Genome Biol , IF:13.583 , 2023 May , V24 (1) : P108 doi: 10.1186/s13059-023-02909-w
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize.
Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA. hartwit@hhu.de.; Heinrich-Heine University, Universitatsstrasse 1, Dusseldorf, NRW, 40225, Germany. hartwit@hhu.de.; Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, NRW, 50829, Germany. hartwit@hhu.de.; Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.; Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Seeland, SA, 06466, Germany.; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 339A Bessey Hall, Ames, IA, 50011, USA.; Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, NRW, 50829, Germany.; School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, 413 Bradfield Hall, Ithaca, NY, 14853, USA.; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 363 Keim Hall, Lincoln, NE, 68583, USA.; Heinrich-Heine University, Universitatsstrasse 1, Dusseldorf, NRW, 40225, Germany.; Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA. zywang24@stanford.edu.
BACKGROUND: Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches. RESULTS: Here, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits. CONCLUSION: Our study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
PMID: 37158941
J Hazard Mater , IF:10.588 , 2023 May , V449 : P131026 doi: 10.1016/j.jhazmat.2023.131026
Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus.
Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China.; Centre for Environmental Policy, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China. Electronic address: hfqian@zjut.edu.cn.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, China.
Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter's microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.
PMID: 36812731
New Phytol , IF:10.151 , 2023 Jun , V238 (6) : P2410-2426 doi: 10.1111/nph.18885
A conserved gene regulatory network controls root epidermal cell patterning in superrosid species.
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved. In this study, we analyzed superrosid species Rhodiola rosea, Boehmeria nivea, and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, and major changes in C. sativus. We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.
PMID: 36932734
New Phytol , IF:10.151 , 2023 Jun , V238 (5) : P2064-2079 doi: 10.1111/nph.18840
A comprehensive metabolic map reveals major quality regulations in red-flesh kiwifruit (Actinidia chinensis).
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.; Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, 610213, Sichuan, China.; GBF Laboratory, Universite de Toulouse, INRA, Castanet-Tolosan, 31320, France.; School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.; School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK.; Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
Kiwifruit (Actinidia chinensis) is one of the popular fruits world-wide, and its quality is mainly determined by key metabolites (sugars, flavonoids, and vitamins). Previous works on kiwifruit are mostly done via a single omics approach or involve only limited metabolites. Consequently, the dynamic metabolomes during kiwifruit development and ripening and the underlying regulatory mechanisms are poorly understood. In this study, using high-resolution metabolomic and transcriptomic analyses, we investigated kiwifruit metabolic landscapes at 11 different developmental and ripening stages and revealed a parallel classification of 515 metabolites and their co-expressed genes into 10 distinct metabolic vs gene modules (MM vs GM). Through integrative bioinformatics coupled with functional genomic assays, we constructed a global map and uncovered essential transcriptomic and transcriptional regulatory networks for all major metabolic changes that occurred throughout the kiwifruit growth cycle. Apart from known MM vs GM for metabolites such as soluble sugars, we identified novel transcription factors that regulate the accumulation of procyanidins, vitamin C, and other important metabolites. Our findings thus shed light on the kiwifruit metabolic regulatory network and provide a valuable resource for the designed improvement of kiwifruit quality.
PMID: 36843264
New Phytol , IF:10.151 , 2023 Aug , V239 (3) : P992-1004 doi: 10.1111/nph.18788
A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO(2).
IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France.; IMAG, Univ. Montpellier, CNRS, 34000, Montpellier, France.; Universite Paul-Valery-Montpellier 3, 34000, Montpellier, France.
The elevation of CO(2) in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO(2) on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO(2) , nitrate, and iron. We demonstrated that elevated CO(2) has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO(2) negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO(2) . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO(2) . Our approach identified key features and regulators of the plant response to elevated CO(2) , with the objective of developing crops resilient to climate change.
PMID: 36727308
Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Arterioscler Thromb Vasc Biol , IF:8.311 , 2023 Jun , V43 (6) : P813-823 doi: 10.1161/ATVBAHA.122.318332
Molecular Interaction Networks and Cardiovascular Disease Risk: The Role of Food Bioactive Small Molecules.
Network Science Institute, Department of Physics, Northeastern University, Boston, MA (F.N., G.M.).; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (G.M.).
