subunits in the cytoplasmic foci which colocalized with the endoplasmic reticulum. In physiological assays, similar to SnRK1α1 overexpression line, flz mutants showed compromised growth. Further, the growth promotion in response to favourable growth conditions was found to be attenuated in the mutants. The enhanced SnRK1 activity in the mutants resulted in a reduction in the level of phosphorylated RIBOSOMAL S6 KINASE and the expression of E2Fa and its targets indicating that TARGET OF RAPAMYCIN-dependent promotion of protein synthesis and cell cycle progression is impaired. Taken together, this study uncovers a plant-specific modulation of SnRK1 signalling.
The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions
(The American Society for Biochemistry and Molecular Biology, 2018) Jamsheer, K Muhammed; Shukla, Brihaspati N.; Jindal, Sunita; Gopan, Nandu; Mannully, Chanchal Thomas; Laxmi, Ashverya
The SNF1-related protein kinase 1 (SnRK1) is a heterotrimeric eukaryotic kinase that interacts with diverse proteins and regulates their activity in response to starvation and stress signals. Recently, the FCS-like zinc finger (FLZ) proteins were identified as a potential scaffold for SnRK1 in plants. However, the evolutionary and mechanistic aspect of this complex formation is currently unknown. Here, in silico analyses predicted that FLZ proteins possess conserved intrinsically disordered regions (IDRs) with a propensity for protein binding in the N and C termini across the plant lineage. We observed that the Arabidopsis FLZ proteins promiscuously interact with SnRK1 subunits, which formed different isoenzyme complexes. The FLZ domain was essential for mediating the interaction with SnRK1α subunits, whereas the IDRs in the N termini facilitated interactions with the β and βγ subunits of SnRK1. Furthermore, the IDRs in the N termini were important for mediating dimerization of different FLZ proteins. Of note, the interaction of FLZ with SnRK1 was confined to cytoplasmic foci, which colocalized with the endoplasmic reticulum. An evolutionary analysis revealed that in general, the IDR-rich regions are under more relaxed selection than the FLZ domain. In summary, the findings in our study reveal the structural details, origin, and evolution of a land plant–specific scaffold of SnRK1 formed by the coordinated actions of IDRs and structured regions in the FLZ proteins. We propose that the FLZ protein complex might be involved in providing flexibility, thus enhancing the binding repertoire of the SnRK1 hub in land plants.
Genome-wide identification and expression, protein-protein interaction and evolutionary analysis of the seed plant-specific BIG GRAIN and BIG GRAIN LIKE gene family
(Frontiers Media S.A., 2017) Mishra, Bhuwaneshwar S.; Jamsheer, K Muhammed; Singh, Dhriti; Sharma, Manvi; Laxmi, Ashverya
BIG GRAIN1 (BG1) is an auxin-regulated gene which functions in auxin pathway and positively regulates biomass, grain size and yield in rice. However, the evolutionary origin and divergence of these genes are still unknown. In this study, we found that BG genes are probably originated in seed plants. We also identified that seed plants evolved a class of BIG GRAIN LIKE (BGL) genes which share conserved middle and C-terminal motifs with BG. The BG genes were present in all monocot and eudicot species analyzed; however, the BGL genes were absent in few monocot lineages. Both BG and BGL were found to be serine-rich proteins; however, differences in expansion and rates of retention after whole genome duplication events were observed. Promoters of BG and BGL genes were found to be enriched with auxin-responsive elements and the Arabidopsis thaliana BG and BGL genes were found to be auxin-regulated. The auxin-induced expression of AthBG2 was found to be dependent on the conserved ARF17/19 module. Protein-protein interaction analysis identified that AthBG2 interact with regulators of splicing, transcription and chromatin remodeling. Taken together, this study provides interesting insights about BG and BGL genes and incentivizes future work in this gene family which has the potential to be used for crop manipulation.