New Phytol , IF:10.151 , 2024 Sep , V243 (5) : P1855-1869 doi: 10.1111/nph.19949
The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm.
State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
Grain filling in maize (Zea mays) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol, and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
PMID: 38962989
Bioresour Technol , IF:9.642 , 2024 Sep , V413 : P131484 doi: 10.1016/j.biortech.2024.131484
Microbial community dynamics in different floc size aggregates during nitrogen removal process upgrading in a full-scale landfill leachate treatment plant.
School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China. Electronic address: shengbb@gdpu.edu.cn.; School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou 510006, PR China. Electronic address: rxzhang@gdpu.edu.cn.
Upgrading processes to reduce biodegradable organic substance addition is crucial for treating landfill leachate with high pollutant concentrations, aiding carbon emission reduction. Aggregate size in activated sludge processes impacts pollutant removal and sludge/water separation. This study investigated microbial community succession and driving mechanisms in different floc-size aggregates during nitrogen removal progress upgrade from conventional to partial nitrification-denitrification in a full-scale landfill leachate treatment plant (LLTP) using 16S rRNA gene sequencing. The upgrade and floc sizes significantly influenced microbial diversity and composition. After upgrading, ammonia-oxidizing bacteria were enriched while nitrite-oxidizing bacteria suppressed in small flocs with homogeneity and high mass transfer efficiency. Larger flocs enriched Defluviicoccus, Thauera, and Truepera, while smaller flocs enriched Nitrosomonas, suggesting their potential as biomarkers. Multi-network analyses revealed microbial interactions. A deep learning model with convolutional neural networks predicted nitrogen removal efficiency. These findings guide optimizing LLTP processes and understanding microbial community dynamics based on floc size.
PMID: 39277056
Food Chem , IF:7.514 , 2024 Dec , V460 (Pt 3) : P140771 doi: 10.1016/j.foodchem.2024.140771
Transcriptome and metabolome analyses provide insights into the fruit softening disorder of papaya fruit under postharvest heat stress.
Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.; Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China. Electronic address: xiaoyang_zhu@scau.edu.cn.
Heat stress in summer causes softening disorder in papaya but the molecular mechanism is not clear. In this study, papaya fruit stored at 35 degrees C showed a softening disorder termed rubbery texture. Analysis of the transcriptome and metabolome identified numerous differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) between the fruit stored at 25 degrees C and 35 degrees C. The DEGs and DAMs related to lignin biosynthesis were upregulated, while those related to ethylene biosynthesis, sucrose metabolism, and cell wall degradation were downregulated under heat stress. Co-expression network analysis highlighted the correlation between the DEGs and metabolites associated with lignin biosynthesis, ethylene biosynthesis, and cell wall degradation under heat stress. Finally, the correlation analysis identified the key factors regulating softening disorder under heat stress. The study's findings reveal that heat stress inhibited papaya cell wall degradation and ethylene production, delaying fruit ripening and softening and ultimately resulting in a rubbery texture.
PMID: 39128369
Plant Cell Environ , IF:7.228 , 2024 Sep , V47 (9) : P3654-3667 doi: 10.1111/pce.14950
Regulatory networks of senescence-associated gene-transcription factors promote degradation in Moso bamboo shoots.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.; College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China.; International Center for Bamboo and Rattan, Beijing, China.; Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Bamboo cultivation, particularly Moso bamboo (Phyllostachys edulis), holds significant economic importance in various regions worldwide. Bamboo shoot degradation (BSD) severely affects productivity and economic viability. However, despite its agricultural consequences, the molecular mechanisms underlying BSD remain unclear. Consequently, we explored the dynamic changes of BSD through anatomy, physiology and the transcriptome. Our findings reveal ruptured protoxylem cells, reduced cell wall thickness and the accumulation of sucrose and reactive oxygen species (ROS) during BSD. Transcriptomic analysis underscored the importance of genes related to plant hormone signal transduction, sugar metabolism and ROS homoeostasis in this process. Furthermore, BSD appears to be driven by the coexpression regulatory network of senescence-associated gene transcription factors (SAG-TFs), specifically PeSAG39, PeWRKY22 and PeWRKY75, primarily located in the protoxylem of vascular bundles. Yeast one-hybrid and dual-luciferase assays demonstrated that PeWRKY22 and PeWRKY75 activate PeSAG39 expression by binding to its promoter. This study advanced our understanding of the molecular regulatory mechanisms governing BSD, offering a valuable reference for enhancing Moso bamboo forest productivity.
