Plant Biotechnol J , IF:9.803 , 2022 May doi: 10.1111/pbi.13833
Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.; College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
Adventitious rooting is an essential biological process in the vegetative propagation of economically important horticultural and forest tree species. It enables utilization of the elite genotypes in breeding programmes and production. Promotion of adventitious root (AR) formation has been associated with starvation of inorganic phosphate and some factors involved in low phosphorus (LP) signalling. However, the regulatory mechanism underlying LP-mediated AR formation remains largely elusive. We established an efficient experimental system that guaranteed AR formation through short-term LP treatment in Populus ussuriensis. We then generated a time-course RNA-seq data set to recognize key regulatory genes and regulatory cascades positively regulating AR formation through data analysis and gene network construction, which were followed by experimental validation and characterization. We constructed a multilayered hierarchical gene regulatory network, from which PuMYB40, a typical R2R3-type MYB transcription factor (TF), and its interactive partner, PuWRKY75, as well as their direct targets, PuLRP1 and PuERF003, were identified to function upstream of the known adventitious rooting genes. These regulatory genes were functionally characterized and proved their roles in promoting AR formation in P. ussuriensis. In conclusion, our study unveiled a new hierarchical regulatory network that promoted AR formation in P. ussuriensis, which was activated by short-term LP stimulus and primarily governed by PuMYB40 and PuWRKY75.
PMID: 35514032
Environ Pollut , IF:8.071 , 2022 May , V307 : P119516 doi: 10.1016/j.envpol.2022.119516
Effects of soil protists on the antibiotic resistome under long term fertilization.
Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.; Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China. Electronic address: dongzhu@rcees.ac.cn.; Key Laboratory for Humid Subtropical Ecogeographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871, Frederiksberg, Denmark; Sino-Danish Center for Education and Research, Beijing, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.
PMID: 35609845
BMC Biol , IF:7.431 , 2022 Apr , V20 (1) : P83 doi: 10.1186/s12915-022-01273-8
Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response.
Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.; Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.; Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.; Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.; Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.; Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.; Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.; Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. motoaki.seki@riken.jp.; Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. motoaki.seki@riken.jp.; Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK. Alessandra.Devoto@rhul.ac.uk.
BACKGROUND: Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS: We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS: The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
PMID: 35399062
Comput Struct Biotechnol J , IF:7.271 , 2022 , V20 : P2001-2012 doi: 10.1016/j.csbj.2022.04.027
A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets.
Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.; Nutrition Obesity Research Center, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.; General Surgery Gastrointestinal Section, Department of Surgery, UAB School of Medicine, Birmingham, AL 35294, USA.
Network science identifies key players in diverse biological systems including host-pathogen interactions. We demonstrated a scale-free network property for a comprehensive rice protein-protein interactome (RicePPInets) that exhibits nodes with increased centrality indices. While weighted k-shell decomposition was shown efficacious to predict pathogen effector targets in Arabidopsis, we improved its computational code for a broader implementation on large-scale networks including RicePPInets. We determined that nodes residing within the internal layers of RicePPInets are poised to be the most influential, central, and effective information spreaders. To identify central players and modules through network topology analyses, we integrated RicePPInets and co-expression networks representing susceptible and resistant responses to strains of the bacterial pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola (Xoc) and generated a RIce-Xanthomonas INteractome (RIXIN). This revealed that previously identified candidate targets of pathogen transcription activator-like (TAL) effectors are enriched in nodes with enhanced connectivity, bottlenecks, and information spreaders that are located in the inner layers of the network, and these nodes are involved in several important biological processes. Overall, our integrative multi-omics network-based platform provides a potentially useful approach to prioritizing candidate pathogen effector targets for functional validation, suggesting that this computational framework can be broadly translatable to other complex pathosystems.
PMID: 35521542
J Exp Bot , IF:6.992 , 2022 Apr , V73 (8) : P2487-2498 doi: 10.1093/jxb/erac044
Custom methods to identify conserved genetic modules applied to novel transcriptomic data from Amborella trichopoda.
Laboratoire Reproduction et Developpement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, Lyon, France.; Universite Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.; Universite de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.; UMR 1318 INRAe-AgroParisTech, Route de Saint Cyr, 78026 Versailles cedex, France.
We have devised a procedure for the inter-species comparison of transcriptomic data and used this procedure to reconstruct the expression dynamics of major genetic modules that were present at least 149 million years ago in the most recent common ancestor of living angiosperms. We began by using laser-assisted microdissection to generate novel transcriptomic data from female flower tissues of Amborella trichopoda, the likely sister to all other living angiosperms. We then employed a gene-expression clustering method, followed by a custom procedure to compare genetic modules on the basis of gene orthology between Amborella and the molecular-genetic model angiosperm Arabidopsis thaliana. Using this protocol, we succeeded in identifying nine major genetic modules that appear to have conserved their expression dynamics from an early stage in angiosperm evolution. The genes of these modules, representing over 5000 orthogroups, include around one third of those known to control female reproductive development in Arabidopsis. Our study constitutes a proof of concept for the comparison of transcriptomic data between widely diverged plant species and represents a first step in the large-scale analysis of gene expression dynamics in a macro-evolutionary context.
PMID: 35134938
Cells , IF:6.6 , 2022 Apr , V11 (9) doi: 10.3390/cells11091420
Transcriptomic, Hormonomic and Metabolomic Analyses Highlighted the Common Modules Related to Photosynthesis, Sugar Metabolism and Cell Division in Parthenocarpic Tomato Fruits during Early Fruit Set.
Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan.; Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan.; RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.; Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan.; Graduate School of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan.; Graduate School and Faculty of Bioresources, Mie University, Tsu 514-8507, Japan.; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.; Rijk Zwaan Breeding Japan K.K., Chiba 289-1608, Japan.; Research Institute, Kagome Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Japan.
