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1.
BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut.
Zhang, K, Yuan, M, Xia, H, He, L, Ma, J, Wang, M, Zhao, H, Hou, L, Zhao, S, Li, P, et al
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2022;(5):1529-1540
Abstract
The candidate recessive gene AhRt2 responsible for red testa of peanut was identified through combined BSA-seq and linkage mapping approaches. The testa color of peanuts (Arachis hypogaea L.) is an important trait, and those with red testa are particularly popular owing to the high-anthocyanin content. However, the identification of genes underlying the regulation of the red testa trait in peanut are rarely reported. In order to fine map red testa gene, two F2:4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and ZH2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identified on chromosome 12, which was further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Furthermore, functional annotation, expression profiling, and the analyses of sequence variation confirmed that the anthocyanin reductase namely (Arahy.IK60LM) was the most likely candidate gene for AhRt2. It was found that a SNP in the third exon of AhRt2 altered the encoding amino acids, and was associated with red testa in peanut. In addition, a closely linked molecular marker linked with red testa trait in peanut was also developed for future studies. Our results provide valuable insight into the molecular mechanism underlying peanut testa color and present significant diagnostic marker resources for marker-assisted selected breeding in peanut.
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2.
An Anecdote on Prospective Protein Targets for Developing Novel Plant Growth Regulators.
Patel, R, Mehta, K, Goswami, D, Saraf, M
Molecular biotechnology. 2022;(2):109-129
Abstract
Phytohormones are the main regulatory molecules of core signalling networks associated with plant life cycle regulation. Manipulation of hormone signalling cascade enables the control over physiological traits of plant, which has major applications in field of agriculture and food sustainability. Hence, stable analogues of these hormones are long sought after and many of them are currently known, but the quest for more effective, stable and economically viable analogues is still going on. This search has been further strengthened by the identification of the components of signalling cascade such as receptors, downstream cascade members and transcription factors. Furthermore, many proteins of phytohormone cascades are available in crystallized forms. Such crystallized structures can provide the basis for identification of novel interacting compounds using in silico approach. Plenty of computational tools and bioinformatics software are now available that can aid in this process. Here, the metadata of all the major phytohormone signalling cascades are presented along with discussion on major protein-ligand interactions and protein components that may act as a potential target for manipulation of phytohormone signalling cascade. Furthermore, structural aspects of phytohormones and their known analogues are also discussed that can provide the basis for the synthesis of novel analogues.
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3.
The phosphoinositide PI(3,5)P2 inhibits the activity of plant NHX proton/potassium antiporters: Advantages of a novel electrophysiological approach.
Gradogna, A, Pardo, JM, Carpaneto, A
Biomolecular concepts. 2022;(1):119-125
Abstract
In the present work, we discuss the way in which the parallel application of the patch-clamp technique and the 2',7'-bis-(2-carboxyethyl)-5(6)-carboxyfluorescein (BCECF) fluorescence detection for recording luminal proton changes allows the functional characterization of nonelectrogenic potassium/proton vacuolar antiporters of the NHX (Na+/H+ exchanger) family. Moreover, we review the functional role of the tonoplast-specific phosphoinositide PI(3,5)P2, able to simultaneously inhibit the activity of NHXs and CLC-a transporters, whose coordinated action can play an important role in the water balance of plant cells.
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4.
Brassinosteroids (BRs) Role in Plant Development and Coping with Different Stresses.
Manghwar, H, Hussain, A, Ali, Q, Liu, F
International journal of molecular sciences. 2022;(3)
Abstract
Plants are vulnerable to a number of abiotic and biotic stresses that cause a substantial decrease in the production of plants. Plants respond to different environmental stresses by experiencing a series of molecular and physiological changes coordinated by various phytohormones. The use of phytohormones to alleviate stresses has recently achieved increasing interest. Brassinosteroids (BRs) are a group of polyhydroxylated steroidal phytohormones that are required for the development, growth, and productivity of plants. These hormones are involved in regulating the division, elongation, and differentiation of numerous cell types throughout the entire plant life cycle. BR studies have drawn the interest of plant scientists over the last few decades due to their flexible ability to mitigate different environmental stresses. BRs have been shown in numerous studies to have a positive impact on plant responses to various biotic and abiotic stresses. BR receptors detect the BR at the cell surface, triggering a series of phosphorylation events that activate the central transcription factor (TF) Brassinazole-resistant 1 (BZR1), which regulates the transcription of BR-responsive genes in the nucleus. This review discusses the discovery, occurrence, and chemical structure of BRs in plants. Furthermore, their role in the growth and development of plants, and against various stresses, is discussed. Finally, BR signaling in plants is discussed.