PMID: 38752443
Chemosphere , IF:7.086 , 2024 Sep , V364 : P143013 doi: 10.1016/j.chemosphere.2024.143013
Reutilization of post-adsorption lanthanum-loaded straw alleviates phosphorus pollution in rice-wheat system: Subsequent performance and underlying mechanisms.
Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China. Electronic address: yangbeimail@126.com.; Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.; Centro de Biotecnologia y Genomica de Plantas (UPM-INIA), Universidad Politecnica de Madrid, Madrid, 28223, Spain. Electronic address: qingnan.chu@upm.es.; Newcastle University, School of Engineering, Newcastle Upon Tyne, NE1 7RU, England, UK.; Nanjing Ningliang Biotechnology Co., Ltd, Nanjing, 211135, China.; Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.; Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. Electronic address: njxuelihong@gmail.com.
Adsorption technology for phosphorus (P) removal is considered promising and reutilization of post-adsorbent can contribute to promoting sustainable agricultural production. However, the long-lasting impact of the post-adsorbent on crop growth and P remains unclear. This study assessed the effects of P-adsorbed lanthanum-modified straw (La@straw-P) on the rice yield, P fractionation and associated water quality parameters. The findings indicated that, compared with traditional fertilizer regimes, La@straw-P expedited the P reduction in the flooding water achieving a rate of decline to the tertiary standard for surface water (0.20 mg/L) 3.8 times faster and enhanced increased the P harvest index by 17.00 %. Economic estimation proved the positive benefits of La@straw-P in planting-breeding combination system. Redundancy analysis (RDA) and co-occurrence network analysis (CONA) revealed that electrical conductivity (EC) and dissolved Fe played primary roles in regulating total P. Fourier transform infrared spectra (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectra (XPS), and soil P fractions collectively demonstrated that the abundant adsorption sites on La@straw-P could facilitate the transformation of active P into moderately Ca-bound P. This study proposes a strategy for recycling P-adsorbed materials to mitigate agricultural non-point P pollution.
PMID: 39111671
J Environ Manage , IF:6.789 , 2024 Sep , V370 : P122428 doi: 10.1016/j.jenvman.2024.122428
Opposite effects of soil pH on bacteria and fungi beta diversity in forests at a continental scale.
Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China.; Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai, 200030, China.; Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China.; Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China.; Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS), CSIC, Sevilla, Spain.; Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China; Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China. Electronic address: xhzhou@des.ecnu.edu.cn.
Soil microbial diversity is crucial for regulating biogeochemical cycles, including soil carbon (C) dynamics and nutrient cycling. However, how climate, plants, and soil properties influence the microbiome in forests remains unclear, especially at the continental scale, hindering us to better understand forest C-climate change feedback. Here, we investigated the spatial patterns of microbial diversity across China's forests and explored the controlling factors of microbial beta diversity and network complexity. Our results showed that soil pH strongly influenced bacterial and fungal beta diversity compared to climate, soil nutrient and plant properties. To further investigate the environmental preference of the microbial networks, we classified the amplicon sequence variants (ASVs) into five groups ranging from acidic to alkaline soils. Co-occurrence network analysis revealed that the topological structure of the bacterial network (e.g., edge and degree) increased with pH and was negatively correlated with beta diversity but not for fungal diversity. Soil fungi exhibited higher beta diversity and network complexity (i.e., degree and betweenness) than bacteria in acidic soils (pH < 5.1), and vice versa in neutral and alkaline soils (pH > 5.5). Within the pH range of 5.1-5.5, the bacterial-fungal network displayed the highest network complexity with the lowest fungal beta diversity, and significant positive correlations were found between fungal beta diversity and soil properties. In addition, bacterial growth in acidic soil (pH < 5.5) showed positive correlations with acid phosphatase (AP), but negative ones with beta-1,4-glucosidase (BG), and vice versa in neutral and alkaline soils (pH > 5.5). Furthermore, 46 bacterial core species were identified, and their abundance had significant correlation with soil pH. These findings highlight the critical role of soil pH in driving soil microbial beta diversity across China's forests and reveal the effects of pH thresholds on changes in the soil microbial network and core species.