Parthenocarpy, the pollination-independent fruit set, can raise the productivity of the fruit set even under adverse factors during the reproductive phase. The application of plant hormones stimulates parthenocarpy, but artificial hormones incur extra financial and labour costs to farmers and can induce the formation of deformed fruit. This study examines the performance of parthenocarpic mutants having no transcription factors of SlIAA9 and SlTAP3 and sldella that do not have the protein-coding gene, SlDELLA, in tomato (cv. Micro-Tom). At 0 day after the flowering (DAF) stage and DAFs after pollination, the sliaa9 mutant demonstrated increased pistil development compared to the other two mutants and wild type (WT). In contrast to WT and the other mutants, the sliaa9 mutant with pollination efficiently stimulated the build-up of auxin and GAs after flowering. Alterations in both transcript and metabolite profiles existed for WT with and without pollination, while the three mutants without pollination demonstrated the comparable metabolomic status of pollinated WT. Network analysis showed key modules linked to photosynthesis, sugar metabolism and cell proliferation. Equivalent modules were noticed in the famous parthenocarpic cultivars 'Severianin', particularly for emasculated samples. Our discovery indicates that controlling the genes and metabolites proffers future breeding policies for tomatoes.
PMID: 35563726
Neuroimage , IF:6.556 , 2022 Aug , V256 : P119246 doi: 10.1016/j.neuroimage.2022.119246
Diurnal variations of resting-state fMRI data: A graph-based analysis.
Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Computational Neuroergonomics Laboratory, Department of Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA. Electronic address: ffaraha2@jhu.edu.; Computational Neuroergonomics Laboratory, Department of Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA.; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA; Department of Psychology, University of California, Berkeley, CA, USA.; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA.; Institute for Simulation and Training, University of Central Florida, Orlando, FL, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA.; Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, Krakow, Poland.; Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, Krakow, Poland; Department of Psychology of Individual Differences, Psychological Diagnosis, and Psychometrics, Institute of Psychology, University of Social Sciences and Humanities, Warsaw, Poland.; Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland. Electronic address: magda.fafrowicz@uj.edu.pl.
Circadian rhythms (lasting approximately 24 h) control and entrain various physiological processes, ranging from neural activity and hormone secretion to sleep cycles and eating habits. Several studies have shown that time of day (TOD) is associated with human cognition and brain functions. In this study, utilizing a chronotype-based paradigm, we applied a graph theory approach on resting-state functional MRI (rs-fMRI) data to compare whole-brain functional network topology between morning and evening sessions and between morning-type (MT) and evening-type (ET) participants. Sixty-two individuals (31 MT and 31 ET) underwent two fMRI sessions, approximately 1 hour (morning) and 10 h (evening) after their wake-up time, according to their declared habitual sleep-wake pattern on a regular working day. In the global analysis, the findings revealed the effect of TOD on functional connectivity (FC) patterns, including increased small-worldness, assortativity, and synchronization across the day. However, we identified no significant differences based on chronotype categories. The study of the modular structure of the brain at mesoscale showed that functional networks tended to be more integrated with one another in the evening session than in the morning session. Local/regional changes were affected by both factors (i.e., TOD and chronotype), mostly in areas associated with somatomotor, attention, frontoparietal, and default networks. Furthermore, connectivity and hub analyses revealed that the somatomotor, ventral attention, and visual networks covered the most highly connected areas in the morning and evening sessions: the latter two were more active in the morning sessions, and the first was identified as being more active in the evening. Finally, we performed a correlation analysis to determine whether global and nodal measures were associated with subjective assessments across participants. Collectively, these findings contribute to an increased understanding of diurnal fluctuations in resting brain activity and highlight the role of TOD in future studies on brain function and the design of fMRI experiments.
PMID: 35477020
Food Res Int , IF:6.475 , 2022 May , V155 : P111071 doi: 10.1016/j.foodres.2022.111071
MicroRNA-dependent regulation of targeted mRNAs for improved muscle texture in crisp grass carp fed with broad bean.
Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Marine Sciences, South China Agricultural University, Guangzhou 510640, China.; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.; School of Arts & Sciences, University of Houston-Victoria, Victoria, TX 77901, USA.; College of Marine Sciences, South China Agricultural University, Guangzhou 510640, China.; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China. Electronic address: yem@prfri.ac.cn.
Among legumes, broad bean (Vicia faba L.) has received particular attention due to its nutraceutical, functional and economic importance. The plant-derived microRNAs (miRNAs), as novel dietary functional components, are found to regulate the expression of endogenous mRNAs in vertebrates. To understand the role of broad bean miRNAs in the regulation of muscle texture, we investigated the miRNA-mRNA network in the established crisp grass carp model fed with broad bean. We identified various miRNAs that potentially improved muscle texture; miR-101b-3p activated Wnt signaling and satellite cell proliferation; miR-126-3p, miR-29a and miR-148b promoted hyperplasia by targeting muscle structure genes (tln2, TPM1, etc.); miR-152-5p and miR-185 regulated collagen expression via Smads signaling pathways; and miR-146a and miR-371-3p increased reactive oxygen species (ROS) by suppressing cat and prdx6. Among these changes, at least the Wnt signal activation was driven by broad bean-derived miR-101b-3p. This paper was conducted to investigate the cross-kingdom regulatory effects of broad bean miRNA on muscle structure and provide basic data for the development and application of broad bean.
PMID: 35400449
Plant J , IF:6.417 , 2022 May doi: 10.1111/tpj.15838
CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice.
UMR DIADE, Universite de Montpellier, IRD, CIRAD, 911 Avenue Agropolis, 34394, Montpellier, France.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, CNRS, INRAE, INRIA, UCB Lyon 1, Lyon, 69007, France.; Agricultural Genetic Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE2, 11300, Hanoi, Vietnam.; CIRAD, UMR AGAP, F-34398, Montpellier, France.; Universite de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.; University of Science and Technology of Hanoi, LMIRICE2, Vietnam Academy of Science and Technology, 11300.; Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052, Ghent, Belgium.; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.; Palacky University Olomouc, Czech Advanced Technology and Research Institute, Centre of Region Hana for Biotechnological and Agricultural Research.; Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain-Centre de Recherche, Route d'Ennezat, Chappes, France.
In cereals, the root system is mainly composed of postembryonic shoot borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family is a key regulator of crown root initiation in rice. Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or a LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and a LBD -box in their promoter show that CRL1 binds preferentially the LBD-box in these promoter contexts. CRISPR-Cas9 targeted mutation of these two CRL1-regulated genes, that encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
PMID: 35596715
Int J Mol Sci , IF:5.923 , 2022 Apr , V23 (8) doi: 10.3390/ijms23084455
Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.
Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Institute of Computational Mathematics and Mathematical Geophysics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.
The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes.
PMID: 35457273
Int J Mol Sci , IF:5.923 , 2022 Apr , V23 (8) doi: 10.3390/ijms23084124
The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response.
Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China.; College of Life Science, Northeast Forestry University, Harbin 150040, China.; Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China.
Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.
PMID: 35456943
Front Plant Sci , IF:5.753 , 2022 , V13 : P860455 doi: 10.3389/fpls.2022.860455
Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Nicotiana tabacum L.).
College of Agriculture, Guizhou University, Guiyang, China.; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China.; College of Tobacco, Guizhou University, Guiyang, China.
Nicotine is a unique alkaloid present in tobacco that is widely used in cigarettes and in the agricultural, chemical, and pharmaceutical industries. However, the research on nicotine is mostly limited to its synthesis pathways, and only a few studies have explored the effects of other metabolic pathways on nicotine precursors. Regulating the nicotine content in tobacco can greatly promoting the application of nicotine in other fields. In this study, we performed global data-independent acquisition proteomics analysis of four tobacco varieties. Of the four varieties, one had high nicotine content and three had a low nicotine content. A total of 31,259 distinct peptides and 6,018 proteins across two samples were identified. A total of 45 differentially expressed proteins (DEPs) co-existed in the three comparison groups and were mainly involved in the transport and metallic processes of the substances. Most DEPs were enriched in the biosynthesis of secondary metals, glutathione metabolism, carbon metabolism, and glycolysis/gluconeogenesis. In addition, the weighted gene co-expression network analysis identified an expression module closely related to the nicotine content (Brown, r = 0.74, P = 0.006). Gene Ontology annotation and Kyoto Encyclopaedia of Genes and Genomes enrichment analysis showed that the module proteins were mainly involved in the synthesis and metabolism of nicotine precursors such as arginine, ornithine aspartate, proline, and glutathione. The increased levels of these precursors lead to the synthesis and accumulation of nicotine in plants. More importantly, these proteins regulate nicotine synthesis by affecting the formation of putrescine, which is the core intermediate product in nicotine anabolism. Our results provide a reference for tobacco variety selection with a suitable nicotine content and regulation of the nicotine content. Additionally, the results highlight the importance of other precursor metabolism in nicotine synthesis.
PMID: 35574122
Front Plant Sci , IF:5.753 , 2022 , V13 : P864605 doi: 10.3389/fpls.2022.864605
Photosynthetic Carbon Fixation and Sucrose Metabolism Supplemented by Weighted Gene Co-expression Network Analysis in Response to Water Stress in Rice With Overlapping Growth Stages.
Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China.
Drought stress at jointing and booting phases of plant development directly affects plant growth and productivity in rice. Limited by natural factors, the jointing and booting stages in rice varieties are known to overlap in high-latitude areas that are more sensitive to water deficit. However, the regulation of photosynthetic carbon fixation and sucrose metabolism in rice leaves under different degrees of drought stress remains unclear. In this study, rice plants were subjected to three degrees of drought stress (-10, -25, -and 40 kPa) for 15 days during the jointing-booting stage, we investigated photosynthetic carbon sequestration and sucrose metabolism pathways in rice leaves and analyzed key genes and regulatory networks using transcriptome sequencing in 2016. And we investigated the effects of drought stress on the growth periods of rice with overlapping growth periods in 2016 and 2017. The results showed that short-term drought stress promoted photosynthetic carbon fixation. However, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) activity significantly decreased, resulting in a significant decrease in photosynthetic rate. Drought stress increased the maximum activity of fructose-1,6-bisphosphate aldolase (FBA). FBA maintains the necessary photosynthetic rate during drought stress and provides a material base after the resumption of irrigation in the form of controlling the content of its reaction product triose phosphate. Drought stress significantly affected the activities of sucrose synthase (SuSase) and sucrose phosphate synthase (SPS). Vacuoles invertase (VIN) activity increased significantly, and the more severe the drought, the higher the VIN activity. Severe drought stress at the jointing-booting stage severely restricted the growth process of rice with overlapping growth stages and significantly delayed heading and anthesis stages. Transcriptome analysis showed that the number of differentially expressed genes was highest at 6-9 days after drought stress. Two invertase and four beta-amylase genes with time-specific expression were involved in sucrose-starch metabolism in rice under drought stress. Combined with weighted gene co-expression network analysis, VIN and beta-amylase genes up-regulated throughout drought stress were regulated by OsbZIP04 and OsWRKY62 transcription factors under drought stress. This study showed that any water deficit at the jointing-booting stage would have a serious effect on sucrose metabolism in leaves of rice with overlapping growth stages.
PMID: 35528941
Front Plant Sci , IF:5.753 , 2022 , V13 : P852511 doi: 10.3389/fpls.2022.852511
Analysis of the Expression and Function of Key Genes in Pepper Under Low-Temperature Stress.
College of Horticulture, Hunan Agricultural University, Changsha, China.; Longping Branch, Graduate School of Hunan University, Changsha, China.; ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China.; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China.
The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.
PMID: 35599873
Front Plant Sci , IF:5.753 , 2022 , V13 : P864422 doi: 10.3389/fpls.2022.864422
Cell Fate Decisions Within the Vascular Cambium-Initiating Wood and Bast Formation.
Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.; RIKEN Center for Sustainable Resource Science (CSRS), Tsurumi-Yokohama, Japan.; Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Japan.
Precise coordination of cell fate decisions is a hallmark of multicellular organisms. Especially in tissues with non-stereotypic anatomies, dynamic communication between developing cells is vital for ensuring functional tissue organization. Radial plant growth is driven by a plant stem cell niche known as vascular cambium, usually strictly producing secondary xylem (wood) inward and secondary phloem (bast) outward, two important structures serving as much-needed CO2 depositories and building materials. Because of its bidirectional nature and its developmental plasticity, the vascular cambium serves as an instructive paradigm for investigating principles of tissue patterning. Although genes and hormones involved in xylem and phloem formation have been identified, we have a yet incomplete picture of the initial steps of cell fate transitions of stem cell daughters into xylem and phloem progenitors. In this mini-review perspective, we describe two possible scenarios of cell fate decisions based on the current knowledge about gene regulatory networks and how cellular environments are established. In addition, we point out further possible research directions.