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5.
PIP aquaporin pH-sensing is regulated by the length and charge of the C-terminal region.
Scochera, F, Zerbetto De Palma, G, Canessa Fortuna, A, Chevriau, J, Toriano, R, Soto, G, Zeida, A, Alleva, K
The FEBS journal. 2022;(1):246-261
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Abstract
Plant PIP aquaporins play a central role in controlling plant water status. The current structural model for PIP pH-gating states that the main pH sensor is located in loopD and that all the mobile cytosolic elements participate in a complex interaction network that ensures the closed structure. However, the precise participation of the last part of the C-terminal domain (CT) in PIP pH gating remains unknown. This last part has not been resolved in PIP crystal structures and is a key difference between PIP1 and PIP2 paralogues. Here, by a combined experimental and computational approach, we provide data about the role of CT in pH gating of Beta vulgaris PIP. We demonstrate that the length of CT and the positive charge located among its last residues modulate the pH at which the open/closed transition occurs. We also postulate a molecular-based mechanism for the differential pH sensing in PIP homo- or heterotetramers by performing atomistic molecular dynamics simulations (MDS) on complete models of PIP tetramers. Our findings show that the last part of CT can affect the environment of loopD pH sensors in the closed state. Results presented herein contribute to the understanding of how the characteristics of CT in PIP channels play a crucial role in determining the pH at which water transport through these channels is blocked, highlighting the relevance of the differentially conserved very last residues in PIP1 and PIP2 paralogues.
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6.
Structural and functional analysis of Chitinase-IV of Brassica juncea: molecular modeling and dynamic simulation study.
Ayyamperumal, S, Jade, D, Tallapaneni, V, Mohan, S, Barge, S, Moola Joghee, N, M J N, C
Journal of biomolecular structure & dynamics. 2022;(4):1830-1842
Abstract
Brassica juncea is an important oil seed crop. The productivity of this plant, however, is known to be low due to the attack of plant pathogens. The plant chitinase-IV is known to hydrolyse the chitin present in the cell walls of the plant pathogens and thus enhance the plant defense systems. In this connection, studies were carried out by us on the prediction and characterization of the 3D structure of chitinase-IV, the structural changes that take place when the protein is in complex with Allosamidin and the chitin fragments (Tri-oligosaccharide and N-acetyl glucosamine) that act as elicitors to induce plant innate immunity against the invading pathogens, and molecular dynamic simulation studies on the stability of these complexes. These studies are expected to give us an insight into the chitin-binding domain and information on the dynamics and energetics of the protein, which is not possible to obtain by experimental methods. The predicted 3D structure of the protein should give us a better understanding of the molecular function of the chitinase gene in Brassica juncea for devising better methods of biocontrol against fungal phytopathogens and harmful insects so as to increase the crop yield.
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7.
The Role of Hydrogen Sulfide in Plant Roots during Development and in Response to Abiotic Stress.
Li, H, Chen, H, Chen, L, Wang, C
International journal of molecular sciences. 2022;(3)
Abstract
Hydrogen sulfide (H2S) is regarded as a "New Warrior" for managing plant stress. It also plays an important role in plant growth and development. The regulation of root system architecture (RSA) by H2S has been widely recognized. Plants are dependent on the RSA to meet their water and nutritional requirements. They are also partially dependent on the RSA for adapting to environment change. Therefore, a good understanding of how H2S affects the RSA could lead to improvements in both crop function and resistance to environmental change. In this review, we summarized the regulating effects of H2S on the RSA in terms of primary root growth, lateral and adventitious root formation, root hair development, and the formation of nodules. We also discussed the genes involved in the regulation of the RSA by H2S, and the relationships with other signal pathways. In addition, we discussed how H2S regulates root growth in response to abiotic stress. This review could provide a comprehensive understanding of the role of H2S in roots during development and under abiotic stress.