PMID: 39260281
Int J Mol Sci , IF:5.923 , 2024 Sep , V25 (17) doi: 10.3390/ijms25179658
Exploring the Rhizospheric Microbial Communities under Long-Term Precipitation Regime in Norway Spruce Seed Orchard.
Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycka 129, Suchdol, 165 21 Prague, Czech Republic.; Faculty of Science, Charles University in Prague, BIOCEV, Prumyslova 595, Vestec, 252 42 Prague, Czech Republic.; Molecular Plant and Microbiology Laboratory (MPML), Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, India.
The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipova Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations.
PMID: 39273604
Gene , IF:3.688 , 2024 Dec , V931 : P148899 doi: 10.1016/j.gene.2024.148899
Multiple functions and regulatory networks of WRKY33 and its orthologs.
School of Life Sciences, Nantong University, Nantong, China; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China. Electronic address: chenyh@ntu.edu.cn.; School of Life Sciences, Nantong University, Nantong, China; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China.
Arabidopsis thaliana WRKY33 is currently one of the most studied members of the Group I WRKY transcription factor family. Research has confirmed that WRKY33 is involved in the regulation of various biological and abiotic stresses and occupies a central position in the regulatory network. The functional studies of orthologous genes of WRKY33 from other species are also receiving increasing attention. In this article, we summarized thirty-eight orthologous genes of AtWKRY33 from twenty-five different species. Their phylogenetic relationship and conserved WRKY domain were analyzed and compared. Similar to AtWKRY33, the well-studied orthologous gene members from rice and tomato also have multiple functions. In addition to playing important regulatory roles in responding to their specific pathogens, they are also involved in regulating various abiotic stresses and development. AtWKRY33 exerts its multiple functions through a complex regulatory network. Upstream transcription factors or other regulatory factors activate or inhibit the expression of AtWKRY33 at the chromatin and transcriptional levels. Interacting proteins affect the transcriptional activity of AtWKRY33 through phosphorylation, ubiquitination, SUMOylation, competition, or cooperation. The downstream genes are diverse and include three major categories: transcription factors, synthesis, metabolism, and signal transduction of various hormones, and disease resistance genes. In the regulatory network of AtWRKY33 orthologs, many conserved regulatory characteristics have been discovered, such as self-activation and phosphorylation by MAP kinases. This can provide a comparative reference for further studying the functions of other orthologous genes of AtWKRY33.
PMID: 39209179
BMC Microbiol , IF:3.605 , 2024 Sep , V24 (1) : P322 doi: 10.1186/s12866-024-03468-1
Disruption of bacterial interactions and community assembly in Babesia-infected Haemaphysalis longicornis following antibiotic treatment.
Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia. mariem.kratou@hotmail.com.; UMR BIPAR, Laboratoire de Sante Animale, ANSES, INRAE, Ecole Nationale Veterinaire d'Alfort, Maisons-Alfort, 94700, France.; INRAE, UR 0045 Laboratoire de Recherches Sur Le Developpement de L'Elevage (SELMET LRDE), Corte, France.; EA 7310, Laboratoire de Virologie, Universite de Corse, Corte, France.; Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Avenue 31 Between 158 and 190, Havana, 10600, Cuba.; Direction of Animal Health, National Center for Animal and Plant Health, Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San Jose de Las Lajas, Mayabeque, 32700, Cuba.; Immunology and Vaccines Laboratory, C. A. Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Queretaro, Mexico.; C.A. Salud Animal y Microbiologia Ambiental. Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Queretaro, Mexico.; Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Cordel de Merinas, 40-52, Salamanca, 37008, Spain.; Department of Biological Sciences, Microbiology Unit, Kings University, Odeomu, Osun State, Nigeria.; National Agency for Food and Drug Control and Administration (NAFDAC), Isolo, Lagos State, Nigeria.; School of Environmental Sciences, University of Guelph, Guelph, ON, Canada.; Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia.; Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia.; UMR BIPAR, Laboratoire de Sante Animale, ANSES, INRAE, Ecole Nationale Veterinaire d'Alfort, Maisons-Alfort, 94700, France. alejandro.cabezas@vet-alfort.fr.