Diet is a well-known modifiable risk factor for cardiovascular diseases, which are the leading cause of death worldwide. However, our current understanding of the human diet is still limited in terms of fully capturing the role of dietary compounds in the intraspecies and interspecies biochemical networks that determine our health. This is due, in part, to a lack of detailed information on the presence of small molecules in food (molecular weight
PMID: 37128923
Sci Total Environ , IF:7.963 , 2023 Jun , V892 : P164506 doi: 10.1016/j.scitotenv.2023.164506
Diversity of fungal microbiome obtained from plant rhizoplanes.
Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA.; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA.; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA. Electronic address: dfrigirodrigues@uh.edu.
Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.
PMID: 37295515
Sci Total Environ , IF:7.963 , 2023 Jun , V879 : P163244 doi: 10.1016/j.scitotenv.2023.163244
Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties.
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; RDFZ Chaoyang School, Beijing 100028, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: xinzhang@rcees.ac.cn.
Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.
PMID: 37004770
Sci Total Environ , IF:7.963 , 2023 Jun , V877 : P162517 doi: 10.1016/j.scitotenv.2023.162517
Gene co-expression network analysis for the selection of candidate early warning indicators of heat and nutrient stress in Posidonia oceanica.
Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy. Electronic address: alex.santillan@szn.it.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Department of Life Sciences, University of Trieste, Trieste, Italy.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.; Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.; Dead Sea and Arava Science Center (DSASC), Masada National Park, Mount Masada 8698000, Israel.; Eilat Campus, Ben-Gurion University of the Negev, Hatmarim Blv, Eilat 8855630, Israel.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy. Electronic address: gpro@szn.it.
The continuous worldwide seagrasses decline calls for immediate actions in order to preserve this precious marine ecosystem. The main stressors that have been linked with decline in seagrasses are 1) the increasing ocean temperature due to climate change and 2) the continuous inputs of nutrients (eutrophication) associated with coastal human activities. To avoid the loss of seagrass populations, an "early warning" system is needed. We used Weighed Gene Co-expression Network Analysis (WGCNA), a systems biology approach, to identify potential candidate genes that can provide an early warning signal of stress in the Mediterranean iconic seagrass Posidonia oceanica, anticipating plant mortality. Plants were collected from both eutrophic (EU) and oligotrophic (OL) environments and were exposed to thermal and nutrient stress in a dedicated mesocosm. By correlating the whole-genome gene expression after 2-weeks exposure with the shoot survival percentage after 5-weeks exposure to stressors, we were able to identify several transcripts that indicated an early activation of several biological processes (BP) including: protein metabolic process, RNA metabolic process, organonitrogen compound biosynthetic process, catabolic process and response to stimulus, which were shared among OL and EU plants and among leaf and shoot apical meristem (SAM), in response to excessive heat and nutrients. Our results suggest a more dynamic and specific response of the SAM compared to the leaf, especially the SAM from plants coming from a stressful environment appeared more dynamic than the SAM from a pristine environment. A vast list of potential molecular markers is also provided that can be used as targets to assess field samples.
PMID: 36868282
Sci Total Environ , IF:7.963 , 2023 May , V871 : P162034 doi: 10.1016/j.scitotenv.2023.162034
Biodegradable mulch films significantly affected rhizosphere microbial communities and increased peanut yield.
Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China.; Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing 100125, China.; Liaoning Academy of Agricultural Sciences, Shenyang 110161, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: dcjin@rcees.ac.cn.
Biodegradable mulch films are widely used to replace conventional plastic films in agricultural fields. However, their ecological effects on different microbial communities that naturally inhabit agricultural fields are scarcely explored. Herein, differences in bacterial communities recovered from biofilms, bulk soil, and rhizosphere soil were comparatively assessed for polyethylene film (PE) and biodegradable mulch film (BDM) application in peanut planted fields. The results showed that the plastic film type significantly influenced the bacterial community in different ecological niches of agricultural fields (P < 0.001). Specifically, BDMs significantly increased the diversity and abundance of bacteria in the rhizosphere soil. The bacterial communities in each ecological niche were distinguishable from each other; bacterial communities in the rhizosphere soil showed the most pronounced response among different treatments. Acidobacteria and Pseudomonas were significantly enriched in the rhizosphere soil when BDMs were used. BDMs also increased the rhizosphere soil bacterial network complexity and stability. The enrichment of beneficial bacteria in the rhizosphere soil under BDMs may also have implications for the observed increase in peanut yield. Deepening analyses indicated that Pseudoxanthomonas and Glutamicibacter are biomarkers in biofilms of PE and BDMs respectively. Our study provides new insights into the consequences of the application of different types of plastic films on microbial communities in different ecological niches of agricultural fields.
