Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae040
Transcription factor PagMYB31 positively regulates cambium activity and negatively regulates xylem development in poplar.
State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.; Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100091, China.; Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China.; Poplar Research Center, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
Wood formation involves consecutive developmental steps, including cell division of vascular cambium, xylem cell expansion, secondary cell wall (SCW) deposition, and programmed cell death. In this study, we identified PagMYB31 as a coordinator regulating these processes in Populus alba x Populus glandulosa and built a PagMYB31-mediated transcriptional regulatory network. PagMYB31 mutation caused fewer layers of cambial cells, larger fusiform initials, ray initials, vessels, fiber and ray cells, and enhanced xylem cell SCW thickening, showing that PagMYB31 positively regulates cambial cell proliferation and negatively regulates xylem cell expansion and SCW biosynthesis. PagMYB31 repressed xylem cell expansion and SCW thickening through directly inhibiting wall-modifying enzyme genes and the transcription factor genes that activate the whole SCW biosynthetic program, respectively. In cambium, PagMYB31 could promote cambial activity through TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF)/PHLOEM INTERCALATED WITH XYLEM (PXY) signaling by directly regulating CLAVATA3/ESR-RELATED (CLE) genes, and it could also directly activate WUSCHEL HOMEOBOX RELATED4 (PagWOX4), forming a feedforward regulation. We also observed that PagMYB31 could either promote cell proliferation through the MYB31-MYB72-WOX4 module, or inhibit cambial activity through the MYB31-MYB72-VASCULAR CAMBIUM-RELATED MADS2 (VCM2)/PIN-FORMED5 (PIN5) modules, suggesting its role in maintaining the homeostasis of vascular cambium. PagMYB31 could be a potential target to manipulate different developmental stages of wood formation.
PMID: 38339982
New Phytol , IF:10.151 , 2024 Feb , V241 (3) : P1193-1209 doi: 10.1111/nph.19420
A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1.
Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autonoma de Madrid, 28049, Madrid, Spain.; Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Cientificas, Ave. Americo Vespucio 49, 41092, Seville, Spain.; Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Ave. Reina Mercedes s/n, 41012, Seville, Spain.; Bioinformatics, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Department of Systems Biology, Centro Nacional de Biotecnologia/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autonoma de Madrid, 28049, Madrid, Spain.
The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::beta-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.
PMID: 38009929
New Phytol , IF:10.151 , 2024 Feb , V241 (4) : P1421-1434 doi: 10.1111/nph.19527
Receptor-like kinases and their signaling cascades for plant male fertility: loyal messengers.
Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China.; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China.; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China.
Receptor-like kinases (RLKs) are evolved for plant cell-cell communications. The typical RLK protein contains an extracellular and hypervariable N-terminus to perceive various signals, a transmembrane domain to anchor into plasma membrane, and a cytoplasmic, highly conserved kinase domain to phosphorylate target proteins. To date, RLKs have manifested their significance in a myriad of biological processes during plant reproductive growth, especially in male fertility. This review first summarizes a recent update on RLKs and their interacting protein partners controlling anther and pollen development, pollen release from dehisced anther, and pollen function during pollination and fertilization. Then, regulatory networks of RLK signaling pathways are proposed. In addition, we predict RLKs in maize and rice genome, obtain homologs of well-studied RLKs from phylogeny of three subfamilies and then analyze their expression patterns in developing anthers of maize and rice to excavate potential RLKs regulating male fertility in crops. Finally, current challenges and future prospects regarding RLKs are discussed. This review will contribute to a better understanding of plant male fertility control by RLKs, creating potential male sterile lines, and inspiring innovative crop breeding methods.
PMID: 38174365
Plant Biotechnol J , IF:9.803 , 2024 Feb doi: 10.1111/pbi.14309
Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield.
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P.R. China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, P.R. China.; Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, P.R. China.
Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.
PMID: 38386569
Elife , IF:8.14 , 2024 Feb , V12 doi: 10.7554/eLife.87895
How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution.