BACKGROUND: A previous study highlighted the role of antibiotic-induced dysbiosis in the tick microbiota, facilitating the transstadial transmission of Babesia microti from nymph to adult in Haemaphysalis longicornis. This study builds on previous findings by analyzing sequence data from an earlier study to investigate bacterial interactions that could be linked to enhanced transstadial transmission of Babesia in ticks. The study employed antibiotic-treated (AT) and control-treated (CT) Haemaphysalis longicornis ticks to investigate shifts in microbial community assembly. Network analysis techniques were utilized to assess bacterial interactions, comparing network centrality measures between AT and CT groups, alongside studying network robustness and connectivity loss. Additionally, functional profiling was conducted to evaluate metabolic diversity in response to antibiotic treatment. RESULTS: The analysis revealed notable changes in microbial community assembly in response to antibiotic treatment. Antibiotic-treated (AT) ticks displayed a greater number of connected nodes but fewer correlations compared to control-treated (CT) ticks, indicating a less interactive yet more connected microbial community. Network centrality measures such as degree, betweenness, closeness, and eigenvector centrality, differed significantly between AT and CT groups, suggesting alterations in local network dynamics due to antibiotic intervention. Coxiella and Acinetobacter exhibited disrupted connectivity and roles, with the former showing reduced interactions in AT group and the latter displaying a loss of connected nodes, emphasizing their crucial roles in microbial network stability. Robustness tests against node removal showed decreased stability in AT networks, particularly under directed attacks, confirming a susceptibility of the microbial community to disturbances. Functional profile analysis further indicated a higher diversity and richness in metabolic capabilities in the AT group, reflecting potential shifts in microbial metabolism as a consequence of antimicrobial treatment. CONCLUSIONS: Our findings support that bacterial interaction traits boosting the transstadial transmission of Babesia could be associated with reduced colonization resistance. The disrupted microbial interactions and decreased network robustness in AT ticks suggest critical vulnerabilities that could be targeted for managing tick-borne diseases.
PMID: 39237861
Photosynth Res , IF:3.573 , 2024 Sep , V161 (3) : P213-232 doi: 10.1007/s11120-024-01103-8
Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium.
Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.; Competence Network IBD, Hopfenstrasse 60, 24103, Kiel, Germany.; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.; Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA. sabeeha@berkeley.edu.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA. sabeeha@berkeley.edu.; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA. sabeeha@berkeley.edu.; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. sabeeha@berkeley.edu.; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. sabeeha@berkeley.edu.
Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
PMID: 39017982
Animal , IF:3.24 , 2024 Sep , V18 (9) : P101259 doi: 10.1016/j.animal.2024.101259
Gene co-expression network analysis for porcine intramuscular fatty acid composition.
Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciencia Animal i dels Aliments, Facultat de Veterinaria, Universitat Autonoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain. Electronic address: cristina.sebastia@cragenomica.es.; Institute for Integrative Biology of the Cell (I2BC), Universite Paris-Saclay, CEA, CNRS, 1, Avenue de la Terrasse, Batiment 21, 91190 Gif-sur-Yvette, France.; Departament de Genetica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain.; Universite Paris-Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy-en-Josas, France.; Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, C. de la Vall Moronta, 08193 Bellaterra, Spain; Departament de Ciencia Animal i dels Aliments, Facultat de Veterinaria, Universitat Autonoma de Barcelona (UAB), Edifici V, Travessera dels Turons, 08193 Bellaterra, Spain.; Departament de Genetica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain; R&D Department, Cuarte S.L., Grupo Jorge, Autov. Zaragoza-Logrono, km.9, 50120 Monzalbarba, Spain.
