Trends Plant Sci , IF:14.416 , 2020 Jun doi: 10.1016/j.tplants.2020.05.009
Altering Plant Architecture to Improve Performance and Resistance.
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.; The Unidad de Genomica Avanzada (Langebio), Centro de Investigacion y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico; Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, TX, USA.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China. Electronic address: caodong@caas.cn.; Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan. Electronic address: tranplamson@duytan.edu.vn.
High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change.
PMID: 32595089
New Phytol , IF:8.512 , 2020 Jun doi: 10.1111/nph.16778
PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.; Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230000, China.; Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was rapidly induced (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression of PuHox52 significantly increased the number of ARs while suppression of PuHox52 had the opposite effect. A multilayered hierarchical gene regulatory network (ML-hGRN) mediated by PuHox52 was reverse-engineered and demonstrated to govern AR formation process. PuHox52 regulated AR formation through up-regulation of nine hub regulators, including a jasmonate signaling pathway gene, PuMYC2. and an auxin signaling pathway gene, PuAGL12. We also identified coherent type 4 feed-forward loops within this ML-hGRN; PuHox52 repressed PuHDA9 that encodes a histone deacetylase and led to an increase in acetylation and presumably expression of three hub regulators, PuWRKY51, PuLBD21, and PuIAA7. Our results indicate that the ML-hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.
PMID: 32589766
Cell Mol Life Sci , IF:6.496 , 2020 Jun , V77 (12) : P2343-2354 doi: 10.1007/s00018-019-03407-8
Control of cell fate during axillary meristem initiation.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. yljiao@genetics.ac.cn.; University of Chinese Academy of Sciences, Beijing, 100049, China. yljiao@genetics.ac.cn.
Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.
PMID: 31807816
Plant J , IF:6.141 , 2020 Jun doi: 10.1111/tpj.14887
Systems biology of responses to simultaneous copper and iron deficiency in Arabidopsis.
Faculty of Biology, Plant Molecular Biology (Botany), Ludwig-Maximilians Universitat Munchen, Grosshadernerstr. 2-4, Planegg-Martinsried, D-82152, Germany.
Plant responses to coincident nutrient deficiencies cannot be predicted from the responses to individual deficiencies. Although copper (Cu) and iron (Fe) are essential micronutrients for plant growth that are often and concurrently limited in soils, the combinatorial response to Cu-Fe deficiency remains elusive. In the present study, we characterised the responses of Arabidopsis thaliana plants deprived of Cu, Fe or both (-Cu-Fe) at the level of plant development, mineral composition, and reconfiguration of transcriptomes, proteomes and metabolomes. Compared to single deficiencies, simultaneous -Cu-Fe leads to a distinct pattern in leaf physiology and microelement concentration characterised by lowered protein content and enhanced manganese and zinc levels. Conditional networking analysis of molecular changes indicates that biological processes also display different co-expression patterns among single and double deficiencies. Indeed, the interaction between Cu and Fe deficiencies causes distinct expression profiles for 15% of all biomolecules, leading to specific enhancement of general stress responses and protein homeostasis mechanisms, at the same time as severely arresting photosynthesis. Accordingly, central carbon metabolites, in particular photosynthates, decrease especially under -Cu-Fe conditions, whereas the pool of free amino acids increases. Further meta-analysis of transcriptomes and proteomes corroborated that protein biosynthesis and folding capacity were readjusted during the combinatorial response and unveiled important rearrangements in the metabolism of organic acids. Consequently, our results demonstrate that the response to -Cu-Fe imposes a distinct reconfiguration of large sets of molecules, not triggered by single deficiencies, resulting into a switch from autotrophy to heterotrophy and involving organic acids such as fumaric acid as central mediators of the response.
PMID: 32578228
Plant J , IF:6.141 , 2020 Jun doi: 10.1111/tpj.14892
Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor.
Departamento de Ciencias - Quimica, Centro de Espectroscopia de Resonancia Magnetica Nuclear (CERMN), Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, Lima, Lima 32, Peru.; Genetics and Crop Improvement, International Potato Center, Av. La Molina 1895, Lima, Lima 12, Peru.
Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water-deficit and recovery conditions in Ica, Peru. All potato genotypes were profiled for 45 morphological traits and 42 central metabolites via nuclear magnetic resonance. Statistical tests and norm of reaction analysis revealed that the observed variations were trait specific, that is, genotypic versus environmental. Principal component analysis showed a separation of samples as a result of conditional changes. To explore the relational ties between morphological traits and metabolites, correlation-based network analysis was employed, constructing one network for normal irrigation and one network for water-recovery samples. Community detection and difference network analysis highlighted the differences between the two networks, revealing a significant correlational link between fumarate and plant vigor. A genome-wide association study was performed for each metabolic trait. Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. Three of the 11 SNPs were located within genes, coding for a protein of unknown function, a RING domain protein and a zinc finger protein ZAT2. Our findings have important implications for future potato breeding regimes, especially in countries suffering from climate change.