Courant Institute of Mathematical Sciences, New York University, New York, United States.; Janelia Research Campus, Ashburn, United States.; Department of Mathematics, University of Wisconsin-Madison, Madison, United States.; Mathematics Group, Lawrence Berkeley National Laboratory, Berkeley, United States.; Weizmann Institute of Science, Rehovot, Israel.; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States.
The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population's mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn.
PMID: 38376390
Sci Total Environ , IF:7.963 , 2024 Mar , V918 : P170707 doi: 10.1016/j.scitotenv.2024.170707
Strategies for regulating the intensity of different cyanobacterial blooms: Insights from the dynamics and stability of bacterioplankton communities.
Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.; Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China.; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.; Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China. Electronic address: wuzhx@swu.edu.cn.
The occurrence of cyanobacterial blooms is increasing in frequency and magnitude due to climate change and human activities, which poses a direct threat to drinking water security. The impacts of abiotic and biotic factors on the development of blooms have been well studied; however, control strategies for different bloom intensities have rarely been explored from the perspective of the dynamics and stability of bacterioplankton communities. Here, a network analysis was used to investigate the interactions and stability of microbial communities during different periods of R. raciborskii bloom in an inland freshwater lake. The abundance and diversity of rare taxa were significantly higher than that of abundant taxa throughout the bloom cycle. At the pre-bloom (PB) stage, microbial interactions among the different bacterial groups were weak but strongly negatively correlated, indicating low robustness and weak disturbance resistance within the community. However, community stability was better, and microbial interactions became more complicated at the high-bloom (HB) and low-bloom (LB) stages. Interestingly, rare taxa were significantly responsible for community stability and connectivity despite their low relative abundance. The Mantel test revealed that Secchi depth (SD), orthophosphate (PO(4)(3-)-P), and dissolved oxygen (DO) were significantly positively correlated with abundant taxa, rare taxa and PB. DO was significantly positively correlated with HB, intermediate taxa, and rare taxa, while water temperature (WT), N/P and total nitrogen (TN) were significantly positively correlated with LB, abundant taxa, intermediate taxa, and rare taxa. These findings suggest that reducing the PO(4)(3-)-P concentration at the PB stage may be an effective approach to preventing the development of R. raciborskii blooms, while regulating rare taxa at the HB and LB stages may be a key factor in controlling R. raciborskii blooms.
PMID: 38325489
Sci Total Environ , IF:7.963 , 2024 Mar , V914 : P169824 doi: 10.1016/j.scitotenv.2023.169824
The impact of various forms of silver nanoparticles on the rhizosphere of wheat (Triticum aestivum L.) - Shifts in microbiome structure and predicted microbial metabolic functions.
Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawochenskiego 17, 10-720 Olsztyn, Poland. Electronic address: sebastian.przemieniecki@uwm.edu.pl.; Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland. Electronic address: karolina.ruraz@ujk.edu.pl.; Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawochenskiego 17, 10-720 Olsztyn, Poland. Electronic address: olga.kosewska@uwm.edu.pl.; Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland. Electronic address: magdalena.ocwieja@ikifp.edu.pl.; Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, 31-120 Krakow, Poland. Electronic address: anna.gorczyca@urk.edu.pl.
The study investigated the effects of different silver nanoparticles (AgNPs) on the soil microbiome and wheat growth. For comparison purposes, a commercial fungicide and silver nitrate (AgNO(3)) were used. The results revealed three distinct groups of nanoparticles based on their impacts. Small-size AgNPs (10 nm) with a negative charge, as well as fungicide had limited effects on the microbiome, similar to the no-treatment control. Bigger in size (30-60 nm) and a negative charge AgNPs showed the most beneficial effects on soil microbiota shifts. These AgNPs increased the abundance of bacteria with beneficial traits such as nitrogen-fixing, urease, protease, and lignin degradation bacteria. The third type of AgNPs had a positive charge of nanostructure and influenced specific microbial populations, increasing the abundance of anaerobic and autotrophic groups of microorganisms, which could be assessed as a harmful shift for plants growth promotions and was similar to the AgNO(3) treatment. Overall, the study emphasized the potential of AgNPs in agriculture not only as biocidal. The conducted study proved that AgNPs with bigger size/negative charge, used in low concentration can have a surprisingly stimulating effect on the positive characteristics of the rhizosphere microbiome. Moreover, the surface charge of AgNPs is a significant factor affecting microbial activity of wheat rhizosphere soil, which in this treatment is significantly similar to the AgNO(3) treatment.