PMID: 35548289
Front Plant Sci , IF:5.753 , 2022 , V13 : P855486 doi: 10.3389/fpls.2022.855486
Transcriptome and Small RNA Sequencing Reveal the Mechanisms Regulating Harvest Index in Brassica napus.
Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.; Academy of Agricultural Sciences, Southwest University, Chongqing, China.; Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China.
Harvest index (HI), the ratio of harvested seed weight to total aboveground biomass weight, is an economically critical value reflecting the convergence of complex agronomic traits. HI values in rapeseed (Brassica napus) remain much lower than in other major crops, and the underlying regulatory network is largely unknown. In this study, we performed mRNA and small RNA sequencing to reveal the mechanisms shaping HI in B. napus during the seed-filling stage. A total of 8,410 differentially expressed genes (DEGs) between high-HI and low-HI accessions in four tissues (silique pericarp, seed, leaves, and stem) were identified. Combining with co-expression network, 72 gene modules were identified, and a key gene BnaSTY46 was found to participate in retarded establishment of photosynthetic capacity to influence HI. Further research found that the genes involved in circadian rhythms and response to stimulus may play important roles in HI and that their transcript levels were modulated by differentially expressed microRNAs (DEMs), and we identified 903 microRNAs (miRNAs), including 46 known miRNAs and 857 novel miRNAs. Furthermore, transporter activity-related genes were critical to enhancing HI in good cultivation environments. Of 903 miRNAs, we found that the bna-miR396-Bna.A06SRp34a/Bna.A01EMB3119 pair may control the seed development and the accumulation of storage compounds, thus contributing to higher HI. Our findings uncovered the underlying complex regulatory network behind HI and offer potential approaches to rapeseed improvement.
PMID: 35444672
Genomics , IF:5.736 , 2022 Apr , V114 (3) : P110374 doi: 10.1016/j.ygeno.2022.110374
Transcriptome mining of genes in Zanthoxylum armatum revealed ZaMYB86 as a negative regulator of prickly development.
College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.; School of Horticulture and Landscape, Wuhan University of Bioengineering, Wuhan, China.; College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China.; College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China; Spice Crops Research Institute, Yangtze University, Jingzhou 434025, Hubei, China. Electronic address: wwzhangchn@163.com.; School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, Hubei, China.; School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, Hubei, China; National Selenium Rich Product Quality Supervision and Inspection Center, Enshi 445000, Hubei, China.; Sichuan Academy of Forestry, Chengdu 610081, Sichuan, China.; College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China. Electronic address: xufeng198@126.com.
Zanthoxylum armatum DC. is an important economic tree species. Prickle is a type of trichome with special morphology, and there are a lot of prickles on the leaves of Z. armatum, which seriously restricts the development of Z. armatum industry. In this study, the leaves of Z. armatum cv. Zhuye (ZY) and its budding variety 'Rongchangwuci' (WC) (A less prickly mutant variety) at different developmental stages were used as materials, and the transcriptome sequencing data were analyzed. A total of 96,931 differentially expressed genes (DEGs) were identified among the samples, among which 1560 were candidate DEGs that might be involved in hormone metabolism. The contents of JA, auxin and CK phytohormones in ZY leaves were significantly higher than those in WC leaves. Combined with weighted gene co-expression network analysis, eight genes (MYC, IAA, ARF, CRE/AHK, PP2C, ARR-A, AOS and LOX) were identified, including 25 transcripts, which might affect the metabolism of the three hormones and indirectly participate in the formation of prickles. Combining with the proteins successfully reported in other plants to regulate trichome formation, ZaMYB86, a transcription factor of R2R3 MYB family, was identified through local Blast and phylogenetic tree analysis, which might regulate prickle formation of Z. armatum. Overexpression of ZaMYB86 in mutant A. thaliana resulted in the reduction of trichomes in A. thaliana leaves, which further verified that ZaMYB86 was involved in the formation of pickles. Yeast two-hybrid results showed that ZaMYB86 interacted with ZaMYB5. Furthermore, ZaMYB5 was highly homologous to AtMYB5, a transcription factor that regulated trichomes development, in MYB DNA binding domain. Taken together, these results indicated that ZaMYB86 and ZaMYB5 act together to regulate the formation of prickles in Z. armatum. Our findings provided a new perspective for revealing the molecular mechanism of prickly formation.
PMID: 35489616
Front Microbiol , IF:5.64 , 2022 , V13 : P864619 doi: 10.3389/fmicb.2022.864619
Bacteria Community Inhabiting Heterobasidion Fruiting Body and Associated Wood of Different Decay Classes.
Department of Forest Sciences, University of Helsinki, Helsinki, Finland.; Natural Resources Institute of Finland (Luke), Helsinki, Finland.
The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.
PMID: 35591994
Viruses , IF:5.048 , 2022 Apr , V14 (4) doi: 10.3390/v14040837
Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs.
Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695, USA.; Program in Genetics, Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.; College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that caused the coronavirus disease 2019 (COVID-19) pandemic. Though previous studies have suggested that SARS-CoV-2 cellular tropism depends on the host-cell-expressed proteins, whether transcriptional regulation controls SARS-CoV-2 tropism factors in human lung cells remains unclear. In this study, we used computational approaches to identify transcription factors (TFs) regulating SARS-CoV-2 tropism for different types of lung cells. We constructed transcriptional regulatory networks (TRNs) controlling SARS-CoV-2 tropism factors for healthy donors and COVID-19 patients using lung single-cell RNA-sequencing (scRNA-seq) data. Through differential network analysis, we found that the altered regulatory role of TFs in the same cell types of healthy and SARS-CoV-2-infected networks may be partially responsible for differential tropism factor expression. In addition, we identified the TFs with high centralities from each cell type and proposed currently available drugs that target these TFs as potential candidates for the treatment of SARS-CoV-2 infection. Altogether, our work provides valuable cell-type-specific TRN models for understanding the transcriptional regulation and gene expression of SARS-CoV-2 tropism factors.