PMID: 36754316
J Exp Bot , IF:6.992 , 2023 May doi: 10.1093/jxb/erad178
Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis.
State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing 100193, China.; North China Key Laboratory for Crop Germplasm Resources, Ministry of Education, State Key Laboratory of North China Crop Improvement and Regulation & College of Agronomy, Hebei Agricultural University, Baoding, Hebei 071001, China.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
Basal internode length is important for lodging resistance of maize (Zea mays L.). In this study, foliar application of coronatine (COR) at the V8 stage differentially suppressed the length of the eighth internode of 10 cultivars, and three, five, and two cultivars were demonstrated to have strong (SC), moderate (MC), and weak (WC) degrees of internode shortening, respectively. RNA-Seq of the eighth internode of these cultivars revealed a total of 7895 internode elongation-regulating genes (IEGs, including 777 transcription factors (TFs)). Compared with those in WC, the hormone-related genes of cytokinin (CTK), gibberellin (GA), auxin and ethylene (ET) genes in SC were significantly downregulated, and more cell cycle regulatory factors and cell wall related genes showed significant changes, which severely inhibited internode elongation. Furthermore, we explored the direct regulatory relationship between two important TFs and target genes using EMSA, ZmABI7 and ZmMYB117, which regulate the cell cycle and cell wall modification by directly binding to the promoters of ZmCYC1, ZmCYC3, ZmCYC7, and ZmCPP1. The landscape transcriptome atlas reported herein provides a useful resource for studying maize internode development, which may provide a genetic basis for targeted control of internode length to improve lodging tolerance of maize.
PMID: 37170764
Int J Biol Macromol , IF:6.953 , 2023 Jul , V242 (Pt 3) : P124834 doi: 10.1016/j.ijbiomac.2023.124834
Comparative transcriptome analysis reveals the core molecular network in pattern-triggered immunity in Sorghum bicolor.
Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China.; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.; Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China. Electronic address: ippxiexin@163.com.
Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is the first line of defense in plant disease resistance. However, the molecular mechanisms of plant PTI vary across species, making it challenging to identify a core set of trait-associated genes. This study aimed to investigate key factors that influence PTI and identify the core molecular network in Sorghum bicolor, a C4 plant. We performed comprehensive weighted gene co-expression network analysis and temporal expression analysis of large-scale transcriptome data from various sorghum cultivars under different PAMP treatments. Our results revealed that the type of PAMP had a stronger influence on the PTI network than did the sorghum cultivar. Following PAMP treatment, 30 genes with stable downregulated expression and 158 genes with stable upregulated expression were identified, including genes encoding potential pattern recognition receptors whose expression was upregulated within 1 h of treatment. PAMP treatment altered the expression of resistance-related, signaling, salt-sensitive, heavy metal-related, and transporter genes. These findings provide novel insights into the core genes involved in plant PTI and are expected to facilitate the identification and application of resistance genes in plant breeding studies.
PMID: 37207754
Food Res Int , IF:6.475 , 2023 Aug , V170 : P112950 doi: 10.1016/j.foodres.2023.112950
Aroma profiling of Shine Muscat grape provides detailed insights into the regulatory effect of gibberellic acid and N-(2-chloro-4-pyridinyl)-N-phenylurea applications on aroma quality.
Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.; Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China. Electronic address: sdtalibo@163.com.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China. Electronic address: fruit@sjtu.edu.cn.
