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Khan, Deirdre; Ziegler, Dylan J.; Kalichuk, Jenna L.; Hoi, Vanessa; Huynh, Nina; Hajihassani, Abolfazl; Parkin, Isobel A. P.; Robinson, Stephen J.; Belmonte, Mark F.
doi: 10.1111/tpj.15587pmid: 34786793
We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole‐genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive‐lethal phenotype. Global mRNA profiling revealed lower accumulation of Cn subgenome transcripts relative to the An subgenome. Subgenome‐specific transcription factor networks identified distinct transcription factor families enriched in each of the An and Cn subgenomes early in seed development. Analysis of laser‐microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the An subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cn subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the An and Cn genomes of the whole B. napus seed can identify valuable targets for seed development research and that ‐omics level approaches to studying gene regulation in B. napus can benefit from both broad and high‐resolution analyses.
Pedroza‐Garcia, José Antonio; Xiang, Yanli; De Veylder, Lieven
doi: 10.1111/tpj.15567pmid: 34741364
Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant‐specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant‐specific SOG1 transcription factor, which drives the activity of cyclin‐dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species‐specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.
Custódio, Valéria; Gonin, Mathieu; Stabl, Georg; Bakhoum, Niokhor; Oliveira, Maria Margarida; Gutjahr, Caroline; Castrillo, Gabriel
doi: 10.1111/tpj.15568pmid: 34743401
Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota–plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota‐based strategies to preserve natural resources and develop more environmentally friendly agricultural practices.
Liu, Huawei; Jiang, Li; Wen, Zhifeng; Yang, Yingjun; Singer, Stacy D.; Bennett, Dennis; Xu, Wenying; Su, Zhen; Yu, Zhifang; Cohn, Jonathan; Chae, Hyunsook; Que, Qiudeng; Liu, Yue; Liu, Chang; Liu, Zongrang
doi: 10.1111/tpj.15574pmid: 34773305
Insulators characterized in Drosophila and mammals have been shown to play a key role in the restriction of promiscuous enhancer–promoter interactions, as well as reshaping the topological landscape of chromosomes. Yet the role of insulators in plants remains poorly understood, in large part because of a lack of well‐characterized insulators and binding factor(s). In this study, we isolated a 1.2‐kb RS2‐9 insulator from the Oryza sativa (rice) genome that can, when interposed between an enhancer and promoter, efficiently block the activation function of both constitutive and floral organ‐specific enhancers in transgenic Arabidopsis and Nicotiana tabacum (tobacco). In the rice genome, the genes flanking RS2‐9 exhibit an absence of mutual transcriptional interactions, as well as a lack of histone modification spread. We further determined that O. sativa Homeobox 1 (OSH1) bound two regions of RS2‐9, as well as over 50 000 additional sites in the rice genome, the majority of which resided in intergenic regions. Mutation of one of the two OSH1‐binding sites in RS2‐9 impaired insulation activity by up to 60%, whereas the mutation of both binding sites virtually abolished insulator function. We also demonstrated that OSH1 binding sites were associated with 72% of the boundaries of topologically associated domains (TADs) identified in the rice genome, which is comparable to the 77% of TAD boundaries bound by the insulator CCCTC‐binding factor (CTCF) in mammals. Taken together, our findings indicate that OSH1‐RS2‐9 acts as a true insulator in plants, and highlight a potential role for OSH1 in gene insulation and topological organization in plant genomes.
Lu, Yun; Luo, Yunfeng; Zhou, Jiawei; Hu, Tianyuan; Tu, Lichan; Tong, Yuru; Su, Ping; Liu, Yuan; Wang, Jiadian; Jiang, Zhouqian; Wu, Xiaoyi; Chen, Xiaochao; Huang, Luqi; Gao, Wei
doi:
Pfeifer, Lukas; Utermöhlen, Jon; Happ, Kathrin; Permann, Charlotte; Holzinger, Andreas; Schwartzenberg, Klaus; Classen, Birgit
doi: 10.1111/tpj.15577pmid: 34767672
Charophyte green algae (CGA) are assigned to be the closest relatives of land plants and therefore enlighten processes in the colonization of terrestrial habitats. For the transition from water to land, plants needed significant physiological and structural changes, as well as with regard to cell wall composition. Sequential extraction of cell walls of Nitellopsis obtusa (Charophyceae) and Spirogyra pratensis (Zygnematophyceae) offered a comparative overview on cell wall composition of late branching CGA. Because arabinogalactan‐proteins (AGPs) are considered common for all land plant cell walls, we were interested in whether these special glycoproteins are present in CGA. Therefore, we investigated both species with regard to characteristic features of AGPs. In the cell wall of Nitellopsis, no hydroxyproline was present and no AGP was precipitable with the β‐glucosyl Yariv’s reagent (βGlcY). By contrast, βGlcY precipitation of the water‐soluble cell wall fraction of Spirogyra yielded a glycoprotein fraction rich in hydroxyproline, indicating the presence of AGPs. Putative AGPs in the cell walls of non‐conjugating Spirogyra filaments, especially in the area of transverse walls, were detected by staining with βGlcY. Labelling increased strongly in generative growth stages, especially during zygospore development. Investigations of the fine structure of the glycan part of βGlcY‐precipitated molecules revealed that the galactan backbone resembled that of AGPs with 1,3‐ 1,6‐ and 1,3,6‐linked Galp moieties. Araf was present only in small amounts and the terminating sugars consisted predominantly of pyranosidic terminal and 1,3‐linked rhamnose residues. We introduce the term ‘rhamnogalactan‐protein’ for this special AGP‐modification present in S. pratensis.
