Genome Biol , IF:13.583 , 2023 May , V24 (1) : P108 doi: 10.1186/s13059-023-02909-w
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize.
Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA. hartwit@hhu.de.; Heinrich-Heine University, Universitatsstrasse 1, Dusseldorf, NRW, 40225, Germany. hartwit@hhu.de.; Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, NRW, 50829, Germany. hartwit@hhu.de.; Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.; Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Seeland, SA, 06466, Germany.; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 339A Bessey Hall, Ames, IA, 50011, USA.; Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, NRW, 50829, Germany.; School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, 413 Bradfield Hall, Ithaca, NY, 14853, USA.; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 363 Keim Hall, Lincoln, NE, 68583, USA.; Heinrich-Heine University, Universitatsstrasse 1, Dusseldorf, NRW, 40225, Germany.; Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA. zywang24@stanford.edu.
BACKGROUND: Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches. RESULTS: Here, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits. CONCLUSION: Our study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
PMID: 37158941
J Hazard Mater , IF:10.588 , 2023 May , V449 : P131026 doi: 10.1016/j.jhazmat.2023.131026
Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus.
Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China.; Centre for Environmental Policy, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China. Electronic address: hfqian@zjut.edu.cn.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, China.
Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter's microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.
PMID: 36812731
New Phytol , IF:10.151 , 2023 Jun , V238 (6) : P2410-2426 doi: 10.1111/nph.18885
A conserved gene regulatory network controls root epidermal cell patterning in superrosid species.
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved. In this study, we analyzed superrosid species Rhodiola rosea, Boehmeria nivea, and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, and major changes in C. sativus. We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.
PMID: 36932734
New Phytol , IF:10.151 , 2023 Jun , V238 (5) : P2064-2079 doi: 10.1111/nph.18840
A comprehensive metabolic map reveals major quality regulations in red-flesh kiwifruit (Actinidia chinensis).
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.; Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, 610213, Sichuan, China.; GBF Laboratory, Universite de Toulouse, INRA, Castanet-Tolosan, 31320, France.; School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.; School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK.; Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
Kiwifruit (Actinidia chinensis) is one of the popular fruits world-wide, and its quality is mainly determined by key metabolites (sugars, flavonoids, and vitamins). Previous works on kiwifruit are mostly done via a single omics approach or involve only limited metabolites. Consequently, the dynamic metabolomes during kiwifruit development and ripening and the underlying regulatory mechanisms are poorly understood. In this study, using high-resolution metabolomic and transcriptomic analyses, we investigated kiwifruit metabolic landscapes at 11 different developmental and ripening stages and revealed a parallel classification of 515 metabolites and their co-expressed genes into 10 distinct metabolic vs gene modules (MM vs GM). Through integrative bioinformatics coupled with functional genomic assays, we constructed a global map and uncovered essential transcriptomic and transcriptional regulatory networks for all major metabolic changes that occurred throughout the kiwifruit growth cycle. Apart from known MM vs GM for metabolites such as soluble sugars, we identified novel transcription factors that regulate the accumulation of procyanidins, vitamin C, and other important metabolites. Our findings thus shed light on the kiwifruit metabolic regulatory network and provide a valuable resource for the designed improvement of kiwifruit quality.
PMID: 36843264
Arterioscler Thromb Vasc Biol , IF:8.311 , 2023 Jun , V43 (6) : P813-823 doi: 10.1161/ATVBAHA.122.318332
Molecular Interaction Networks and Cardiovascular Disease Risk: The Role of Food Bioactive Small Molecules.
Network Science Institute, Department of Physics, Northeastern University, Boston, MA (F.N., G.M.).; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (G.M.).
Diet is a well-known modifiable risk factor for cardiovascular diseases, which are the leading cause of death worldwide. However, our current understanding of the human diet is still limited in terms of fully capturing the role of dietary compounds in the intraspecies and interspecies biochemical networks that determine our health. This is due, in part, to a lack of detailed information on the presence of small molecules in food (molecular weight
PMID: 37128923
Sci Total Environ , IF:7.963 , 2023 Jun , V879 : P163244 doi: 10.1016/j.scitotenv.2023.163244
Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties.
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; RDFZ Chaoyang School, Beijing 100028, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: xinzhang@rcees.ac.cn.
Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.