PMID: 38185142
Sci Total Environ , IF:7.963 , 2024 Apr , V919 : P170801 doi: 10.1016/j.scitotenv.2024.170801
Quality variation and salt-alkali-tolerance mechanism of Cynomorium songaricum: Interacting from microbiome-transcriptome-metabolome.
Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.; Center for Biotechnology & Microbiology, University of Peshawar, 25000 Peshawar, Pakistan.; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China. Electronic address: peixjin@163.com.; Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China. Electronic address: lfhuang@implad.ac.cn.
Addressing soil salinization and implementing sustainable practices for cultivating cash crops on saline-alkali land is a prominent global challenge. Cynomorium songaricum is an important salt-alkali tolerant medicinal plant capable of adapting to saline-alkali environments. In this study, two typical ecotypes of C. songaricum from the desert-steppe (DS) and saline-alkali land (SAL) habitats were selected. Through the integration of multi-omics with machine learning, the rhizosphere microbial communities, genetic maps, and metabolic profiles of two ecotypes were created and the crucial factors for the adaptation of C. songaricum to saline-alkali stress were identified, including 7 keystone OTUs (i.e. Novosphingobium sp., Sinorhizobium meliloti, and Glycomyces sp.), 5 core genes (cell wall-related genes), and 10 most important metabolites (i.e. cucurbitacin D and 3-Hydroxybutyrate) were identified. Our results indicated that under saline-alkali environments, the microbial competition might become more intense, and the microbial community network had the simple but stable structure, accompanied by the changes in the gene expression related to cell wall for adaptation. However, this regulation led to the reduction in active ingredients, such as the accumulation of flavonoids and organic acid, and enhanced the synthesis of bitter substances (cucurbitacin D), resulting in the decrease in the quality of C. songaricum. Therefore, compared to the SAL ecotype, the DS was more suitable for the subsequent development of medicinal and edible products of C. songaricum. Furthermore, to explore the reasons for this quality variation, we constructed a comprehensive microbial-genetic-metabolic regulatory network, revealing that the metabolism of C. songaricum was primarily influenced by genetic factors. These findings not only offer new insights for future research into plant salt-alkali tolerance strategies but also provide a crucial understanding for cultivating high-quality medicinal plants.
PMID: 38340858
Microbiol Spectr , IF:7.171 , 2024 Feb , V12 (2) : Pe0307623 doi: 10.1128/spectrum.03076-23
Community ecological succession of endophytic fungi associates with medicinal compound accumulation in Sophora alopecuroides.
College of Forestry and Prataculture, Ningxia University, Yinchuan, China.; Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida, USA.; School of Agriculture, Ningxia University, Yinchuan, China.; State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan, China.
Endophytic fungi of medicinal plants are symbiotic with the host and play an important role in determining metabolites. To understand the relationship between the accumulation of Sophora alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi, here we collected samples from S. alopecuroides at four developmental stages (adult, flowering, podding, and mature) and different organs (roots, stems, leaves, and seeds) at the mature stage. We then used high-performance liquid chromatography-mass spectrometry and high-throughput sequencing on the internal transcribed spacer region to identify the medicinal compounds and endophytic fungal communities in each sample. The endophytic fungal community characteristics and accumulation of medicinally bioactive compounds of S. alopecuroides varied with the host's developmental stages and organs, with the highest total alkaloids content of 111.9 mg/g at the mature stage. Membership analysis and network connection analysis showed a total of 15 core endophytic fungi in different developmental stages and 16 core endophytic fungi in different organs at the mature stage. The unclassified Ascomycota, Aspergillus, and Alternaria were significantly and positively correlated with the medicinal compounds of S. alopecuroides at the mature stage (r > 0.6 or r < -0.6; P < 0.05). In this study, we identified key endophytic fungal resources that affect the content of medicinally bioactive compounds in S. alopecuroides. This discovery could lay the foundation for enhancing the yield of medicinally bioactive compounds in S. alopecuroides and the development and application of functional endophytic fungi.IMPORTANCESophora alopecuroides is a traditional Chinese herbal medicine. The major medicinal chemicals are considered to be quinolizidine alkaloids. Quinolizidine alkaloids have been widely used for the treatment of tumors, dysentery, and enteritis. Previous studies have found that endophytic fungi in S. alopecuroides can promote the accumulation of host quinolizidine alkaloids. However, the relationship between the accumulation of S. alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi remains unclear. In this study, we screened the key endophytic fungal resources affecting the content of medicinally bioactive compounds and laid the foundation for subsequent research on the mechanism by which endophytic fungi promote the accumulation of medicinally bioactive compounds in S. alopecuroides.