As plant growth regulators, gibberellic acid (GA(3)) and CPPU [forchlorfenuron, N-(2-chloro-4-pyridinyl)-N-phenylurea] are widely used in the production of table grapes. However, how these compounds regulate the aroma quality remains unclear. By measuring free and bound aroma compounds in Shine Muscat grapes from eight groups during whole growth period, GA(3) and CPPU were both found to significantly promote the synthesis of acyclic monoterpenes and (E)-2-hexenal, and double applications were found to further increase the aroma compound contents. On the other hand, GA(3) and CPPU obviously promoted the expansion of berries, and the effect of promoting the synthesis of aroma compounds was largely diminished. In conclusion, free compound concentrations in berry were almost unaffected by GA(3) and CPPU. From the perspective of aroma compounds, a highly concerted interplay was observed for terpenes, and bound compounds exhibited higher correlations than those of free compounds. In addition, 17 compounds could be used as markers that indicated the developmental timing of berries.
PMID: 37316003
Plant J , IF:6.417 , 2023 May doi: 10.1111/tpj.16330
A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis.
Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.; Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan.; Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.
PMID: 37247130
Int J Mol Sci , IF:5.923 , 2023 May , V24 (11) doi: 10.3390/ijms24119447
The Landscapes of Gluten Regulatory Network in Elite Wheat Cultivars Contrasting in Gluten Strength.
Zhenjiang Academy of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Jurong 212400, China.; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China.; Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.; Testing Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
Yangmai-13 (YM13) is a wheat cultivar with weak gluten fractions. In contrast, Zhenmai-168 (ZM168) is an elite wheat cultivar known for its strong gluten fractions and has been widely used in a number of breeding programs. However, the genetic mechanisms underlying the gluten signatures of ZM168 remain largely unclear. To address this, we combined RNA-seq and PacBio full-length sequencing technology to unveil the potential mechanisms of ZM168 grain quality. A total of 44,709 transcripts were identified in Y13N (YM13 treated with nitrogen) and 51,942 transcripts in Z168N (ZM168 treated with nitrogen), including 28,016 and 28,626 novel isoforms in Y13N and Z168N, respectively. Five hundred and eighty-four differential alternative splicing (AS) events and 491 long noncoding RNAs (lncRNAs) were discovered. Incorporating the sodium-dodecyl-sulfate (SDS) sedimentation volume (SSV) trait, both weighted gene coexpression network analysis (WGCNA) and multiscale embedded gene coexpression network analysis (MEGENA) were employed for network construction and prediction of key drivers. Fifteen new candidates have emerged in association with SSV, including 4 transcription factors (TFs) and 11 transcripts that partake in the post-translational modification pathway. The transcriptome atlas provides new perspectives on wheat grain quality and would be beneficial for developing promising strategies for breeding programs.
PMID: 37298403
Int J Mol Sci , IF:5.923 , 2023 May , V24 (10) doi: 10.3390/ijms24108473
Trichome-Specific Analysis and Weighted Gene Co-Expression Correlation Network Analysis (WGCNA) Reveal Potential Regulation Mechanism of Artemisinin Biosynthesis in Artemisia annua.
Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
Trichomes are attractive cells for terpenoid biosynthesis and accumulation in Artemisia annua. However, the molecular process underlying the trichome of A. annua is not yet fully elucidated. In this study, an analysis of multi-tissue transcriptome data was performed to examine trichome-specific expression patterns. A total of 6646 genes were screened and highly expressed in trichomes, including artemisinin biosynthetic genes such as amorpha-4,11-diene synthase (ADS) and cytochrome P450 monooxygenase (CYP71AV1). Mapman and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that trichome-specific genes were mainly enriched in lipid metabolism and terpenoid metabolism. These trichome-specific genes were analyzed by a weighted gene co-expression network analysis (WGCNA), and the blue module linked to terpenoid backbone biosynthesis was determined. Hub genes correlated with the artemisinin biosynthetic genes were selected based on TOM value. ORA, Benzoate carboxyl methyltransferase (BAMT), Lysine histidine transporter-like 8 (AATL1), Ubiquitin-like protease 1 (Ulp1) and TUBBY were revealed as key hub genes induced by methyl jasmonate (MeJA) for regulating artemisinin biosynthesis. In summary, the identified trichome-specific genes, modules, pathways and hub genes provide clues and shed light on the potential regulatory mechanisms of artemisinin biosynthesis in trichomes in A. annua.
PMID: 37239820
Front Pharmacol , IF:5.81 , 2023 , V14 : P1143768 doi: 10.3389/fphar.2023.1143768
A funnel-type stepwise filtering strategy for identification of potential Q-markers of traditional Chinese medicine formulas.