PMID: 35458567
Genetics , IF:4.562 , 2022 Apr doi: 10.1093/genetics/iyac056
An interolog-based barley interactome as an integration framework for NLR immune signaling.
Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA.; Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.; Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA.
The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem- and stripe rust. We used interolog inference to construct a barley protein interactome (HvInt) comprising 66133 edges and 7181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared to the experimentally validated Arabidopsis interactome of 11253 proteins and 73960 interactions, verifying that the two networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific 'omics' datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant (R) and susceptible (S) subnetworks. The resulting differentially co-expressed (R-S) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to Mla through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli (CC) + nucleotide binding (NB) domains and extended these to additional MLA alleles, orthologs and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.
PMID: 35435213
Plant Physiol Biochem , IF:4.27 , 2022 May , V178 : P40-54 doi: 10.1016/j.plaphy.2022.02.024
Evolutionary and functional characterisation of glutathione peroxidases showed splicing mediated stress responses in Maize.
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India. Electronic address: MG.Mallikarjuna@icar.gov.in.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.; ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.; Department of Genetics and Plant Breeding, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India.; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
Maize (Zea mays L) is an important cereal with extensive adaptability and multifaceted usages. However, various abiotic and biotic stresses limit the productivity of maize across the globe. Exposure of plant to stresses disturb the balance between reactive oxygen species (ROS) production and scavenging, which subsequently increases cellular damage and death of plants. Tolerant genotypes have evolved higher output of scavenging antioxidative defence compounds (ADCs) during stresses as one of the protective mechanisms. The glutathione peroxidases (GPXs) are the broad class of ADCs family. The plant GPXs catalyse the reduction of hydrogen peroxide (H2O2), lipid hydroperoxides and organic hydroperoxides to the corresponding alcohol, and facilitate the regulation of stress tolerance mechanisms. The present investigation was framed to study the maize GPXs using evolutionary and functional analyses. Seven GPX genes with thirteen splice-variants and sixty-three types of cis-acting elements were identified through whole-genome scanning in maize. Evolutionary analysis of GPXs in monocots and dicots revealed mixed and lineage-specific grouping patterns in phylogeny. The expression of ZmGPX splice variants was studied in drought and waterlogging tolerant (L1621701) and sensitive (PML10) genotypes in root and shoot tissues. Further, the differential expression of splice variants of ZmGPX1, ZmGPX3, ZmGPX6 and ZmGPX7 and regulatory network analysis suggested the splicing and regulatory elements mediated stress responses. The present investigation suggests targeting the splicing machinery of GPXs as an approach to enhance the stress tolerance in maize.
PMID: 35276595
BMC Plant Biol , IF:4.215 , 2022 May , V22 (1) : P247 doi: 10.1186/s12870-022-03641-6
Systematic identification of miRNA-regulatory networks unveils their potential roles in sugarcane response to Sorghum mosaic virus infection.
Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; Fuzhou Institute of Agricultural Sciences, Fuzhou, 350018, Fujian, China.; College of Agriculture, Yulin Normal University, Yulin, 537000, Guangxi,, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. xlpmail@126.com.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. queyouxiong@126.com.
BACKGROUND: Sugarcane mosaic disease (SMD) is a major viral disease of sugarcane (Saccharum spp.) worldwide. Sorghum mosaic virus (SrMV) is the dominant pathogen of SMD in the sugarcane planting areas of China. There is no report on miRNAs and their regulatory networks in sugarcane response to SrMV infection. RESULTS: In this study, small RNA sequencing (sRNA-seq) of samples from the leaves of SMD-susceptible variety ROC22 and -resistant variety FN39 infected by SrMV was performed. A total of 132 mature miRNAs (55 known miRNAs and 77 novel miRNAs) corresponding to 1,037 target genes were identified. After the SrMV attack, there were 30 differentially expressed miRNAs (17 up-regulated and 13 down-regulated) in FN39 and 19 in ROC22 (16 up-regulated and 3 down-regulated). Besides, there were 18 and 7 variety-specific differentially expressed miRNAs for FN39 and ROC22, respectively. KEGG enrichment analysis showed that the differentially expressed miRNAs targeted genes involved in several disease resistance-related pathways, such as mRNA surveillance, plant pathway interaction, sulfur metabolism, and regulation of autophagy. The reliability of sequencing data, and the expression patterns / regulation relationships between the selected differentially expressed miRNAs and their target genes in ROC22 and FN39 were confirmed by quantitative real-time PCR. A regulatory network diagram of differentially expressed miRNAs and their predicted target genes in sugarcane response to SrMV infection was sketched. In addition, precursor sequences of three candidate differentially expressed novel miRNAs (nov_3741, nov_22650 and nov_40875) were cloned from the ROC22 leaf infected by SrMV. Transient overexpression demonstrated that they could induce the accumulation of hydrogen peroxide and the expression level of hypersensitive response marker genes, salicylic acid-responsive genes and ethylene synthesis-depended genes in Nicotiana benthamiana. It is thus speculated that these three miRNAs may be involved in regulating the early immune response of sugarcane plants following SrMV infection. CONCLUSIONS: This study lays a foundation for revealing the miRNA regulation mechanism in the interaction of sugarcane and SrMV, and also provides a resource for miRNAs and their predicted target genes for SrMV resistance improvement in sugarcane.
PMID: 35585486
Phytopathology , IF:4.025 , 2022 May doi: 10.1094/PHYTO-02-22-0053-SYM
Why do plant pathogenic fungi produce mycotoxins? Potential roles for mycotoxins in the plant ecosystem.