PMID: 32579242
Toxicology , IF:4.099 , 2020 Jun , V441 : P152531 doi: 10.1016/j.tox.2020.152531
Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells.
Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Italy. Electronic address: daniele.mercatelli2@unibo.it.; Department of Experimental, Diagnostic and Specialty Medicine-DIMES, Alma Mater Studiorum, University of Bologna, Italy. Electronic address: massimo.bortolotti2@unibo.it.; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Italy. Electronic address: federico.giorgi@unibo.it.
Gene-regulatory networks reconstruction has become a very popular approach in applied biology to infer and dissect functional interactions of Transcription Factors (TFs) driving a defined phenotypic state, termed as Master Regulators (MRs). In the present work, cutting-edge bioinformatic methods were applied to re-analyze experimental data on leukemia cells (human myelogenous leukemia cell line THP-1 and acute myeloid leukemia MOLM-13 cells) treated for 6 h with two different Ribosome-Inactivating Proteins (RIPs), namely Shiga toxin type 1 (400 ng/mL) produced by Escherichia coli strains and the plant toxin stenodactylin (60 ng/mL), purified from the caudex of Adenia stenodactyla Harms. This analysis allowed us to identify the common early transcriptional response to 28S rRNA damage based on gene-regulatory network inference and Master Regulator Analysis (MRA). Both toxins induce a common response at 6 h which involves inflammatory mediators triggered by AP-1 family transcriptional factors and ATF3 in leukemia cells. We describe for the first time the involvement of MAFF, KLF2 and KLF6 in regulating RIP-induced apoptotic cell death, while receptor-mediated downstream signaling through ANXA1 and TLR4 is suggested for both toxins.
PMID: 32593706
Biochim Biophys Acta Gene Regul Mech , IF:3.51 , 2020 Jun , V1863 (6) : P194447 doi: 10.1016/j.bbagrm.2019.194447
Inference of plant gene regulatory networks using data-driven methods: A practical overview.
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.; Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium. Electronic address: klaas.vandepoele@psb.vib-ugent.be.
Transcriptional regulation is a complex and dynamic process that plays a vital role in plant growth and development. A key component in the regulation of genes is transcription factors (TFs), which coordinate the transcriptional control of gene activity. A gene regulatory network (GRN) is a collection of regulatory interactions between TFs and their target genes. The accurate delineation of GRNs offers a significant contribution to our understanding about how plant cells are organized and function, and how individual genes are regulated in various conditions, organs or cell types. During the past decade, important progress has been made in the identification of GRNs using experimental and computational approaches. However, a detailed overview of available platforms supporting the analysis of GRNs in plants is missing. Here, we review current databases, platforms and tools that perform data-driven analyses of gene regulation in Arabidopsis. The platforms are categorized into two sections, 1) promoter motif analysis tools that use motif mapping approaches to find TF motifs in the regulatory sequences of genes of interest and 2) network analysis tools that identify potential regulators for a set of input genes using a range of data types in order to generate GRNs. We discuss the diverse datasets integrated and highlight the strengths and caveats of different platforms. Finally, we shed light on the limitations of the above approaches and discuss future perspectives, including the need for integrative approaches to unravel complex GRNs in plants.
PMID: 31678628
BMC Plant Biol , IF:3.497 , 2020 Jun , V20 (1) : P299 doi: 10.1186/s12870-020-02513-1
Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam).
Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China.; Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China.; Jining Academy of Agricultural Sciences, Jining, Shandong, China.; Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China. wang-qm@163.com.; Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China. wang-qm@163.com.; Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China. Zhanglm11@sina.com.; Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China. Zhanglm11@sina.com.
BACKGROUND: Sweet potato (Ipomoea batatas (L.) Lam.) is a highly heterozygous autohexaploid crop with high yield and high anthocyanin content. Purple sweet potato is the main source of anthocyanins, and the mechanism of anthocyanin biosynthesis in storage roots has not been fully revealed. RESULTS: In order to reveal the mechanism of anthocyanin biosynthesis and identify new homologous genes involved in anthocyanin biosynthesis in the storage roots of sweet potato, we used Ningzishu 1 and Jizishu 2 as parents to construct a F1 hybrid population. Seven anthocyanin-containing lines and three anthocyanin-free lines were selected for full-length and second-generation transcriptome analyses. A total of 598,375 circular consensus sequencing reads were identified from full-length transcriptome sequencing. After analysis and correction of second-generation transcriptome data, 41,356 transcripts and 18,176 unigenes were obtained. Through a comparative analysis between anthocyanin-containing and anthocyanin-free groups 2329 unigenes were found to be significantly differentially expressed, of which 1235 were significantly up-regulated and 1094 were significantly down-regulated. GO enrichment analysis showed that the differentially expressed unigenes were significantly enriched in molecular function and biological process. KEGG enrichment analysis showed that the up-regulated unigenes were significantly enriched in the flavonoid biosynthesis and phenylpropanoid biosynthesis pathways, and the down-regulated unigenes were significantly enriched in the plant hormone signal transduction pathway. Weighted gene co-expression network analysis of differentially expressed unigenes revealed that anthocyanin biosynthesis genes were co-expressed with transcription factors such as MYB, bHLH and WRKY at the transcription level. CONCLUSIONS: Our study will shed light on the regulatory mechanism of anthocyanin biosynthesis in sweet potato storage roots at the transcriptome level.