PMID: 37004770
Sci Total Environ , IF:7.963 , 2023 Jun , V877 : P162517 doi: 10.1016/j.scitotenv.2023.162517
Gene co-expression network analysis for the selection of candidate early warning indicators of heat and nutrient stress in Posidonia oceanica.
Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy. Electronic address: alex.santillan@szn.it.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Department of Life Sciences, University of Trieste, Trieste, Italy.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.; Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.; Dead Sea and Arava Science Center (DSASC), Masada National Park, Mount Masada 8698000, Israel.; Eilat Campus, Ben-Gurion University of the Negev, Hatmarim Blv, Eilat 8855630, Israel.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain.; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy. Electronic address: gpro@szn.it.
The continuous worldwide seagrasses decline calls for immediate actions in order to preserve this precious marine ecosystem. The main stressors that have been linked with decline in seagrasses are 1) the increasing ocean temperature due to climate change and 2) the continuous inputs of nutrients (eutrophication) associated with coastal human activities. To avoid the loss of seagrass populations, an "early warning" system is needed. We used Weighed Gene Co-expression Network Analysis (WGCNA), a systems biology approach, to identify potential candidate genes that can provide an early warning signal of stress in the Mediterranean iconic seagrass Posidonia oceanica, anticipating plant mortality. Plants were collected from both eutrophic (EU) and oligotrophic (OL) environments and were exposed to thermal and nutrient stress in a dedicated mesocosm. By correlating the whole-genome gene expression after 2-weeks exposure with the shoot survival percentage after 5-weeks exposure to stressors, we were able to identify several transcripts that indicated an early activation of several biological processes (BP) including: protein metabolic process, RNA metabolic process, organonitrogen compound biosynthetic process, catabolic process and response to stimulus, which were shared among OL and EU plants and among leaf and shoot apical meristem (SAM), in response to excessive heat and nutrients. Our results suggest a more dynamic and specific response of the SAM compared to the leaf, especially the SAM from plants coming from a stressful environment appeared more dynamic than the SAM from a pristine environment. A vast list of potential molecular markers is also provided that can be used as targets to assess field samples.
PMID: 36868282
Sci Total Environ , IF:7.963 , 2023 May , V871 : P162034 doi: 10.1016/j.scitotenv.2023.162034
Biodegradable mulch films significantly affected rhizosphere microbial communities and increased peanut yield.
Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China.; Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing 100125, China.; Liaoning Academy of Agricultural Sciences, Shenyang 110161, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: dcjin@rcees.ac.cn.
Biodegradable mulch films are widely used to replace conventional plastic films in agricultural fields. However, their ecological effects on different microbial communities that naturally inhabit agricultural fields are scarcely explored. Herein, differences in bacterial communities recovered from biofilms, bulk soil, and rhizosphere soil were comparatively assessed for polyethylene film (PE) and biodegradable mulch film (BDM) application in peanut planted fields. The results showed that the plastic film type significantly influenced the bacterial community in different ecological niches of agricultural fields (P < 0.001). Specifically, BDMs significantly increased the diversity and abundance of bacteria in the rhizosphere soil. The bacterial communities in each ecological niche were distinguishable from each other; bacterial communities in the rhizosphere soil showed the most pronounced response among different treatments. Acidobacteria and Pseudomonas were significantly enriched in the rhizosphere soil when BDMs were used. BDMs also increased the rhizosphere soil bacterial network complexity and stability. The enrichment of beneficial bacteria in the rhizosphere soil under BDMs may also have implications for the observed increase in peanut yield. Deepening analyses indicated that Pseudoxanthomonas and Glutamicibacter are biomarkers in biofilms of PE and BDMs respectively. Our study provides new insights into the consequences of the application of different types of plastic films on microbial communities in different ecological niches of agricultural fields.
PMID: 36754316
J Exp Bot , IF:6.992 , 2023 Apr doi: 10.1093/jxb/erad135
An Evo-Devo view of the gynoecium.
International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.; Laboratorio de Genetica Molecular, Epigenetica, Desarrollo y Evolucion de Plantas, Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria, Av. Universidad 3000, Coyoacan, Mexico D.F. 04510, Mexico.; Faculty of Advanced Science and Technology (FAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.; Unidad de Genomica Avanzada (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, Mexico.