PMID: 38236025
J Integr Plant Biol , IF:7.061 , 2024 Feb , V66 (2) : P265-284 doi: 10.1111/jipb.13608
MdbHLH162 connects the gibberellin and jasmonic acid signals to regulate anthocyanin biosynthesis in apple.
Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China.; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China.; College of Biology and Oceanography, Weifang University, Weifang, 261061, China.
Anthocyanins are secondary metabolites induced by environmental stimuli and developmental signals. The positive regulators of anthocyanin biosynthesis have been reported, whereas the anthocyanin repressors have been neglected. Although the signal transduction pathways of gibberellin (GA) and jasmonic acid (JA) and their regulation of anthocyanin biosynthesis have been investigated, the cross-talk between GA and JA and the antagonistic mechanism of regulating anthocyanin biosynthesis remain to be investigated. In this study, we identified the anthocyanin repressor MdbHLH162 in apple and revealed its molecular mechanism of regulating anthocyanin biosynthesis by integrating the GA and JA signals. MdbHLH162 exerted passive repression by interacting with MdbHLH3 and MdbHLH33, which are two recognized positive regulators of anthocyanin biosynthesis. MdbHLH162 negatively regulated anthocyanin biosynthesis by disrupting the formation of the anthocyanin-activated MdMYB1-MdbHLH3/33 complexes and weakening transcriptional activation of the anthocyanin biosynthetic genes MdDFR and MdUF3GT by MdbHLH3 and MdbHLH33. The GA repressor MdRGL2a antagonized MdbHLH162-mediated inhibition of anthocyanins by sequestering MdbHLH162 from the MdbHLH162-MdbHLH3/33 complex. The JA repressors MdJAZ1 and MdJAZ2 interfered with the antagonistic regulation of MdbHLH162 by MdRGL2a by titrating the formation of the MdRGL2a-MdbHLH162 complex. Our findings reveal that MdbHLH162 integrates the GA and JA signals to negatively regulate anthocyanin biosynthesis. This study provides new information for discovering more anthocyanin biosynthesis repressors and explores the cross-talk between hormone signals.
PMID: 38284786
J Exp Bot , IF:6.992 , 2024 Feb doi: 10.1093/jxb/erae051
Current understanding of gene regulatory networks underlying the sulfate deficiency response in plants.
Centro de Genomica y Bioinformatica, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745, Santiago, Chile.; Agencia Nacional de Investigacion y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile.; Programa de Doctorado en Genomica Integrativa, Vicerrectoria de Investigacion, Universidad Mayor, 8580745, Santiago, Chile.; Instituto de Bioquimica y Microbiologia, Facultad de Ciencias, Universidad Austral de Chile, 5110566, Valdivia, Chile.; Escuela de Biotecnologia, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745, Santiago, Chile.
Sulfur (S) is an essential macronutrient for plants and its availability in soils is a relevant determinant for plant growth and development. Current regulatory policies aimed at reducing industrial S emissions and changes in agronomical practices have caused a decline in S contents in soils worldwide. Deficiency of sulfate - the primary form of S accessible to plants in soil - has adverse effects on both crop yield and nutritional quality. Therefore, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis thaliana, with a few studies centering on crop species such as wheat, rice or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize the knowledge on gene expression responses to sulfate deficiency and current efforts on the identification of transcription factors relevant for controlling this response. We further compare the transcriptional response and putative regulators between Arabidopsis thaliana and two relevant crop plants, rice and tomato, to gain insights into common mechanisms of response to sulfate deficiency.