PMID: 32600332
Plants (Basel) , IF:2.762 , 2020 Jun , V9 (6) doi: 10.3390/plants9060713
Transcriptome and Network Analyses of Heterostyly in Turnera subulata Provide Mechanistic Insights: Are S-Loci a Red-Light for Pistil Elongation?
School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA.; Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J1P3, Canada.
Heterostyly employs distinct hermaphroditic floral morphs to enforce outbreeding. Morphs differ structurally in stigma/anther positioning, promoting cross-pollination, and physiologically blocking self-fertilization. Heterostyly is controlled by a self-incompatibility (S)-locus of a small number of linked S-genes specific to short-styled morph genomes. Turnera possesses three S-genes, namely TsBAHD (controlling pistil characters), TsYUC6, and TsSPH1 (controlling stamen characters). Here, we compare pistil and stamen transcriptomes of floral morphs of T. subulata to investigate hypothesized S-gene function(s) and whether hormonal differences might contribute to physiological incompatibility. We then use network analyses to identify genetic networks underpinning heterostyly. We found a depletion of brassinosteroid-regulated genes in short styled (S)-morph pistils, consistent with hypothesized brassinosteroid-inactivating activity of TsBAHD. In S-morph anthers, auxin-regulated genes were enriched, consistent with hypothesized auxin biosynthesis activity of TsYUC6. Evidence was found for auxin elevation and brassinosteroid reduction in both pistils and stamens of S- relative to long styled (L)-morph flowers, consistent with reciprocal hormonal differences contributing to physiological incompatibility. Additional hormone pathways were also affected, however, suggesting S-gene activities intersect with a signaling hub. Interestingly, distinct S-genes controlling pistil length, from three species with independently evolved heterostyly, potentially intersect with phytochrome interacting factor (PIF) network hubs which mediate red/far-red light signaling. We propose that modification of the activities of PIF hubs by the S-locus could be a common theme in the evolution of heterostyly.
PMID: 32503265
Biosystems , IF:1.808 , 2020 Jun : P104175 doi: 10.1016/j.biosystems.2020.104175
A computational approach to validate novel drug targets of gentianine from Swertiya chirayita in Plasmodium falciparum.
School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, 751024, Odisha, India. Electronic address: rmahapatra@kiitbiotech.ac.in.; School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, 751024, Odisha, India.
Gentianine is one of the compounds found in the plant Swertiya chirayita that is known for its antimalarial activity. However, its exact molecular mechanism of action is yet to be understood. In our present study, we applied several computational approaches to filter out and determine possible targets of gentianine in Plasmodium falciparum 3D7. Protein-protein networks formed the basis of one of our strategies along with orthologous protein analysis to establish essentiality. Out of 6 essential proteins from unique pathways, haloacid dehalogenase like-hydrolase (PfHAD1), phosphoenolpyruvate carboxykinase (PfPEPCK) and fumarate hydratase (PfFH) were screened as drug targets through this approach. Through our other strategy we established the predicted IC50 (PIC50) value of gentianine with a set of molecular descriptors from 123 Pathogen Box anti-malarial compounds. Afterwards through 2D structural similarity, L-lactate dehydrogenase (PfLDH) was established as another possible target. In our work, we performed in silico docking and analysed the binding of gentianine to the proteins. All of the proteins were reported with favourable binding results and were considered for complex molecular dynamics simulation approach. Our research clears up the molecular mechanism of antimalarial activity of gentianine to some extent paving way for experimental validation of the same in future.
PMID: 32593550
Heliyon , 2020 Jun , V6 (6) : Pe04293 doi: 10.1016/j.heliyon.2020.e04293
Panama Papers' offshoring network behavior.
Escuela Politecnica Superior, Universidad Autonoma de Madrid, 28049 Madrid, Spain.; SIGTI-Research Group, Escuela Politecnica Nacional, Quito, Ecuador.; SI2-Lab, FICA, Universidad de las Americas, Quito, Ecuador.; FCEE, Universidad Autonoma de Madrid, 28049 Madrid, Spain.
The present study analyzes the offshoring network constructed from the information contained in the Panama Papers, characterizing worldwide regions and countries as well as their intra- and inter-relationships. The Panama Papers 2016 divulgence is the largest leak of offshoring and tax avoidance documentation. The document leak, with a volume content of approximately 2.6 terabytes, involves more than two hundred thousand enterprises in more than two hundred countries. From this information, the offshore connections of individuals and companies are constructed and aggregated using their countries of origin. The top offshore financial regions and countries of the network are identified, and their intra- and inter-relationship are mapped and described. We are able to identify the top countries in the offshoring network and characterize their connectivity structure, discovering the more prominent actors in the worldwide offshoring scenario and their range of influence.
PMID: 32637690