The appearance of the flower marks a key event in the evolutionary history of plants. Among the four types of floral organs, the gynoecium represents the major adaptive advantage of the flower. The gynoecium is an enclosing structure that protects and facilitates the fertilisation of the ovules, which then mature as seeds. Upon fertilisation, in many species, the gynoecium itself eventually becomes the fruit, which contributes to the dispersal of the seeds. However, despite its importance and the recent advances in our understanding of the genetic regulatory network (GRN) guiding early gynoecium development, many questions remain to be resolved regarding the extent of the conservation of the molecular mechanisms for gynoecium development among different taxa, and how these mechanisms give origin and diversification to the gynoecium. In this review, we compile the existing knowledge about the evolution, development and molecular mechanisms involved in the origin and evolution of the gynoecium.
PMID: 37075814
Int J Biol Macromol , IF:6.953 , 2023 May : P124834 doi: 10.1016/j.ijbiomac.2023.124834
Comparative transcriptome analysis reveals the core molecular network in pattern-triggered immunity in Sorghum bicolor.
Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China.; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.; Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China. Electronic address: ippxiexin@163.com.
Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is the first line of defense in plant disease resistance. However, the molecular mechanisms of plant PTI vary across species, making it challenging to identify a core set of trait-associated genes. This study aimed to investigate key factors that influence PTI and identify the core molecular network in Sorghum bicolor, a C4 plant. We performed comprehensive weighted gene co-expression network analysis and temporal expression analysis of large-scale transcriptome data from various sorghum cultivars under different PAMP treatments. Our results revealed that the type of PAMP had a stronger influence on the PTI network than did the sorghum cultivar. Following PAMP treatment, 30 genes with stable downregulated expression and 158 genes with stable upregulated expression were identified, including genes encoding potential pattern recognition receptors whose expression was upregulated within 1 h of treatment. PAMP treatment altered the expression of resistance-related, signaling, salt-sensitive, heavy metal-related, and transporter genes. These findings provide novel insights into the core genes involved in plant PTI and are expected to facilitate the identification and application of resistance genes in plant breeding studies.
PMID: 37207754
Plant J , IF:6.417 , 2023 May doi: 10.1111/tpj.16330
A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis.
Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.; Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan.; Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFAs levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. Additionally, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle (RCC), which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through RCC formation.
PMID: 37247130
Plant J , IF:6.417 , 2023 Apr doi: 10.1111/tpj.16260
Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.; Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.; HainanYazhou Bay Seed Lab, Sanya, 572025, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.
PMID: 37186341
Plant J , IF:6.417 , 2023 Apr doi: 10.1111/tpj.16248
Co-expression network analysis of diverse wheat landraces reveals markers of early thermotolerance and a candidate master regulator of thermotolerance genes.
Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, YO10 5DD, UK.
Triticum aestivum L. (bread wheat) is a crop relied upon by billions of people around the world, as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprising 342 accessions that show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110 790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and to identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat-shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belong to the same module, with one (TraesCS4D01G207500.1) being a candidate master-regulator potentially controlling the expression of the other two hub genes, as well as a suite of other HSPs and heat-stress transcription factors (HSFs). In this work, therefore, we identify three validated hub genes, the expression of which can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and HSF expression - presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops.
PMID: 37077043
Plant J , IF:6.417 , 2023 Apr doi: 10.1111/tpj.16229
The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice.
Dipartimento di Bioscienze, Universita degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.; Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA.; DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France.
The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.
PMID: 37009647
Int J Mol Sci , IF:5.923 , 2023 Apr , V24 (8) doi: 10.3390/ijms24087349
Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis.
Department of Biology, 464 Campbell Hall, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.; Nutrition Obesity Research Center, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA.; Department of Surgery, University of Alabama at Birmingham, 1808 7th Ave S, Birmingham, AL 35294, USA.
Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of high-priority transcription factors (TFs), dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We identified distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficient nodes. Dynamic transcriptional regulatory modeling of integrated TF targets and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs, as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that could potentially be used in future genetic crop engineering programs.
PMID: 37108512
Int J Mol Sci , IF:5.923 , 2023 May , V24 (10) doi: 10.3390/ijms24108473
Trichome-Specific Analysis and Weighted Gene Co-Expression Correlation Network Analysis (WGCNA) Reveal Potential Regulation Mechanism of Artemisinin Biosynthesis in Artemisia annua.
Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
Trichomes are attractive cells for terpenoid biosynthesis and accumulation in Artemisia annua. However, the molecular process underlying the trichome of A. annua is not yet fully elucidated. In this study, an analysis of multi-tissue transcriptome data was performed to examine trichome-specific expression patterns. A total of 6646 genes were screened and highly expressed in trichomes, including artemisinin biosynthetic genes such as amorpha-4,11-diene synthase (ADS) and cytochrome P450 monooxygenase (CYP71AV1). Mapman and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that trichome-specific genes were mainly enriched in lipid metabolism and terpenoid metabolism. These trichome-specific genes were analyzed by a weighted gene co-expression network analysis (WGCNA), and the blue module linked to terpenoid backbone biosynthesis was determined. Hub genes correlated with the artemisinin biosynthetic genes were selected based on TOM value. ORA, Benzoate carboxyl methyltransferase (BAMT), Lysine histidine transporter-like 8 (AATL1), Ubiquitin-like protease 1 (Ulp1) and TUBBY were revealed as key hub genes induced by methyl jasmonate (MeJA) for regulating artemisinin biosynthesis. In summary, the identified trichome-specific genes, modules, pathways and hub genes provide clues and shed light on the potential regulatory mechanisms of artemisinin biosynthesis in trichomes in A. annua.
PMID: 37239820
Front Plant Sci , IF:5.753 , 2023 , V14 : P1108351 doi: 10.3389/fpls.2023.1108351
Applying network and genetic analysis to the potato metabolome.
School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.; Cayuga Genetics Consulting Group LLC, Ithaca, NY, United States.; Department of Mechanical Engineering, Penn State University, State College, PA, United States.; Bioanalysis and Omics Team, Colorado State University, Fort Collins, CO, United States.
Compositional traits in potato [Solanum tuberosum L.] are economically important but genetically complex, often controlled by many loci of small effect; new methods need to be developed to accelerate analysis and improvement of such traits, like chip quality. In this study, we used network analysis to organize hundreds of metabolic features detected by mass spectrometry into groups, as a precursor to genetic analysis. 981 features were condensed into 44 modules; module eigenvalues were used for genetic mapping and correlation analysis with phenotype data collected by the Solanaceae Coordinated Agricultural Project. Half of the modules were associated with at least one SNP according to GWAS; 11 of those modules were also significantly correlated with chip color. Within those modules features associated with chipping provide potential targets for selection in addition to selection for reduced glucose. Loci associated with module eigenvalues were not evenly distributed throughout the genome but were instead clustered on chromosomes 3, 7, and 8. Comparison of GWAS on single features and modules of clustered features often identified the same SNPs. However, features with related chemistries (for example, glycoalkaloids with precursor/product relationships) were not found to be near neighbors in the network analysis and did not share common SNPs from GWAS. Instead, the features within modules were often structurally disparate, suggesting that linkage disequilibrium complicates network analyses in potato. This result is consistent with recent genomic studies of potato showing that chromosomal rearrangements that create barriers to recombination are common in cultivated germplasm.
PMID: 37152172
Front Plant Sci , IF:5.753 , 2023 , V14 : P1158965 doi: 10.3389/fpls.2023.1158965
Alternative splicing: transcriptional regulatory network in agroforestry.
State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.; Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China.; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.; Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, United States.; Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.; Department of Chemical and Biomolecular Engineering, The University of Tennessee-Knoxville, Knoxville, TN, United States.
Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNA(ir)) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.
PMID: 37123829
Front Plant Sci , IF:5.753 , 2023 , V14 : P1149879 doi: 10.3389/fpls.2023.1149879
The genetic architecture of trait covariation in Populus euphratica, a desert tree.