PMID: 38366662
Plant J , IF:6.417 , 2024 Feb doi: 10.1111/tpj.16690
Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems.
Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA.; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA.; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA.; DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA.; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA.; Pacific Northwest National Laboratory, Richland, Washington, 99354, USA.
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).
PMID: 38407828
Plant J , IF:6.417 , 2024 Mar , V117 (5) : P1574-1591 doi: 10.1111/tpj.16548
Dynamic transcriptome landscape of maize pericarp development.
State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China.; Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, P. R. China.; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China.
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome-wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA-seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non-seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp-specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene-related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
PMID: 37970738
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (4) doi: 10.3390/ijms25042171
The Construction of lncRNA/circRNA-miRNA-mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba.
Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China.
Schima superba is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in S. superba growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 S. superba individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including Ss4CL2, SsCSL1, and SsCSL2, and transcription factors, including SsDELLA2 (SsSLR), SsDELLA3 (SsSLN), SsDELLA5 (SsGAI-like2), and SsNAM1, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of S. superba. The results not merely provide candidate functional genes related to S. superba growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species.
PMID: 38396847
J Proteome Res , IF:4.466 , 2024 Feb doi: 10.1021/acs.jproteome.3c00485
Longitudinal Transcriptomic, Proteomic, and Metabolomic Response of Citrus sinensis to Diaphorina citri Inoculation of Candidatus Liberibacter asiaticus.
Department of Food Science and Technology, University of California Davis, Davis, California 95616, United States.; Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, United States.; Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.; Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States.; Department of Nutrition, University of California Davis, Davis, California 95616, United States.
Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Candidatus Liberibacter asiaticus (CLas), is vectored by Diaphorina citri, known as the Asian citrus psyllid (ACP). Understanding the details of CLas infection in HLB disease has been hindered by its Candidatus nature and the inability to confidently detect it in diseased trees during the asymptomatic stage. To identify early changes in citrus metabolism in response to inoculation of CLas using its natural psyllid vector, leaves from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck) trees were exposed to CLas-positive ACP or CLas-negative ACP and longitudinally analyzed using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry; data available in Dryad: 10.25338/B83H1Z), and metabolomics (proton nuclear magnetic resonance). At 4 weeks postexposure (wpe) to psyllids, the initial HLB plant response was primarily to the ACP and, to a lesser extent, the presence or absence of CLas. Additionally, analysis of 4, 8, 12, and 16 wpe identified 17 genes and one protein as consistently differentially expressed between leaves exposed to CLas-positive ACP versus CLas-negative ACP. This study informs identification of early detection molecular targets and contributes to a broader understanding of vector-transmitted plant pathogen interactions.
PMID: 38373055
BMC Plant Biol , IF:4.215 , 2024 Feb , V24 (1) : P109 doi: 10.1186/s12870-024-04790-6
Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars.
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, No. 229 Tabi Rd., Xi'an, 710069, China.; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an, 710061, Shaanxi, China.; Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Academy of Forestry, Guiyang, 55005, China. houna1018@163.com.; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, No. 229 Tabi Rd., Xi'an, 710069, China. pengzhao@nwu.edu.cn.
BACKGROUND: The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known. RESULTS: To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways. CONCLUSIONS: This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.
PMID: 38350847
BMC Plant Biol , IF:4.215 , 2024 Feb , V24 (1) : P84 doi: 10.1186/s12870-024-04754-w
Integrated transcriptomics and metabolomics analysis provides insights into aromatic volatiles formation in Cinnamomum cassia bark at different harvesting times.
College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China.; Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China.; College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China. Hrshao802@163.com.; Key Laboratory of Protection and Utilization of Traditional Chinese Medicine and Ethnic Medicine Resources, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530200, China. Hrshao802@163.com.; Guangxi Scientific Experimental Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China. yaochun111111@163.com.