Rog, Ido; Chaturvedi, Amit Kumar; Tiwari, Vivekanand; Danon, Avihai
doi: 10.1111/tpj.15579pmid: 34767654
Disulfide‐based regulation links the activity of numerous chloroplast proteins with photosynthesis‐derived redox signals. The plastid terminal oxidase (PTOX) is a thylakoid‐bound plastoquinol oxidase that has been implicated in multiple roles in the light and in the dark, which could require different levels of PTOX activity. Here we show that Arabidopsis PTOX contains a conserved C‐terminus domain (CTD) with cysteines that evolved progressively following the colonization of the land by plants. Furthermore, the CTD contains a regulatory disulfide that is in the oxidized state in the dark and is rapidly reduced, within 5 min, in low light intensity (1–5 µE m−2 sec−1). The reduced PTOX form in the light was reoxidized within 15 min after transition to the dark. Mutation of the cysteines in the CTD prevented the formation of the oxidized form. This resulted in higher levels of reduced plastoquinone when measured at transition to the onset of low light. This is consistent with the reduced state of PTOX exhibiting diminished PTOX oxidase activity under conditions of limiting PQH2 substrate. Our findings suggest that AtPTOX‐CTD evolved to provide light‐dependent regulation of PTOX activity for the adaptation of plants to terrestrial conditions.
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The translocation of photosynthate carbohydrates, such as sucrose, is critical for plant growth and crop yield. Previous studies have revealed that sugar transporters, plasmodesmata and sieve plates act as important controllers in sucrose loading into and unloading from phloem in the vascular system. However, other pivotal steps for the regulation of sucrose movement remain largely elusive. In this study, characterization of two starch excesses in mesophyll (sem) mutants and dye and sucrose export assays were performed to provide insights into the regulatory networks that drive source–sink relations in rice. Map‐based cloning identified two allelic mutations in a gene encoding a GLUCAN SYNTHASE‐LIKE (GSL) protein, thus indicating a role for SEM1 in callose biosynthesis. Subcellular localization in rice showed that SEM1 localized to the plasma membrane. In situ expression analysis and GUS staining showed that SEM1 was mainly expressed in vascular phloem cells. Reduced sucrose transport was found in the sem1‐1/1‐2 mutant, which led to excessive starch accumulation in source leaves and inhibited photosynthesis. Paraffin section and transmission electron microscopy experiments revealed that less‐developed vascular cells (VCs) in sem1‐1/1‐2 potentially disturbed sugar movement. Moreover, dye and sugar trafficking experiments revealed that aberrant VC development was the main reason for the pleiotropic phenotype of sem1‐1/1‐2. In total, efficient sucrose loading into the phloem benefits from an optional number of VCs with a large vacuole that could act as a buffer holding tank for sucrose passing from the vascular bundle sheath.
Triterpenes are among the most diverse plant natural products, and their diversity is closely related to various triterpene skeletons catalyzed by different 2,3‐oxidosqualene cyclases (OSCs). Celastrol, a friedelane‐type triterpene with significant bioactivities, is specifically distributed in higher plants, such as Celastraceae species. Friedelin is an important precursor for the biosynthesis of celastrol, and it is synthesized through the cyclization of 2,3‐oxidosqualene, with the highest number of rearrangements being catalyzed by friedelane‐type triterpene cyclases. However, the molecular mechanisms underlying the catalysis of friedelin production by friedelane‐type triterpene cyclases have not yet been fully elucidated. In this study, transcriptome data of four celastrol‐producing plants from Celastraceae were used to identify a total of 21 putative OSCs. Through functional characterization, the friedelane‐type triterpene cyclases were separately verified in the four plants. Analysis of the selection pressure showed that purifying selection acted on these OSCs, and the friedelane‐type triterpene cyclases may undergo weaker selective restriction during evolution. Molecular docking and site‐directed mutagenesis revealed that changes in some amino acids that are unique to friedelane‐type triterpene cyclases may lead to variations in catalytic specificity or efficiency, thereby affecting the synthesis of friedelin. Our research explored the functional diversity of triterpene synthases from a multispecies perspective. It also provides some references for further research on the relative mechanisms of friedelin biosynthesis.