Regulatory mechanisms of the LBD40 transcription factor in Arabidopsis thaliana somatic embryogenesis

IF 2.3 3区 生物学 Q2 PLANT SCIENCES Plant Direct Pub Date : 2023-12-06 DOI:10.1002/pld3.547
Sanjay Joshi, Kristine Hill, Manohar Chakrabarti, Sharyn E. Perry
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Abstract

Somatic embryogenesis (SE) is a process by which an embryo is derived from somatic tissue. Transcription factors (TFs) have been identified that control this process. One such TF that promotes SE is AGAMOUS-like 15 (AGL15). Prior work has shown that AGL15 can both induce and repress gene expression. One way this type of dual function TF works is via protein interactions, so a yeast 2-hybrid (Y2H) screen was undertaken. One intriguing protein with which AGL15 interacted in Y2H was LBD40. LBD40 encodes a LATERAL ORGAN BOUNDARIES (LOB)-domain TF that is unique to plants and is primarily expressed during seed development. Here, we confirm the AGL15-LBD40 interaction by quantitative assays and in planta co-immunoprecipation. We also document a role for LBD40, and the closely related protein LBD41, in supporting SE. To determine downstream genes potentially controlled by LBD40, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) was used. More than 400 binding regions for LBD40 were consistently found genome-wide. To determine genes responsive to LBD40/41 accumulation, RNA-seq analysis of transcriptomes of wild-type control and loss-of-function lbd40/lbd41 was performed. Combining these datasets provides insight into genes directly and indirectly controlled by these LOB domain TFs. The gene ontology (GO) enrichment analysis of these regulated genes showed an overrepresentation of biological processes that are associated with SE, further indicating the importance of LBD40 in SE. This work provides insight into SE, a poorly understood, but essential process to generate transgenic plants to meet agricultural demands or test gene function. This manuscript reports on experiments to understand the role that LDB40, a TF, plays in support of SE by investigating genes directly and indirectly controlled by LBD40 and examining physical and genetic interactions with other TFs active in SE. We uncover targets of LBD40 and an interacting TF of the MADS family and investigate targets involvement in SE.
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拟南芥体细胞胚胎发生中 LBD40 转录因子的调控机制
体细胞胚胎发生(SE)是胚胎从体细胞组织中产生的过程。目前已发现转录因子(TF)可控制这一过程。AGAMOUS-like 15(AGL15)就是促进体细胞胚胎发生的转录因子之一。先前的研究表明,AGL15 既能诱导基因表达,也能抑制基因表达。这种双功能 TF 的一种工作方式是通过蛋白质相互作用,因此我们进行了酵母 2-杂交(Y2H)筛选。在 Y2H 中与 AGL15 发生相互作用的一个有趣的蛋白质是 LBD40。LBD40 编码一种 LATERAL ORGAN BOUNDARIES(LOB)-domain TF,它是植物所特有的,主要在种子发育过程中表达。在这里,我们通过定量测定和植物共沉淀证实了 AGL15-LBD40 的相互作用。我们还记录了 LBD40 和密切相关的蛋白 LBD41 在支持 SE 中的作用。为了确定可能受 LBD40 控制的下游基因,我们使用了染色质免疫共沉淀和高通量测序(ChIP-seq)技术。在全基因组范围内持续发现了 400 多个与 LBD40 结合的区域。为了确定对 LBD40/41 积累有反应的基因,对野生型对照和功能缺失的 lbd40/lbd41 的转录组进行了 RNA-seq 分析。结合这些数据集,可以深入了解受这些 LOB domain TFs 直接和间接控制的基因。对这些受调控基因进行的基因本体(GO)富集分析表明,与 SE 相关的生物过程的代表性过高,这进一步表明了 LBD40 在 SE 中的重要性。这项工作为人们深入了解 SE 提供了机会,SE 虽然鲜为人知,但却是生成转基因植物以满足农业需求或测试基因功能的重要过程。本手稿报告了为了解 LDB40(一种 TF)在支持 SE 方面所起的作用而进行的实验,这些实验调查了直接和间接受 LBD40 控制的基因,并研究了与 SE 中活跃的其他 TF 之间的物理和遗传相互作用。我们发现了 LBD40 和 MADS 家族一个相互作用 TF 的靶标,并研究了参与 SE 的靶标。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Plant Direct
Plant Direct Environmental Science-Ecology
CiteScore
5.00
自引率
3.30%
发文量
101
审稿时长
14 weeks
期刊介绍: Plant Direct is a monthly, sound science journal for the plant sciences that gives prompt and equal consideration to papers reporting work dealing with a variety of subjects. Topics include but are not limited to genetics, biochemistry, development, cell biology, biotic stress, abiotic stress, genomics, phenomics, bioinformatics, physiology, molecular biology, and evolution. A collaborative journal launched by the American Society of Plant Biologists, the Society for Experimental Biology and Wiley, Plant Direct publishes papers submitted directly to the journal as well as those referred from a select group of the societies’ journals.
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