In pigs, meat quality depends markedly on the fatty acid (FA) content and composition of the intramuscular fat, which is partly determined by the gene expression in this tissue. The aim of this work was to identify the link between muscle gene expression and its FA composition. In an (Iberian x Duroc) x Duroc backcrossed pig population, we identified modules of co-expressed genes, and correlation analyses were performed for each of them versus the phenotypes, finding four relevant modules. Two of the modules were positively correlated with saturated FAs (SFAs) and monounsaturated FAs (MUFAs), while negatively correlated with polyunsaturated FAs (PUFAs) and the omega-6/omega-3 ratio. The gene-enrichment analysis showed that these modules had over-representation of pathways related with the biosynthesis of unsaturated FAs, the Peroxisome proliferator-activated receptor signalling pathway and FA elongation. The two other relevant modules were positively correlated with PUFA and the n-6/n-3 ratio, but negatively correlated with SFA and MUFA. In this case, they had an over-representation of pathways related with fatty and amino acid degradation, and with oxidative phosphorylation. Using a graphical Gaussian model, we inferred a network of connections between the genes within each module. The first module had 52 genes with 87 connections, and the most connected genes were ADIPOQ, which is related with FA oxidation, and ELOVL6 and FABP4, both involved in FA metabolism. The second module showed 196 genes connected by 263 edges, being FN1 and MAP3K11 the most connected genes. On the other hand, the third module had 161 genes connected by 251 edges and ATG13 was the top neighbouring gene, while the fourth module had 224 genes and 655 connections, and its most connected genes were related with mitochondrial pathways. Overall, this work successfully identified relevant muscle gene networks and modules linked with FA composition, providing further insights on how the physiology of the pigs influences FA composition.
PMID: 39137614
STAR Protoc , 2024 Sep , V5 (3) : P103211 doi: 10.1016/j.xpro.2024.103211
Protocol for collecting xylem sap from drought-treated tomato plants using a pressure chamber.
Food Science Department, Aarhus University, 8200 Aarhus N, Denmark.; Food Science Department, Aarhus University, 8200 Aarhus N, Denmark. Electronic address: apetridis@food.au.dk.
When plants are subjected to drought, it is impossible to obtain xylem sap for subsequent biochemical and molecular analysis using root pressure exudate, the conventional approach. Here, we present a protocol for collecting xylem sap from drought-treated tomato plants using a pressure chamber. We describe steps for how to prepare plants, apply drought, and use the pressure chamber to collect the xylem sap. Using this technique, one can obtain 500-700 muL of xylem sap in just 5-7 min. For complete details on the use and execution of this protocol, please refer to Alexou and Peuke.(1).
PMID: 39068658
Plant Commun , 2024 Sep : P101130 doi: 10.1016/j.xplc.2024.101130
Regulatory Networks of Coresident Subgenomes during Rapid Fiber Cell Elongation in Upland Cotton.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang, 455000, China.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450000, Zhengzhou, China.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang, 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450000, Zhengzhou, China.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang, 455000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450000, Zhengzhou, China. Electronic address: yangzhaoen0925@126.com.
Cotton, an intriguing plant species shaped by polyploidization, evolution, and domestication, holds particular interest due to the complex mechanisms governing fiber traits across its two subgenomes. However, the regulatory elements or transcriptional networks between subgenomes during fiber elongation remain elusive. Here, we analyzed 1,462 cotton fiber samples to reconstruct gene expression regulatory networks influencing fiber cell elongation. Inter-subgenomic eQTLs largely dictate gene transcription, with a notable tendency for the D subgenome to regulate A subgenome eGenes. This regulation showcases synchronized homoeologous gene expression driven by colocalized eQTLs and divergent patterns that diminish genetic correlations, thus leading to preferential expression in the A and D subgenomes. Hotspot456 emerged as a key regulator of fiber initiation and elongation, and artificial selection of trans-eQTLs in hotspot456 positively regulating KCS1 has facilitated cell elongation. To elucidate the roles of trans-eQTL in improved fiber breeding, experimentation confirmed the inhibition of GhTOL9 by a specific trans-eQTL via GhWRKY28, which negatively impacts fiber elongation. We propose a model where the GhWRKY28-GhTOL9 module, through the Endosomal Sorting Complex Required for Transport pathway, regulates this process. This research significantly advances our understanding of cotton's evolutionary, domestication processes, and the intricate regulatory mechanisms underlying significant plant traits.
PMID: 39257006