School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
Quality marker (Q-marker) serves as an important driver for the standardization of quality control in traditional Chinese medicine (TCM) formulas. However, it is still challenging to discover comprehensive and representative Q-markers. This study aimed to identify Q-markers of Hugan tablet (HGT), a famous TCM formula with ideal clinical effects in liver diseases. Here, we proposed a funnel-type stepwise filtering strategy that integrated secondary metabolites characterization, characteristic chromatogram, quantitative analysis, literature mining, biotransformation rules and network analysis. Firstly, the strategy of "secondary metabolites-botanical drugs-TCM formula" was applied to comprehensively identify the secondary metabolites of HGT. Then, the secondary metabolites with specificity and measurability in each botanical drug were identified by HPLC characteristic chromatogram, biosynthesis pathway and quantitative analysis. Based on literature mining, the effectiveness of botanical metabolites that met the above conditions was evaluated. Furthermore, the metabolism of the above metabolites in vivo was studied to reveal their biotransformation forms, which were used for network analysis. At last, according to biotransformation rules of the prototype drugs in vivo, the secondary metabolites were traced and preliminarily chosen as Q-markers. As a result, 128 plant secondary metabolites were identified in HGT, and 11 specific plant secondary metabolites were screened out. Then, the content of specific plant secondary metabolites in 15 batches of HGT was determined, which confirmed their measurability. And the results of literature mining showed that eight secondary metabolites had therapeutic effects in treating liver disease at the in vivo level, and three secondary metabolites inhibited liver disease-related indicators at the in vitro level. After that, 26 compounds absorbed into the blood (11 specific plant metabolites and their 15 metabolites in vivo) were detected in rats. Moreover, 14 compounds, including prototype components and their metabolites, were selected as Q-marker candidates by the "TCM formula-botanical drugs-compounds-targets-pathways" network. Finally, 9 plant secondary metabolites were defined as comprehensive and representative Q-markers. Our study not only provides a scientific basis for the improvement and secondary development of the quality standard of HGT, but also proposes a reference method for discovering and identifying Q-markers of TCM preparations.
PMID: 37251316
Front Plant Sci , IF:5.753 , 2023 , V14 : P1161245 doi: 10.3389/fpls.2023.1161245
Potential role of the regulatory miR1119-MYC2 module in wheat (Triticum aestivum L.) drought tolerance.
Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran.; Department of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas, Iran.; Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden.
MicroRNA (miRNA)-target gene modules are essential components of plants' abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module's expression profiles and ABA hormone content, water relations, photosynthetic activities, H(2)O(2) levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat's drought tolerance.
PMID: 37324698
Front Plant Sci , IF:5.753 , 2023 , V14 : P1193284 doi: 10.3389/fpls.2023.1193284
Drought and recovery in barley: key gene networks and retrotransposon response.
HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland.; Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.; Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland.; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
INTRODUCTION: During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses. METHODS: Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis. RESULTS: The varieties differed by their critical SWC (Ï´(crit)), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated. DISCUSSION: The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.
PMID: 37377802
J Agric Food Chem , IF:5.279 , 2023 Jun , V71 (25) : P9573-9598 doi: 10.1021/acs.jafc.2c07741
Root Hair Development and Adaptation to Abiotic Stress.
Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Shandong 250014, China.; Dongying Institute, Shandong Normal University, Dongying 257000, China.
Root hairs tie the root system to the soil substrate, facilitate water and nutrient absorption, and enable the interaction with microbes in the soil. Root hair development can be classified into three main development types (I-III). Root hair development type III has been extensively studied, mainly represented using the model plant Arabidopsis thaliana. Transcription factors, plant hormones, and proteins are involved at different root hair developmental stages. The mechanisms underlying development in types I and II have been examined using other representative plant species but have not been studied as intensively. Many key developmental genes in types I and II are highly homologous with those in type III, exhibiting conservation of related mechanisms. Root hairs are also involved in the regulation of plant response to abiotic stress by altering developmental patterns. Abiotic stress, regulatory genes, and plant hormones jointly regulate root hair development and growth; however, few studies have focused on how root hair recognizes abiotic stress signals. This review examines the molecular mechanisms of root hair development and adaptations under stress, and prospective future developments in root hair research are also discussed.