USDA Agricultural Research Service, 17123, Food and Feed Safety Research Unit, Southern Regional Research Center, New Orleans, Louisiana, United States; rebecca.sweany@usda.gov.; Michigan State College of Agriculture and Applied Science, 3078, Department of Plant, Soil, and Microbial Sciences, East Lansing, Michigan, United States; mikaela.breunig@bayer.com.; USDA Agricultural Research Service, 17123, Pest Management and Biological Control Research Unit, US Arid-land Agricultural Research Center, Tucson, Arizona, United States; Joseph.Opoku@usda.gov.; Tulane University, 5783, Department of Ecology and Evolutionary Biology, New Orleans, Louisiana, United States; clay@tulane.edu.; Oregon State University, 2694, Botany and Plant Pathology, Corvallis, Oregon, United States; joseph.spatafora@oregonstate.edu.; University of Wisconsin-Madison, 5228, Department of Medical Microbiology and Immunology, Madison, Wisconsin, United States; mdrott@wisc.edu.; North Dakota State University, 3323, Department of Plant Pathology, Fargo, North Dakota, United States; thomas.t.baldwin@ndsu.edu.; Mississippi State University, 5547, Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Starkville, Mississippi, United States; jcf416@msstate.edu.
For many plant pathogenic or endophytic fungi, production of mycotoxins, which are toxic to humans, may present a fitness gain. However, associations between mycotoxin production and plant pathogenicity or virulence is inconsistent and difficult due to the complexity of these host-pathogen interactions and the influences of environmental and insect factors. Aflatoxin receives a lot of attention due to its potent toxicity and carcinogenicity, but the connection between aflatoxin production and pathogenicity is complicated by the pathogenic ability and prevalence of n on-aflatoxigenic isolates in crops. Other toxins directly aid fungi in planta, trichothecenes are important virulence factors and ergot alkaloids limit herbivory and fungal consumption due to insect toxicity. We review a panel discussion at Amercian Phytopathological Society's Plant Health 2021 conference, which gathered diverse experts representing different research sectors, career stages, ethnicities and genders to discuss the diverse roles of mycotoxins in the lifestyles of filamentous fungi of the families: Clavicipitaceae, Trichocomaceae (Eurotiales), Nectriaceae (Hypocreales).
PMID: 35502928
Plants (Basel) , IF:3.935 , 2022 Apr , V11 (9) doi: 10.3390/plants11091111
Grape Cultivar Features Differentiate the Grape Rhizosphere Microbiota.
Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; College of Resources and Environment, Henan University of Engingeering, Zhengzhou 451191, China.; Xiongan Institute of Innovation, Xiongan New Area Baoding 071000, China.
Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants' metabolisms and activation of plants' responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes.
PMID: 35567111
Life (Basel) , IF:3.817 , 2022 Apr , V12 (5) doi: 10.3390/life12050650
Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow.
Malaysian Agricultural Research & Development Institute (MARDI), Serdang 43400, Malaysia.; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia.; UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia.; Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
Protein-protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI network has been widely applied in biomedical research to understand the pathobiology of human diseases. It has also been used to understand the plant physiology that relates to crop improvement. However, the application of the PPI network in aquaculture is limited as compared to humans and plants. This review aims to demonstrate the workflow and step-by-step instructions for constructing a PPI network using bioinformatics tools and PPI databases that can help to predict potential interaction between proteins. We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network. Thus, serving as a guide for future steps in exploring potential mechanisms on the organismal physiology of interest that ultimately benefit aquaculture research.
PMID: 35629318
Gene , IF:3.688 , 2022 Apr , V820 : P146114 doi: 10.1016/j.gene.2021.146114
Genome-wide evaluation of transcriptomic responses of human tissues to smoke: A systems biology study.
Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran. Electronic address: m_rashidi80@yahoo.com.; Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.; Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran.; Department of Immunology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.; Razi Herbal Medicines Research Center and Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran.
The harmful compounds in various sources of smoke threaten human health. So far, many studies have investigated the effects of compounds of smoke on transcriptome changes in different human tissues. However, no study has been conducted on the effects of these compounds on transcriptome changes in different human tissues simultaneously. Hence, the present study was conducted to identify smoke-related genes (SRGs) and their response mechanisms to smoke in various human cells and tissues using systems biology based methods. A total of 6,484 SRGs were identified in the studied tissues, among which 4,095 SRGs were up-regulated and 2,389 SRGs were down-regulated. Totally, 459 SRGs were smoke-related transcription factors (SRTFs). Gene regulatory network analysis showed that the studied cells and tissues have different gene regulation and responses to compounds of smoke. The comparison of different tissues revealed no common SRG among the all studied tissues. However, the CYP1B1 gene was common among seven cells and tissues, and had the same expression trend. Network analysis showed that the CYP1B1 is a hub gene among SRGs in various cells and tissues. To the best of our knowledge, for the first time, our results showed that compounds of smoke induce and increase the expression of CYP1B1 key gene in all target and non-target tissues of human. Moreover, despite the specific characteristics of CYP1B1 gene and its identical expression trend in target and non-target tissues, it can be used as a biomarker for diagnosis and prognosis.
PMID: 35077830
Gene , IF:3.688 , 2022 Apr , V819 : P146233 doi: 10.1016/j.gene.2022.146233
Different gene co-expression patterns of aortic intima-media and adventitia in thoracic aortic aneurysm.
Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. Electronic address: lcx_pumc@163.com.; Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China.; Department of Neurosurgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. Electronic address: yuehongzheng@yahoo.com.
BACKGROUND: Due to permanent aortic dilation, thoracic aortic aneurysm (TAA) is a life-threatening disease. Once ruptured, TAA has a high lethality and disability rate. Although studies have focused on transcriptomic alterations in TAA, more detailed analysis is still lacking, especially the different aortic intima-media and adventitia roles. This study aimed to identify the different co-expression patterns between the aortic intima-media and the adventitia underlying the aortic dilation. METHODS: We analyzed the gene expression profiles obtained from Gene Expression Omnibus (GEO, GSE26155) database. With a false discovery rate (FDR) < 0.05 and |log2FC| >/= 1, 56 and 33 differential genes in the intima-media and adventitia, respectively, between the non-dilated and dilated status. Gene ontology (GO) and gene set enrichment analysis revealed that degranulation and activation of neutrophils play an essential role in the intima-media of dilated aortas. Through weighted gene co-expression network analysis (WGCNA), we identified essential co-expressed modules and hub genes to explore the biological functions of the dysregulated genes. RESULTS: Functional pathway analysis suggested that lipid metabolism, C-C motif chemokine pathways were significantly enriched in the adventitia, whereas ribosome proteins and related mRNA translation pathways were closely related to intima and media. Furthermore, the ssGSEA analysis indicated that macrophages, helper T cells, and neutrophils were higher in the intima-media of the dilated thoracic aorta. Finally, we validated the critical findings of the study with the murine model of TAA. CONCLUSION: This study identified and verified hub genes and pathways in aortic intima-media and adventitia prominently associated with aortic dilation, providing practical understanding in the perspective of searching for new molecular targets.