BACKGROUND: Cinnamomum cassia Presl, classified in the Lauraceae family, is widely used as a spice, but also in medicine, cosmetics, and food. Aroma is an important factor affecting the medicinal and flavoring properties of C. cassia, and is mainly determined by volatile organic compounds (VOCs); however, little is known about the composition of aromatic VOCs in C. cassia and their potential molecular regulatory mechanisms. Here, integrated transcriptomic and volatile metabolomic analyses were employed to provide insights into the formation regularity of aromatic VOCs in C. cassia bark at five different harvesting times. RESULTS: The bark thickness and volatile oil content were significantly increased along with the development of the bark. A total of 724 differentially accumulated volatiles (DAVs) were identified in the bark samples, most of which were terpenoids. Venn analysis of the top 100 VOCs in each period showed that twenty-eight aromatic VOCs were significantly accumulated in different harvesting times. The most abundant VOC, cinnamaldehyde, peaked at 120 months after planting (MAP) and dominated the aroma qualities. Five terpenoids, alpha-copaene, beta-bourbonene, alpha-cubebene, alpha-funebrene, and delta-cadinene, that peaked at 240 MAP could also be important in creating C. cassia's characteristic aroma. A list of 43,412 differentially expressed genes (DEGs) involved in the biosynthetic pathways of aromatic VOCs were identified, including phenylpropanoids, mevalonic acid (MVA) and methylerythritol phosphate (MEP). A gene-metabolite regulatory network for terpenoid and phenylpropanoid metabolism was constructed to show the key candidate structural genes and transcription factors involved in the biosynthesis of terpenoids and phenylpropanoids. CONCLUSIONS: The results of our research revealed the composition and changes of aromatic VOCs in C. cassia bark at different harvesting stages, differentiated the characteristic aroma components of cinnamon, and illuminated the molecular mechanism of aroma formation. These foundational results will provide technical guidance for the quality breeding of C. cassia.
PMID: 38308239
Tree Physiol , IF:4.196 , 2024 Feb , V44 (1) doi: 10.1093/treephys/tpad133
Transcriptome and photosynthetic analyses provide new insight into the molecular mechanisms underlying heat stress tolerance in Rhododendron x pulchrum Sweet.
Jiyang College, Zhejiang A&F University, Zhuji 311800, China.; Hangzhou Animation & Game College, Hangzhou Vocational & Technical College, Hangzhou 310018, China.; School of Life Science and Health, Huzhou College , Huzhou 313000, China.
Rhododendron species provide excellent ornamental use worldwide, yet heat stress (HS) is one of the major threats to their cultivation. However, the intricate mechanisms underlying the photochemical and transcriptional regulations associated with the heat stress response in Rhododendron remain relatively unexplored. In this study, the analyses of morphological characteristics and chlorophyll fluorescence (ChlF) kinetics showed that HS (40 degrees C/35 degrees C) had a notable impact on both the donor's and acceptor's sides of photosystem II (PSII), resulting in reduced PSII activity and electron transfer capacity. The gradual recovery of plants observed following a 5-day period of culture under normal conditions indicates the reversible nature of the HS impact on Rhododendron x pulchrum. Analysis of transcriptome data unveiled noteworthy trends: four genes associated with photosynthesis-antenna protein synthesis (LHCb1, LHCb2 and LHCb3) and the antioxidant system (glutamate-cysteine ligase) experienced significant down-regulation in the leaves of R. x pulchrum during HS. Conversely, aseorbate peroxidase and glutathione S-transferase TAU 8 demonstrated an up-regulated pattern. Furthermore, six down-regulated genes (phos-phoenolpyruvate carboxylase 4, sedoheptulose-bisphosphatase, ribose-5-phosphate isomerase 2, high cyclic electron flow 1, beta glucosidase 32 and starch synthase 2) and two up-regulated genes (beta glucosidase 2 and UDP-glucose pyrophosphorylase 2) implicated in photosynthetic carbon fixation and starch/sucrose metabolism were identified during the recovery process. To augment these insights, a weighted gene co-expression network analysis yielded a co-expression network, pinpointing the hub genes correlated with ChlF dynamics' variation trends. The cumulative results showed that HS inhibited the synthesis of photosynthesis-antenna proteins in R. x pulchrum leaves. This disruption subsequently led to diminished photochemical activities in both PSII and PSI, albeit with PSI exhibiting heightened thermostability. Depending on the regulation of the reactive oxygen species scavenging system and heat dissipation, photoprotection sustained the recoverability of R. x pulchrum to HS.