College of Science, Beijing Forestry University, Beijing, China.; Department of Artificial Intelligence and Data Science, Guangzhou Xinhua University, Guangzhou, China.; College of Biological Sciences and Technology, Center for Computational Biology, Beijing Forestry University, Beijing, China.; Faculty of Science, Yamagata University, Yamagata, Japan.; Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
INTRODUCTION: The cooperative strategy of phenotypic traits during the growth of plants reflects how plants allocate photosynthesis products, which is the most favorable decision for them to optimize growth, survival, and reproduction response to changing environment. Up to now, we still know little about why plants make such decision from the perspective of biological genetic mechanisms. METHODS: In this study, we construct an analytical mapping framework to explore the genetic mechanism regulating the interaction of two complex traits. The framework describes the dynamic growth of two traits and their interaction as Differential Interaction Regulatory Equations (DIRE), then DIRE is embedded into QTL mapping model to identify the key quantitative trait loci (QTLs) that regulate this interaction and clarify the genetic effect, genetic contribution and genetic network structure of these key QTLs. Computer simulation experiment proves the reliability and practicability of our framework. RESULTS: In order to verify that our framework is universal and flexible, we applied it to two sets of data from Populus euphratica, namely, aboveground stem length - underground taproot length, underground root number - underground root length, which represent relationships of phenotypic traits in two spatial dimensions of plant architecture. The analytical result shows that our model is well applicable to datasets of two dimensions. DISCUSSION: Our model helps to better illustrate the cooperation-competition patterns between phenotypic traits, and understand the decisions that plants make in a specific environment that are most conducive to their growth from the genetic perspective.
PMID: 37089657
Plant Sci , IF:4.729 , 2023 Jun , V331 : P111689 doi: 10.1016/j.plantsci.2023.111689
Integrated analysis of smRNAome, transcriptome, and degradome data to decipher microRNAs regulating costunolide biosynthesis in Saussurea lappa.
Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India. Electronic address: ravk14@gmail.com.; Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India.
Saussurea lappa (S. lappa) has been known to synthesize medicinally important, costunolide. Due to its immense therapeutic importance, understanding of regulatory mechanism associated with its biosynthesis is crucial. The identification of genes and transcription factors (TFs) in S. lappa, created a clear picture of costunolide biosynthesis pathways. Further to understand the regulation of costunolide biosynthesis by miRNAs, an integrated study of transcriptome, miRNAs, and degradome was performed. Identified candidate miRNAs and associated feed-forward loops (FFLs) illustrates their regulatory role in secondary metabolite biosynthesis. Small RNA and degradome sequencing were performed for leaf and root tissues to determine miRNAs-targets pairs. A total of 711 and 525 such targets were obtained for novel and known miRNAs respectively. This data was used to generate costunolide-specific miRNA-TF-gene interactome to perform systematic analyses through graph theoretical approach. Interestingly, miR171c.1 and sla-miR121 were identified as key regulators to connect and co-regulate both mevalonate and sesquiterpenoid pathways to bio-synthesize costunolide. Tissue-specific FFLs were identified to be involved in costunolide biosynthesis which further suggests the evolutionary co-relation of root-specific networks in synthesis of secondary metabolites in addition to leaf-specific networks. This integrative approach allowed us to determine candidate miRNAs and associated tissue-specific motifs involved in the diversification of secondary metabolites. MiRNAs identified in present study can provide alternatives for bioengineering tool to enhance the synthesis of costunolide and other secondary metabolites in S. lappa.
PMID: 36965630
Plant Physiol Biochem , IF:4.27 , 2023 Apr , V197 : P107642 doi: 10.1016/j.plaphy.2023.107642
Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice.
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, 210095, China.; State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. Electronic address: zenghq@hznu.edu.cn.
Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.
PMID: 36989993
Planta , IF:4.116 , 2023 May , V257 (6) : P110 doi: 10.1007/s00425-023-04149-5
Dunaliella Ds-26-16 acts as a global regulator to enhance salt tolerance by coordinating multiple responses in Arabidopsis seedlings.
Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.; Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China. xiwenchen@nankai.edu.cn.; Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China. chendefu@nankai.edu.cn.
