Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice

Xiong, Qiangqiang; Zhong, Liang; Du, Jie; Zhu, Changlan; Peng, Xiaosong; He, Xu; Fu, Junru; Ouyang, Liang; Bian, Jianmin; Hu, Lifang; Sun, Xiaotang; Xu, Jie; Zhou, Dahu; Cai, Yicong; Fu, Haihui; He, Haohua; Chen, Xiaorong

doi:10.1016/j.plaphy.2020.07.021

Cited by 34 publications

(33 citation statements)

References 74 publications

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“…Supplementary Figure 2G demonstrates the RPFs length distribution peaked at 31 nt in both M and B groups, which was similar to that reported by other species (21)(22)(23)(24). The pattern of RPF distribution ratios was similar for the M and B groups (Supplementary Figure 2H).…”

Section: Overview Of Trancriptome and Translatomesupporting

confidence: 85%

“…A novel method, ribosome footprints (RFPs) sequencing (Ribo-seq) has recently been proposed, providing a genome-wide view of the translational process by deep sequencing of ribosome-protected fragments (RPFs) ( 18 ). Ribo-seq enables gene identification and quantification at the genomic translational level, which has been widely used in different species including human ( 19 ), mouse ( 20 ), zebrafish ( 21 ), drosophila ( 22 ), rice ( 23 ), and maize ( 24 ). Ribosome profiling data are characterized by 28–32 nt RFP length, RFP distribution, and translation efficiency (TE) ( 25 ), providing valuable information for exploration of biological questions.…”

Section: Introductionmentioning

confidence: 99%

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Integrated Transcriptomic and Translatomic Inquiry of the Role of Betaine on Lipid Metabolic Dysregulation Induced by a High-Fat Diet

et al. 2021

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An excessive high-fat/energy diet is a major cause of obesity and linked complications, such as non-alcoholic fatty liver disease (NAFLD). Betaine has been shown to effectively improve hepatic lipid metabolism. However, the mechanistic basis for this improvement is largely unknown. Herein, integration of mRNA sequencing and ribosome footprints profiling (Ribo-seq) was used to investigate the means by which betaine alleviates liver lipid metabolic disorders induced by a high-fat diet. For the transcriptome, gene set enrichment analysis demonstrated betaine to reduce liver steatosis by up-regulation of fatty acid beta oxidation, lipid oxidation, and fatty acid catabolic processes. For the translatome, 574 differentially expressed genes were identified, 17 of which were associated with the NAFLD pathway. By combined analysis of transcriptome and translatome, we found that betaine had the greater effect on NAFLD at the translational level. Further, betaine decreased translational efficiency (TE) for IDI1, CYP51A1, TM7SF2, and APOA4, which are related to lipid biosynthesis. In summary, this study demonstrated betaine alleviating lipid metabolic dysfunction at the translational level. The transcriptome and translatome data integration approach used herein provides for a new understanding of the means by which to treat NAFLD.

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Section: Overview Of Trancriptome and Translatomesupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Integrated Transcriptomic and Translatomic Inquiry of the Role of Betaine on Lipid Metabolic Dysregulation Induced by a High-Fat Diet

et al. 2021

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“…The extraction of total RNA was achieved with the TRIzol Kit (Invitrogen, USA). RNA quality was evaluated using the Bioanalyzer 2100 (Agilent Technologies, USA) and agarose gel electrophoresis (RNase-free) [ 61 ]. The high-quality RNA samples were used to constructed cDNA libraries for transcriptome sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…The high-quality RNA samples were used to constructed cDNA libraries for transcriptome sequencing. The workflow of cDNA library construction was performed as descripted previously [ 61 , 62 ]. After that, the cDNA library was sequenced using Hiseq 2500 sequencer (Illumina, USA) to generate 150 bp paired-end reads.…”

Section: Methodsmentioning

confidence: 99%

Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism

Zhao

Cheng

et al. 2020

BMC Genomics

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Background Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies. Results Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine. Conclusion Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis.

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“…In addition, the PSM mediated P cycling has been revealed under individual drought events ( Preece et al, 2020 ; Püschel et al, 2021 ), individual flood events ( Bai et al, 2019 ; Bao et al, 2019 ), or the drying-rewetting process ( Brödlin et al, 2019 ; Gao et al, 2020 ), while few on DFAA. What’s more, many studies have addressed the negative impacts of DFAA on agricultural production ( Huang et al, 2019 ; Xiong et al, 2020 ). Therefore, it is necessary to reveal the responses of PSM mediated P cycling to DFAA in agroecosystems, especially in topsoil layers.…”

Section: Introductionmentioning

confidence: 99%

Responses of Phosphate-Solubilizing Microorganisms Mediated Phosphorus Cycling to Drought-Flood Abrupt Alternation in Summer Maize Field Soil

Weng

Yan

et al. 2022

Front. Microbiol.

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Soil microbial communities are essential to phosphorus (P) cycling, especially in the process of insoluble phosphorus solubilization for plant P uptake. Phosphate-solubilizing microorganisms (PSM) are the dominant driving forces. The PSM mediated soil P cycling is easily affected by water condition changes due to extreme hydrological events. Previous studies basically focused on the effects of droughts, floods, or drying-rewetting on P cycling, while few focused on drought-flood abrupt alternation (DFAA), especially through microbial activities. This study explored the DFAA effects on P cycling mediated by PSM and P metabolism-related genes in summer maize field soil. Field control experiments were conducted to simulate two levels of DFAA (light drought-moderate flood, moderate drought-moderate flood) during two summer maize growing periods (seeding-jointing stage, tasseling-grain filling stage). Results showed that the relative abundance of phosphate-solubilizing bacteria (PSB) and phosphate-solubilizing fungi (PSF) increased after DFAA compared to the control system (CS), and PSF has lower resistance but higher resilience to DFAA than PSB. Significant differences can be found on the genera Pseudomonas, Arthrobacter, and Penicillium, and the P metabolism-related gene K21195 under DFAA. The DFAA also led to unstable and dispersed structure of the farmland ecosystem network related to P cycling, with persistent influences until the mature stage of summer maize. This study provides references for understanding the micro process on P cycling under DFAA in topsoil, which could further guide the DFAA regulations.

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Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice

Cited by 34 publications

References 74 publications

Integrated Transcriptomic and Translatomic Inquiry of the Role of Betaine on Lipid Metabolic Dysregulation Induced by a High-Fat Diet

Integrated Transcriptomic and Translatomic Inquiry of the Role of Betaine on Lipid Metabolic Dysregulation Induced by a High-Fat Diet

Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism

Responses of Phosphate-Solubilizing Microorganisms Mediated Phosphorus Cycling to Drought-Flood Abrupt Alternation in Summer Maize Field Soil

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