PMID: 37930230
Plant Mol Biol , IF:4.076 , 2024 Feb , V114 (2) : P21 doi: 10.1007/s11103-024-01422-3
IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss.
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA. hwsedero@ncsu.edu.
Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.
PMID: 38368585
Plant Mol Biol , IF:4.076 , 2024 Feb , V114 (1) : P10 doi: 10.1007/s11103-023-01402-z
Integration of transcriptome and metabolome reveals the accumulation of related metabolites and gene regulation networks during quinoa seed development.
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.; Food Crop Research Institute, Zhaotong Academy of Agricultural Sciences, Zhaotong, 657000, China.; Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China.; College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China. wheat-quinoa@ynau.edu.cn.
Quinoa seeds are gluten- and cholesterol-free, contain all amino acids required by the human body, have a high protein content, provide endocrine regulation, protein supplementation, and cardiovascular protection effects. However, metabolite accumulation and transcriptional regulatory networks in quinoa seed development are not well understood. Four key stages of seed development in Dianli-3260 and Dianli-557 were thus analyzed and 849 metabolites were identified, among which sugars, amino acids, and lipids were key for developmental processes, and their accumulation showed a gradual decrease. Transcriptome analysis identified 40,345 genes, of which 20,917 were differential between the M and F phases, including 8279 and 12,638 up- and down-regulated genes, respectively. Grain development processes were mainly enriched in galactose metabolism, pentose and glucuronate interconversions, the biosynthesis of amino acids, and carbon metabolism pathways, in which raffinose, phosphoenolpyruvate, series and other metabolites are significantly enriched, gene-LOC110689372, Gene-LOC110710556 and gene-LOC110714584 are significantly expressed, and these metabolites and genes play an important role in carbohydrate metabolism, lipid and Amino acid synthesis of quinoa. This study provides a theoretical basis to expand our understanding of the molecular and metabolic development of quinoa grains.
PMID: 38319430
Biochem Biophys Rep , 2024 Mar , V37 : P101620 doi: 10.1016/j.bbrep.2023.101620
Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in Hordeum vulgare L. in response to cold stress.
Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.; Faculty of Agriculture (Meshgin-Shahr Campus), University of Mohaghegh Ardabili, Ardabil, Iran.
Cold stress, as an abiotic stress, is one of the most limiting factors which pose a great threat to the plant's productivity. To understand the transcriptional regulation and connectivity pattern of genes involved in barley cold stress responses, co-expression network analysis was performed based on the global transcriptome profiling. The microarray datasets related to cold stress treatments were retrieved from the Gene Expression Omnibus (GEO) and Array express databases. Four microarray datasets related to cold stress-responsive transcriptome in barley were included in our study. Gene co-expression analysis was constructed using WGCNA method. Module-Trait Relationships (MTR) analysis and hub genes determination and validation were carried out. Finally, transcription factor and kinase regulatory networks were Inferred using machine learning algorithm. The co-expression modules were determined using beta index = 10. In total 13 co-expressed modules were identified with an average size of 153 genes. Functional enrichment based on gene ontology (GO) showed that each of the stress related significant modules were enriched in different biological processes. Annotation of significant modules identifies some TFs and Kinases such as ethylene-responsive transcription factor 1-like, transcription factor PCL1-like, transcription factor MYC2, WRKY, serine/threonine-protein kinase PBL7, and receptor-like protein kinase At2g42960 were contributed in barley cold stress response. Our analysis highlighted the functional importance of ABA signaling pathway, ROS signaling, defensive and protective proteins, degrading protein, Ca2(+) related signaling, ribosome-mediated translation and etc. in responding of barley to cold stress condition. The current findings add substantially to our understanding of the cold responsive underlying mechanism of barley which can serve in future studies and breeding programs.
PMID: 38155945