PMID: 35121027
Virus Res , IF:3.303 , 2022 Apr , V311 : P198704 doi: 10.1016/j.virusres.2022.198704
Complex small RNA-mediated regulatory networks between viruses/viroids/satellites and host plants.
Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Plant Protection, China Agricultural University, Beijing 100193, China.; Chinese Academy of Inspection and Quarantine, Beijing 100176, China.; Chinese Academy of Inspection and Quarantine, Beijing 100176, China. Electronic address: zhusf@caiq.org.cn.
Host plants deploy the small RNA (sRNA)-directed RNA silencing pathway to resist invasion by acellular microorganisms (viruses/viroids/satellites), and, in turn, this pathway is exploited by pathogenic agents to create an environment conducive to infection. Previous known sRNA-RNA systems consist of host endogenous microRNAs (miRNAs) mediating the regulation of host mRNAs and virus/viroid/satellite-derived small interfering RNAs (vsiRNAs) targeting their genomic RNAs. However, more in-depth explorations have substantially expanded the understanding of the complexity of sRNA-RNA regulatory networks. Here, we review some recently discovered sRNA-mediated regulatory systems. Specifically, in addition to virus-encoded proteins acting as virulence factors, vsiRNAs can serve as important pathogenic determinants targeting host mRNAs and noncoding RNAs to promote virus/viroid/satellite infection and trigger symptoms that may be side effects of infection. Additionally, virus-activated but host-derived siRNAs (vasiRNAs) regulate endogenous plant gene expression related to virus resistance or pathogenicity. The inhibitory effect of miRNAs on plant endogenous mRNAs and viral RNAs (vRNAs) has also been identified. Furthermore, siRNA-based interregulation occurring between viruses and their parasite satellite RNAs (satRNAs) enables coexisting virus-satRNA-plant homoeostasis. Thus, the underlying mechanisms of plant-virus/viroid/satellite competition and symbiosis are largely obscured by these diverse sRNA-RNA combinations. Guided by the intricate regulatory network-based principle at the RNA level, practically applicable and feasible strategies have been developed for the management of plant viruses/viroids/satellites for which effective control measures are lacking.
PMID: 35139407
Bioengineered , IF:3.269 , 2022 May , V13 (5) : P12475-12488 doi: 10.1080/21655979.2022.2076009
Differences between the effects of plant species and compartments on microbiome composition in two halophyte Suaeda species.
College of Biological Science and Technology, Hubei Minzu University, Hubei, China.; College of Life Sciences, Northeast Forestry University, Harbin, China.; Zibo Academy of Agricultural Sciences, Zibo, China.
Root-related or endophytic microbes in halophytes play an important role in adaptation to extreme saline environments. However, there have been few comparisons of microbial distribution patterns in different tissues associated with halophytes. Here, we analyzed the bacterial communities and distribution patterns of the rhizospheres and tissue endosphere in two Suaeda species (S. salsa and S. corniculata Bunge) using the 16S rRNA gene sequencing. The results showed that the bacterial abundance and diversity in the rhizosphere were significantly higher than that of endophytic, but lower than that of bulk soil. Microbial-diversity analysis showed that the dominant phyla of all samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria and Firmicutes, among which Proteobacteria were extremely abundant in all the tissue endosphere. Heatmap and Linear discriminant analysis Effect Size (LEfSe) results showed that there were notable differences in microbial community composition related to plant compartments. Different networks based on plant compartments exhibited distinct topological features. Additionally, the bulk soil and rhizosphere networks were more complex and showed higher centrality and connectedness than the three endosphere networks. These results strongly suggested that plant compartments, and not species, affect microbiome composition.
PMID: 35593105
BMC Bioinformatics , IF:3.169 , 2022 May , V23 (1) : P165 doi: 10.1186/s12859-022-04696-w
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique.
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. zhangxj@wbgcas.cn.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China. zhangxj@wbgcas.cn.
BACKGROUND: Current gene regulatory network (GRN) inference methods are notorious for a great number of indirect interactions hidden in the predictions. Filtering out the indirect interactions from direct ones remains an important challenge in the reconstruction of GRNs. To address this issue, we developed a redundancy silencing and network enhancement technique (RSNET) for inferring GRNs. RESULTS: To assess the performance of RSNET method, we implemented the experiments on several gold-standard networks by using simulation study, DREAM challenge dataset and Escherichia coli network. The results show that RSNET method performed better than the compared methods in sensitivity and accuracy. As a case of study, we used RSNET to construct functional GRN for apple fruit ripening from gene expression data. CONCLUSIONS: In the proposed method, the redundant interactions including weak and indirect connections are silenced by recursive optimization adaptively, and the highly dependent nodes are constrained in the model to keep the real interactions. This study provides a useful tool for inferring clean networks.
PMID: 35524190
3 Biotech , IF:2.406 , 2022 Jun , V12 (6) : P127 doi: 10.1007/s13205-022-03182-7
Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.).
ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India.grid.418105.90000 0001 0643 7375; Department of Botany, National College, Tiruchirapalli, Tamil Nadu 620001 India.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.grid.418196.30000 0001 2172 0814; Tamil Nadu Agricultural University, Coimbatore, India.grid.412906.80000 0001 2155 9899
A wealth of microarray and RNA-seq data for studying abiotic stress tolerance in rice exists but only limited studies have been carried out on multiple stress-tolerance responses and mechanisms. In this study, we identified 6657 abiotic stress-responsive genes pertaining to drought, salinity and heat stresses from the seedling stage microarray data of 83 samples and used them to perform unweighted network analysis and to identify key hub genes or master regulators for multiple abiotic stress tolerance. Of the total 55 modules identified from the analysis, the top 10 modules with 8-61 nodes comprised 239 genes. From these 10 modules, 10 genes common to all the three stresses were selected. Further, based on the centrality properties and highly dense interactions, we identified 7 intra-modular hub genes leading to a total of 17 potential candidate genes. Out of these 17 genes, 15 were validated by expression analysis using a panel of 4 test genotypes and a pair of standard check genotypes for each abiotic stress response. Interestingly, all the 15 genes showed upregulation under all stresses and in all the genotypes, suggesting that they could be representing some of the core abiotic stress-responsive genes. More pertinently, eight of the genes were found to be co-localized with the stress-tolerance QTL regions. Thus, in conclusion, our study not only provided an effective approach for studying abiotic stress tolerance in rice, but also identified major candidate genes which could be further validated by functional genomics for abiotic stress tolerance. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03182-7.
PMID: 35573803
J Comput Biol , IF:1.479 , 2022 May doi: 10.1089/cmb.2021.0600
Extracting Information from Gene Coexpression Networks of Rhizobium leguminosarum.
Department of Statistics, University of Oxford, Oxford, United Kingdom.; Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.; Department of the Mathematical Institute, University of Oxford, Oxford, United Kingdom.
Nitrogen uptake in legumes is facilitated by bacteria such as Rhizobium leguminosarum. For this bacterium, gene expression data are available, but functional gene annotation is less well developed than for other model organisms. More annotations could lead to a better understanding of the pathways for growth, plant colonization, and nitrogen fixation in R. leguminosarum. In this study, we present a pipeline that combines novel scores from gene coexpression network analysis in a principled way to identify the genes that are associated with certain growth conditions or highly coexpressed with a predefined set of genes of interest. This association may lead to putative functional annotation or to a prioritized list of genes for further study.
PMID: 35588362
Proc SPIE Int Soc Opt Eng , 2022 Feb-Mar , V12032 doi: 10.1117/12.2611845
Longitudinal changes of connectomes and graph theory measures in aging.
Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA.; Department of Radiology and Radiological Science, Vanderbilt University Medical Center, Nashville, TN, USA.; Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.; Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
Changes in brain structure and connectivity in aging can be probed through diffusion weighted MRI and summarized with structural connectome matrices. Complex network analysis based on graph theory has been applied to provide measures that are correlated with neurobiological variations and can help guide quantitative study of brain function. However, the understanding of how connectomes change longitudinally is limited. In this work, we evaluate modern pipelines to obtain the connectomics data from diffusion weighted MRI scans across different sessions from control subjects (55-99 years old) in the Baltimore Longitudinal Study of Aging and Cambridge Centre for Ageing and Neuroscience. From the connectivity matrices, we compute graph theory measures to understand their brain networks and apply a linear mixed-effects model to study their longitudinal changes with respect to age. With this approach, we computed 14 graph theory measures of 1469 healthy subjects (2476 scans) and found statistically significant correlations between all 14 measures and age. In this analysis: 1) the brain becomes more segregated but less integrated in aging; 2) the overall network cost increases for older subjects; 3) the small-world organizations remain stable; and 4) due to high intra-subject variance, there is not clear trend for longitudinal changes of graph theory measures of individual subjects. Therefore, while useful to investigate brain evolution in aging at the population level, improvements in the connectome reconstruction are needed to decrease single subject variability for individual inference.
PMID: 35506128
Emerg Top Life Sci , 2022 Apr , V6 (2) : P137-139 doi: 10.1042/ETLS20220020
How 'omics technologies can drive plant engineering, ecosystem surveillance, human and animal health.
La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia.; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia.
'Omics describes a broad collection of research tools and techniques that enable researchers to collect data about biological systems at a very large, or near-complete, scale. These include sequencing of individual and community genomes (genomics, metagenomics), characterization and quantification of gene expression (transcriptomics), metabolite abundance (metabolomics), protein content (proteomics) and phosphorylation (phospho-proteomics), amongst many others. Though initially exploited as tools for fundamental discovery, 'omics techniques are now used extensively in applied and translational research, for example in plant and animal breeding, biomarker development and drug discovery. In this collection of reviews, we aimed to introduce readers to current and future applications of 'omics technologies to solve real-world problems.
PMID: 35403675
Energy Nexus , 2022 Jun , V6 : P100080 doi: 10.1016/j.nexus.2022.100080
Plant-Based Natural Bioactive Compounds 2,4-Ditert-Butylphenolas: A Potential Candidates Against SARS-Cov-2019.
Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, Tamil Nadu, India.; Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous) Chennai 600 042.; Department of Biotechnology, Rathinam College of Arts and Science(Autonomous), Coimbatore 641021, Tamil Nadu, India.; Department of Botany, Thiru Kolanjiyapper Government Arts College, Virudhachalam, Cuddalore 606001, Tamil Nadu, India.; Department of Biotechnology, St Joseph's College (Arts & Science), Kovur, Chennai, Tamil Nadu, India.; Department of Botany, Shri Sakthikailassh Women's college, Salem 636003, Tamil Nadu, India.
The novel coronavirus 2019 is spreading around the world and causing serious concern. However, there is limited information about novel coronavirus that hinders the design of effective drug. Bioactive compounds are rich source of chemo preventive ingredients. In our present research focuses on identifying and recognizing bioactive chemicals in Lantana camara, by evaluating their potential toward new coronaviruses and confirming the findings using molecular docking, ADMET, network analysis and dynamics investigations.. The spike protein receptor binding domain were docked with 25 identified compounds and 2,4-Ditertbutyl-phenol (-6.3kcal/mol) shows highest docking score, its interactions enhances the increase in binding and helps to identify the biological activity. The ADME/toxicity result shows that all the tested compounds can serve as inhibitors of the enzymes CYP1A2 and CYP2D6. In addition, Molecular dynamics simulations studies with reference inhibitors were carried out to test the stability. This study identifies the possible active molecules against the receptor binding domain of spike protein, which can be further exploited for the treatment of novel coronavirus 2019. The results of the toxicity risk for phytocompounds and their active derivatives showed a moderate to good drug score.
PMID: 35578668