Based on phenotypic, physiological and proteomic analysis, the possible mechanism by which Ds-26-16 regulates salt tolerance in Arabidopsis seedlings was revealed. Functional and mechanistic characterization of salt tolerance genes isolated from natural resources is crucial for their application. In this study, we report the possible mechanism by which Ds-26-16, a gene from Dunaliella, and its point mutation gene EP-5, enhance salt tolerance in Arabidopsis seedlings. Both Ds-26-16 and EP-5 transgenic lines displayed higher seed germination rates, cotyledon-greening rates, soluble sugar contents, decreased relative conductivity and ROS accumulation when germinating under 150 mM NaCl conditions. Comparative proteomic analysis revealed that there were 470 or 391 differentially expressed proteins (DEPs) in Ds-26-16 or EP-5, respectively, compared with the control (3301) under salt stress. The GO and KEGG enrichment analyses showed the DEPs in Ds-26-16 vs. 3301 and EP-5 vs. 3301 were similar and mainly enriched in photosynthesis, regulation of gene expression, carbohydrate metabolism, redox homeostasis, hormonal signal and defense, and regulation of seed germination. Thirty-seven proteins were found to be stably expressed under salt stress due to the expression of Ds-26-16, and eleven of them contain the CCACGT motif which could be bound by the transcription factor in ABA signaling to repress gene transcription. Taken together, we propose that Ds-26-16, as a global regulator, improves salt-tolerance by coordinating stress-induced signal transduction and modulating multiple responses in Arabidopsis seedlings. These results provide valuable information for utilizing natural resources in crop improvement for breeding salt-tolerant crops.
PMID: 37149499
AoB Plants , IF:3.276 , 2023 Jun , V15 (3) : Pplad013 doi: 10.1093/aobpla/plad013
Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions.
Sunflower and Plant Biology Research Unit, USDA-ARS-ETSARC, 1616 Albrecht Blvd., Fargo, ND 58102, USA.; Metabolism and Disease Molecular and Systems Biology, North Carolina State University, 120 Broughton Dr., Raleigh, NC 27607, USA.; Wave Life Sciences, 733 Concord Ave, Cambridge, MA 02138, USA.; Massachusetts Institute of Technology, Merkin Building, 415 Main St., Cambridge, MA 02142, USA.
A new paradigm suggests weeds primarily reduce crop yield by altering crop developmental and physiological processes long before the weeds reduce resources through competition. Multiple studies have implicated stress response pathways are activated when crops such as maize are grown in close proximity with weeds during the first 4-8 weeks of growth-the point at which weeds have their greatest impact on subsequent crop yields. To date, these studies have mostly focused on the response of above-ground plant parts and have not examined the early signal transduction processes associated with maize root response to weeds. To investigate the impact of signals from a below-ground competitor on the maize root transcriptome when most vulnerable to weed pressure, a system was designed to expose maize to only below-ground signals. Gene set enrichment analyses identified over-represented ontologies associated with oxidative stress signalling throughout the time of weed exposure, with additional ontologies associated with nitrogen use and transport and abscisic acid (ABA) signalling, and defence responses being enriched at later time points. Enrichment of promoter motifs indicated over-representation of sequences known to bind FAR-RED IMPAIRED RESPONSE 1 (FAR1), several AP2/ERF transcription factors and others. Likewise, co-expression networks were identified using Weighted-Gene Correlation Network Analysis (WGCNA) and Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) algorithms. WGCNA highlighted the potential roles of several transcription factors including a MYB 3r-4, TB1, WRKY65, CONSTANS-like5, ABF3, HOMEOBOX 12, among others. These studies also highlighted the role of several specific proteins involved in ABA signalling as being important for the initiation of the early response of maize to weeds. SC-ION highlighted potential roles for NAC28, LOB37, NAC58 and GATA2 transcription factors, among many others.
PMID: 37228420
BMC Bioinformatics , IF:3.169 , 2023 Apr , V24 (1) : P163 doi: 10.1186/s12859-023-05253-9
A gene regulatory network inference model based on pseudo-siamese network.
School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China.; School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China. guomaozu@bucea.edu.cn.; College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
MOTIVATION: Gene regulatory networks (GRNs) arise from the intricate interactions between transcription factors (TFs) and their target genes during the growth and development of organisms. The inference of GRNs can unveil the underlying gene interactions in living systems and facilitate the investigation of the relationship between gene expression patterns and phenotypic traits. Although several machine-learning models have been proposed for inferring GRNs from single-cell RNA sequencing (scRNA-seq) data, some of these models, such as Boolean and tree-based networks, suffer from sensitivity to noise and may encounter difficulties in handling the high noise and dimensionality of actual scRNA-seq data, as well as the sparse nature of gene regulation relationships. Thus, inferring large-scale information from GRNs remains a formidable challenge. RESULTS: This study proposes a multilevel, multi-structure framework called a pseudo-Siamese GRN (PSGRN) for inferring large-scale GRNs from time-series expression datasets. Based on the pseudo-Siamese network, we applied a gated recurrent unit to capture the time features of each TF and target matrix and learn the spatial features of the matrices after merging by applying the DenseNet framework. Finally, we applied a sigmoid function to evaluate interactions. We constructed two maize sub-datasets, including gene expression levels and GRNs, using existing open-source maize multi-omics data and compared them to other GRN inference methods, including GENIE3, GRNBoost2, nonlinear ordinary differential equations, CNNC, and DGRNS. Our results show that PSGRN outperforms state-of-the-art methods. This study proposed a new framework: a PSGRN that allows GRNs to be inferred from scRNA-seq data, elucidating the temporal and spatial features of TFs and their target genes. The results show the model's robustness and generalization, laying a theoretical foundation for maize genotype-phenotype associations with implications for breeding work.
