Single cell‐type transcriptome profiling reveals genes that promote nitrogen fixation in the infected and uninfected cells of legume nodules

Wang, Longlong; Yu, Zhe; Li, Runhui; Liang, Jiahui; Tian, Tao; Ji, Jie; Chen, Runzhou; Zhou, Yumiao; Fan, Qiuling; Ning, Guogui; Larkin, Robert M.; Becana, Manuel; Duanmu, Deqiang

doi:10.1111/pbi.13778

Cited by 21 publications

(13 citation statements)

References 9 publications

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“…There are four clusters 0, 7, 11 and 12 co-localized in CIZ of nodule (Fig.1d). By examining the expression of orthologs which are up-regulated in Lotus japonocus uninfected cells (UCs) and infected cells (ICs) 5 , we identified cluster 0, 7, 11 as UC and further confirmed cluster 12 as ICs (Fig.2a, Supplementary Fig.7, Supplementary Data 4). In UCs, cluster 0 is shared by nodules at two different developmental stages, while two clusters (7, 11) are almost only found in 21-dpi nodule cells (Fig.2b).…”

Section: Mainmentioning

confidence: 67%

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Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment

Liu

Kong

Long

et al. 2022

Preprint

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Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zone of nodule, we found that uninfected cells specialize into functionally distinct sub-groups during nodule development and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.

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Section: Mainmentioning

confidence: 67%

“…1d). By examining the expression of orthologs which are up-regulated in Lotus japonocus uninfected cells (UCs) and infected cells (ICs) 5 , we identified cluster 0, 7, 11 as UC and further confirmed cluster 12 as ICs (Fig. 2a, Supplementary Fig.…”

Section: Mainmentioning

confidence: 69%

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment

Liu

Kong

Long

et al. 2022

Preprint

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“…Reactive oxygen species (ROS) metabolism in legume nodules. The scheme is based on biochemical studies and on transcriptomic and proteomic data of Lotus japonicus ( https://lotus.au.dk; Wang et al ., 2019, 2022) and Medicago truncatula ( https://medicago.toulouse.inrae.fr/MtExpress; Wienkoop et al ., 2012). Among other ROS metabolic pathways in the bacteroids, the figure shows the generation of ROS through the irreversible oxidation by O 2 of the Fe–S clusters of the nitrogenase enzyme complex.…”

Section: Reactive Oxygen Species In Nodule Host Cellsmentioning

confidence: 99%

“…Reactive nitrogen species (RNS) metabolism in legume nodules. The scheme is based on biochemical studies and on transcriptomic and proteomic data of Lotus japonicus ( https://lotus.au.dk; Wang et al ., 2019, 2022) and Medicago truncatula ( https://medicago.toulouse.inrae.fr/MtExpress; Wienkoop et al ., 2012). Dashed lines indicate reactions that have been demonstrated only in vitro or that have been shown to occur in leaves.…”

Section: Reactive Nitrogen Species In Nodule Host Cellsmentioning

confidence: 99%

Signaling by reactive molecules and antioxidants in legume nodules

et al. 2022

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Legume nodules are symbiotic structures formed as a result of the interaction with rhizobia. Nodules fix atmospheric nitrogen into ammonia that is assimilated by the plant and this process requires strict metabolic regulation and signaling. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are involved as signal molecules at all stages of symbiosis, from rhizobial infection to nodule senescence. Also, reactive sulfur species (RSS) are emerging as important signals for an efficient symbiosis. Homeostasis of reactive molecules is mainly accomplished by antioxidant enzymes and metabolites and is essential to allow redox signaling while preventing oxidative damage. Here, we examine the metabolic pathways of reactive molecules and antioxidants with an emphasis on their functions in signaling and protection of symbiosis. In addition to providing an update of recent findings while paying tribute to original studies, we identify several key questions. These include the need of new methodologies to detect and quantify ROS, RNS, and RSS, avoiding potential artifacts due to their short lifetimes and tissue manipulation; the regulation of redox-active proteins by post-translational modification; the production and exchange of reactive molecules in plastids, peroxisomes, nuclei, and bacteroids; and the unknown but expected crosstalk between ROS, RNS, and RSS in nodules.

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“…The single-cell resolution and relatively large cell/nuclei counts afforded by 10x Genomics Chromium technology allowed detection of a pervasive early response to rhizobium infection two days post inoculation (dpi) across root tissues and identification of a large number of infection-responsive genes, including differential responses of known nodulation genes across tissues 41 . In addition, a limited number of cells derived from determinate Lotus nodules were studied using a Smart-Seq2 protocol 42,43 .…”

Section: Introductionmentioning

confidence: 99%

Single-cell analysis maps distinct cellular responses to rhizobia and identifies the novel infection regulator SYMRKL1 inLotus japonicus

Frank

Fechete

Tedeschi

et al. 2022

Preprint

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Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.

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Single cell‐type transcriptome profiling reveals genes that promote nitrogen fixation in the infected and uninfected cells of legume nodules

Cited by 21 publications

References 9 publications

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment

Signaling by reactive molecules and antioxidants in legume nodules

Single-cell analysis maps distinct cellular responses to rhizobia and identifies the novel infection regulator SYMRKL1 inLotus japonicus

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