PMID: 37314142
Plant Sci , IF:4.729 , 2023 Jun , V331 : P111689 doi: 10.1016/j.plantsci.2023.111689
Integrated analysis of smRNAome, transcriptome, and degradome data to decipher microRNAs regulating costunolide biosynthesis in Saussurea lappa.
Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India. Electronic address: ravk14@gmail.com.; Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India.
Saussurea lappa (S. lappa) has been known to synthesize medicinally important, costunolide. Due to its immense therapeutic importance, understanding of regulatory mechanism associated with its biosynthesis is crucial. The identification of genes and transcription factors (TFs) in S. lappa, created a clear picture of costunolide biosynthesis pathways. Further to understand the regulation of costunolide biosynthesis by miRNAs, an integrated study of transcriptome, miRNAs, and degradome was performed. Identified candidate miRNAs and associated feed-forward loops (FFLs) illustrates their regulatory role in secondary metabolite biosynthesis. Small RNA and degradome sequencing were performed for leaf and root tissues to determine miRNAs-targets pairs. A total of 711 and 525 such targets were obtained for novel and known miRNAs respectively. This data was used to generate costunolide-specific miRNA-TF-gene interactome to perform systematic analyses through graph theoretical approach. Interestingly, miR171c.1 and sla-miR121 were identified as key regulators to connect and co-regulate both mevalonate and sesquiterpenoid pathways to bio-synthesize costunolide. Tissue-specific FFLs were identified to be involved in costunolide biosynthesis which further suggests the evolutionary co-relation of root-specific networks in synthesis of secondary metabolites in addition to leaf-specific networks. This integrative approach allowed us to determine candidate miRNAs and associated tissue-specific motifs involved in the diversification of secondary metabolites. MiRNAs identified in present study can provide alternatives for bioengineering tool to enhance the synthesis of costunolide and other secondary metabolites in S. lappa.
PMID: 36965630
Plant Physiol Biochem , IF:4.27 , 2023 Jun , V201 : P107856 doi: 10.1016/j.plaphy.2023.107856
Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress.
College of Forestry, Nanjing Forestry University, Nanjing, China.; College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.; College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China. Electronic address: fangsz@njfu.edu.cn.
Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.
PMID: 37354727
BMC Plant Biol , IF:4.215 , 2023 May , V23 (1) : P238 doi: 10.1186/s12870-023-04255-2
Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes.
The New Zealand Institute for Plant and Food Research Limited, Palmerston North, 4442, New Zealand. olivia.angelin-bonnet@plantandfood.co.nz.; The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand.; School of Mathematical and Computational Sciences, Massey University, Palmerston North, 4412, New Zealand.; School of Natural Sciences, Massey University, Palmerston North, 4412, New Zealand.; School of Veterinary Science, Massey University, Palmerston North, 4412, New Zealand.
BACKGROUND: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. RESULTS: When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. CONCLUSION: This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.
PMID: 37147582
Planta , IF:4.116 , 2023 May , V257 (6) : P110 doi: 10.1007/s00425-023-04149-5
Dunaliella Ds-26-16 acts as a global regulator to enhance salt tolerance by coordinating multiple responses in Arabidopsis seedlings.
Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.; Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China. xiwenchen@nankai.edu.cn.; Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China. chendefu@nankai.edu.cn.
Based on phenotypic, physiological and proteomic analysis, the possible mechanism by which Ds-26-16 regulates salt tolerance in Arabidopsis seedlings was revealed. Functional and mechanistic characterization of salt tolerance genes isolated from natural resources is crucial for their application. In this study, we report the possible mechanism by which Ds-26-16, a gene from Dunaliella, and its point mutation gene EP-5, enhance salt tolerance in Arabidopsis seedlings. Both Ds-26-16 and EP-5 transgenic lines displayed higher seed germination rates, cotyledon-greening rates, soluble sugar contents, decreased relative conductivity and ROS accumulation when germinating under 150 mM NaCl conditions. Comparative proteomic analysis revealed that there were 470 or 391 differentially expressed proteins (DEPs) in Ds-26-16 or EP-5, respectively, compared with the control (3301) under salt stress. The GO and KEGG enrichment analyses showed the DEPs in Ds-26-16 vs. 3301 and EP-5 vs. 3301 were similar and mainly enriched in photosynthesis, regulation of gene expression, carbohydrate metabolism, redox homeostasis, hormonal signal and defense, and regulation of seed germination. Thirty-seven proteins were found to be stably expressed under salt stress due to the expression of Ds-26-16, and eleven of them contain the CCACGT motif which could be bound by the transcription factor in ABA signaling to repress gene transcription. Taken together, we propose that Ds-26-16, as a global regulator, improves salt-tolerance by coordinating stress-induced signal transduction and modulating multiple responses in Arabidopsis seedlings. These results provide valuable information for utilizing natural resources in crop improvement for breeding salt-tolerant crops.