PMID: 37085776
J Mol Evol , IF:2.395 , 2023 May doi: 10.1007/s00239-023-10109-0
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.
Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, P.O. Box 74135-111, Jahrom, Islamic Republic of Iran. bheghrari@yahoo.com.; Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran.
HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.
PMID: 37191719
Biosystems , IF:1.973 , 2023 Apr , V226 : P104872 doi: 10.1016/j.biosystems.2023.104872
Formal autopoiesis: Solutions of the classical and extended functional closure equations.
Departments of Mathematics and Computer Science, University of Dallas, United States of America. Electronic address: echastain@udallas.edu.
Formalization of autopoiesis is an ongoing effort among theoretical biologists. In this field, Letelier and co-authors proposed that Robert Rosen's (M,R)-systems theory be used as a formalism for autopoiesis. In (M,R)-systems theory, Rosen proposes that one solve a set of functional closure equations (FCEs) which account for all of the components of the system as coming from within the system itself. A key part of the functional closure equations is the repair of the metabolism component of the system. Rosen's theory gives the organizational closure of the components as well as their products, as found in autopoiesis. However, according to Razeto-Barry (M,R)-systems leaves out some of the messiness and approximation that we find in autopoiesis as he reformulates it. A related problem is that though FCEs have a long history, they are difficult in practice to solve due to their mathematical formulation. In this paper we give a novel exact solution for the FCEs for continuous real vector-valued functions which is nevertheless difficult to compute. In addition we propose an extended form of FCEs which both captures more of the messiness of autopoiesis and also helps to make the FCEs more solvable. Finally, we use our solution for the extended FCEs to give an extended repair function for a metabolism taken from a representative class of biological dynamics for gene expression (the repressilator). More generally we show that one can use our solution for the extended FCEs to get an extended repair function for continuous real vector-valued functions.
PMID: 36921792
J Genet Eng Biotechnol , 2023 May , V21 (1) : P69 doi: 10.1186/s43141-023-00515-8
Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa).
Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka.; Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka. weeraman97@gmail.com.
BACKGROUND: The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance. RESULTS: Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs. CONCLUSIONS: These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.
PMID: 37246172
J Biomol Struct Dyn , 2023 May : P1-14 doi: 10.1080/07391102.2023.2213341
Computational investigation of phytochemicals identified from medicinal plant extracts against tuberculosis.
Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.; Sygnature Discovery, Nottingham, United Kingdom.
Tuberculosis (TB) is still one of the world's most challenging infectious diseases and the emergence of drug-resistant Mycobacterium tuberculosis poses a significant threat to the treatment of TB. Identifying new medications based on local traditional remedies has become more essential. Gas Chromatography-Mass spectrometry (GC-MS) (Perkin-Elmer, MA, USA) was used to identify potential bioactive components in Solanum surattense, Piper longum, and Alpinia galanga plants sections. The fruits and rhizomes' chemical compositions were analyzed using solvents like petroleum ether, chloroform, ethyl acetate, and methanol. A total of 138 phytochemicals were identified, further categorized and finalized with 109 chemicals. The phytochemicals were docked with selected proteins (ethA, gyrB, and rpoB) using AutoDock Vina. The top complexes were selected and preceded with molecular dynamics simulation. It was found that the rpoB-sclareol complex is very stable, which means it could be further explored. The compounds were further studied for ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties. Sclareol has obeyed all the rules and it might be a potential chemical to treat TB.Communicated by Ramaswamy H. Sarma.
PMID: 37211911