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8.
Ca2+-CBL-CIPK: a modulator system for efficient nutrient acquisition.
Verma, P, Sanyal, SK, Pandey, GK
Plant cell reports. 2021;(11):2111-2122
Abstract
Calcium (Ca2+) is a universal second messenger essential for the growth and development of plants in normal and stress situations. In plants, the proteins, CBL (calcineurin B-like) and CIPK (CBL-interacting protein kinase), form one of the important Ca2+ decoding complexes to decipher Ca2+ signals elicited by environmental challenges. Multiple interactors distinguish CBL and CIPK protein family members to form a signaling network for regulated perception and transduction of environmental signals, e.g., signals generated under nutrient stress conditions. Conservation of equilibrium in response to varying soil nutrient status is an important aspect for plant vigor and yield. Signaling processes have been reported to observe nutrient fluctuations as a signal responsible for regulated nutrient transport adaptation. Recent studies have identified downstream targets of CBL-CIPK modules as ion channels or transporters and their association in signaling nutrient disposal including potassium, nitrate, ammonium, magnesium, zinc, boron, and iron. Ca2+-CBL-CIPK pathway modulates ion transporters/channels and hence maintains a homeostasis of several important plant nutrients in the cytosol and sub-cellular compartments. In this article, we summarize recent literature to discuss the role of the Ca2+-CBL-CIPK pathway in cellular osmoregulation and homeostasis on exposure to nutrient excess or deprived soils. This further establishes a link between taking up the nutrient in the roots and its distribution and homeostasis during the generation of signal for the development and survival of plants.
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Hydroxyurea and Caffeine Impact pRb-like Protein-Dependent Chromatin Architecture Profiles in Interphase Cells of Vicia faba.
Musiałek, MW, Deckert, J, Rybaczek, D
International journal of molecular sciences. 2021;(9)
Abstract
The survival of cells depends on their ability to replicate correctly genetic material. Cells exposed to replication stress can experience a number of problems that may lead to deregulated proliferation, the development of cancer, and/or programmed cell death. In this article, we have induced prolonged replication arrest via hydroxyurea (HU) treatment and also premature chromosome condensation (PCC) by co-treatment with HU and caffeine (CF) in the root meristem cells of Vicia faba. We have analyzed the changes in the activities of retinoblastoma-like protein (RbS807/811ph). Results obtained from the immunocytochemical detection of RbS807/811ph allowed us to distinguish five unique activity profiles of pRb. We have also performed detailed 3D modeling using Blender 2.9.1., based on the original data and some final conclusions. 3D models helped us to visualize better the events occurring within the nuclei and acted as a high-resolution aid for presenting the results. We have found that, despite the decrease in pRb activity, its activity profiles were mostly intact and clearly recognizable, with some local alterations that may correspond to the increased demand in transcriptional activity. Our findings suggest that Vicia faba's ability to withstand harsh environments may come from its well-developed and highly effective response to replication stress.
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10.
On the biosynthesis and evolution of apocarotenoid plant growth regulators.
Wang, JY, Lin, PY, Al-Babili, S
Seminars in cell & developmental biology. 2021;:3-11
Abstract
Carotenoids are an important source of metabolites with regulatory function, which include the plant hormones abscisic acid (ABA) and strigolactones (SLs), and several recently identified growth regulators and signaling molecules. These carotenoid-derivatives originate from oxidative breakdown of double bonds in the carotenoid polyene, a common metabolic process that gives rise to diverse carbonyl cleavage-products known as apocarotenoids. Apocarotenoids exert biologically important functions in all taxa. In plants, they are a major regulator of plant growth, development and response to biotic and abiotic environmental stimuli, and mediate plant's communication with surrounding organisms. In this article, we provide a general overview on the biology of plant apocarotenoids, focusing on ABA, SLs, and recently identified apocarotenoid growth regulators. Following an introduction on carotenoids, we describe plant apocarotenoid biosynthesis, signal transduction, and evolution and summarize their biological functions. Moreover, we discuss the evolution of these intriguing metabolites, which has not been adequately addressed in the literature.