PMID: 37149499
Genes (Basel) , IF:4.096 , 2023 Jun , V14 (6) doi: 10.3390/genes14061290
Integrated Transcriptomics and Metabolomics Analysis of the Fructan Metabolism Response to Low-Temperature Stress in Garlic.
Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China.; Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China.
As the main reserve carbohydrate in garlic, fructan contributes to garlic's yield and quality formation. Numerous studies have shown that plant fructan metabolism induces a stress response to adverse environments. However, the transcriptional regulation mechanism of garlic fructan in low-temperature environments is still unknown. In this study, the fructan metabolism of garlic seedlings under low-temperature stress was revealed by transcriptome and metabolome approaches. With the extension of stress time, the number of differentially expressed genes and metabolites increased. Using weighted gene co-expression network analysis (WGCNA), three key enzyme genes related to fructan metabolism were screened (a total of 12 transcripts): sucrose: sucrose 1-fructosyltransferase (1-SST) gene; fructan: fructan 6G fructosyltransferase (6G-FFT) gene; and fructan 1-exohydrolase (1-FEH) gene. Finally, two hub genes were obtained, namely Cluster-4573.161559 (6G-FFT) and Cluster-4573.153574 (1-FEH). The correlation network and metabolic heat map analysis between fructan genes and carbohydrate metabolites indicate that the expression of key enzyme genes in fructan metabolism plays a positive promoting role in the fructan response to low temperatures in garlic. The number of genes associated with the key enzyme of fructan metabolism in trehalose 6-phosphate was the highest, and the accumulation of trehalose 6-phosphate content may mainly depend on the key enzyme genes of fructan metabolism rather than the enzyme genes in its own synthesis pathway. This study not only obtained the key genes of fructan metabolism in garlic seedlings responding to low temperatures but also preliminarily analyzed its regulatory mechanism, providing an important theoretical basis for further elucidating the cold resistance mechanism of garlic fructan metabolism.
PMID: 37372470
AoB Plants , IF:3.276 , 2023 Jun , V15 (3) : Pplad013 doi: 10.1093/aobpla/plad013
Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions.
Sunflower and Plant Biology Research Unit, USDA-ARS-ETSARC, 1616 Albrecht Blvd., Fargo, ND 58102, USA.; Metabolism and Disease Molecular and Systems Biology, North Carolina State University, 120 Broughton Dr., Raleigh, NC 27607, USA.; Wave Life Sciences, 733 Concord Ave, Cambridge, MA 02138, USA.; Massachusetts Institute of Technology, Merkin Building, 415 Main St., Cambridge, MA 02142, USA.
A new paradigm suggests weeds primarily reduce crop yield by altering crop developmental and physiological processes long before the weeds reduce resources through competition. Multiple studies have implicated stress response pathways are activated when crops such as maize are grown in close proximity with weeds during the first 4-8 weeks of growth-the point at which weeds have their greatest impact on subsequent crop yields. To date, these studies have mostly focused on the response of above-ground plant parts and have not examined the early signal transduction processes associated with maize root response to weeds. To investigate the impact of signals from a below-ground competitor on the maize root transcriptome when most vulnerable to weed pressure, a system was designed to expose maize to only below-ground signals. Gene set enrichment analyses identified over-represented ontologies associated with oxidative stress signalling throughout the time of weed exposure, with additional ontologies associated with nitrogen use and transport and abscisic acid (ABA) signalling, and defence responses being enriched at later time points. Enrichment of promoter motifs indicated over-representation of sequences known to bind FAR-RED IMPAIRED RESPONSE 1 (FAR1), several AP2/ERF transcription factors and others. Likewise, co-expression networks were identified using Weighted-Gene Correlation Network Analysis (WGCNA) and Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) algorithms. WGCNA highlighted the potential roles of several transcription factors including a MYB 3r-4, TB1, WRKY65, CONSTANS-like5, ABF3, HOMEOBOX 12, among others. These studies also highlighted the role of several specific proteins involved in ABA signalling as being important for the initiation of the early response of maize to weeds. SC-ION highlighted potential roles for NAC28, LOB37, NAC58 and GATA2 transcription factors, among many others.
PMID: 37228420
J Phycol , IF:2.923 , 2023 Jun , V59 (3) : P433-440 doi: 10.1111/jpy.13341
Ulva: An emerging green seaweed model for systems biology.
Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.; Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany.
Green seaweeds exhibit a wide range of morphologies and occupy various ecological niches, spanning from freshwater to marine and terrestrial habitats. These organisms, which predominantly belong to the class Ulvophyceae, showcase a remarkable instance of parallel evolution toward complex multicellularity and macroscopic thalli in the Viridiplantae lineage. Within the green seaweeds, several Ulva species ("sea lettuce") are model organisms for studying carbon assimilation, interactions with bacteria, life cycle progression, and morphogenesis. Ulva species are also notorious for their fast growth and capacity to dominate nutrient-rich, anthropogenically disturbed coastal ecosystems during "green tide" blooms. From an economic perspective, Ulva has garnered increasing attention as a promising feedstock for the production of food, feed, and biobased products, also as a means of removing excess nutrients from the environment. We propose that Ulva is poised to further develop as a model in green seaweed research. In this perspective, we focus explicitly on Ulva mutabilis/compressa as a model species and highlight the molecular data and tools that are currently available or in development. We discuss several areas that will benefit from future research or where exciting new developments have been reported in other Ulva species.
PMID: 37256696
J Mol Evol , IF:2.395 , 2023 Aug , V91 (4) : P424-440 doi: 10.1007/s00239-023-10109-0
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.
Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, P.O. Box 74135-111, Jahrom, Islamic Republic of Iran. bheghrari@yahoo.com.; Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran.
HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.
PMID: 37191719
Heliyon , 2023 Jun , V9 (6) : Pe16811 doi: 10.1016/j.heliyon.2023.e16811
Seiethr: Efficient calculation of robust ensemble gene networks.
Department of Plant Physiology, Umea Plant Science Center, Umea University, Umea, Sweden.; Department of Plant Physiology, Umea Plant Science Center, Swedish University of Agricultural Sciences, Umea, Sweden.
Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few useable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiethr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks. Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms. Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.
PMID: 37313140
J Genet Eng Biotechnol , 2023 May , V21 (1) : P69 doi: 10.1186/s43141-023-00515-8
Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa).
Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka.; Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka. weeraman97@gmail.com.
BACKGROUND: The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance. RESULTS: Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs. CONCLUSIONS: These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.
PMID: 37246172
J Biomol Struct Dyn , 2023 May : P1-14 doi: 10.1080/07391102.2023.2213341
Computational investigation of phytochemicals identified from medicinal plant extracts against tuberculosis.
Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.; Sygnature Discovery, Nottingham, United Kingdom.
Tuberculosis (TB) is still one of the world's most challenging infectious diseases and the emergence of drug-resistant Mycobacterium tuberculosis poses a significant threat to the treatment of TB. Identifying new medications based on local traditional remedies has become more essential. Gas Chromatography-Mass spectrometry (GC-MS) (Perkin-Elmer, MA, USA) was used to identify potential bioactive components in Solanum surattense, Piper longum, and Alpinia galanga plants sections. The fruits and rhizomes' chemical compositions were analyzed using solvents like petroleum ether, chloroform, ethyl acetate, and methanol. A total of 138 phytochemicals were identified, further categorized and finalized with 109 chemicals. The phytochemicals were docked with selected proteins (ethA, gyrB, and rpoB) using AutoDock Vina. The top complexes were selected and preceded with molecular dynamics simulation. It was found that the rpoB-sclareol complex is very stable, which means it could be further explored. The compounds were further studied for ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties. Sclareol has obeyed all the rules and it might be a potential chemical to treat TB.Communicated by Ramaswamy H. Sarma.
PMID: 37211911