Intercellular Communication in Shoot Meristems.

Plant cells utilize mobile transcription factors to transmit intercellular signals when they perceive environmental stimuli or initiate developmental programmes. Studies on these novel cell-to-cell signals have accumulated multiple pieces of evidence showing that non-cell-autonomous transcription factors play pivotal roles in most processes related to the formation and development of plant organs. Recent studies have explored the evolution of mobile transcription factors and proposed mechanisms for their trafficking through plasmodesmata, where a selective system exists to facilitate this process. Mobile transcription factors contribute to the diversity of the intercellular signalling network, which is also established by peptides, hormones, and RNAs. Crosstalk between mobile transcription factors and other intercellular molecules leads to the development of complex biological signalling networks in plants. The regulation of plasmodesmata appears to have been another major step in controlling the intercellular trafficking of transcription factors based on studies of many plasmodesmal components. Furthermore, diverse omics approaches are being successfully applied to explore a large number of candidate transcription factors as mobile signals in plants. Here, we review these fascinating discoveries to integrate current knowledge of non-cell-autonomous transcription factors.

Simple SummarySmall RNA sequencing has been widely used for characterizing the landscape of small non-coding RNAs—the most abundant cargo in extracellular vesicles (EVs). Here, we performed a systematic assessment of the quality, technical, and potential biological biases introduced by different EV isolation methods and the enrichment of specific, small RNA biotypes in EVs. The findings in this study guide the quality control of EV small RNA-seq and the selection of EV isolation techniques and enhance the interpretation of small RNA contents and the preferential loading of specific RNA biotypes into EVs.Motivation: Extracellular vesicles (EVs) are produced and released by most cells and are now recognized to play a role in intercellular communication through the delivery of molecular cargo, including proteins, lipids, and RNA. Small RNA sequencing (small RNA-seq) has been widely used to characterize the small RNA content in EVs. However, there is a lack of a systematic assessment of the quality, technical biases, RNA composition, and RNA biotypes enrichment for small RNA profiling of EVs across cell types, biofluids, and conditions. Methods: We collected and reanalyzed small RNA-seq datasets for 2756 samples from 83 studies involving 55 with EVs only and 28 with both EVs and matched donor cells. We assessed their quality by the total number of reads after adapter trimming, the overall alignment rate to the host and non-host genomes, and the proportional abundance of total small RNA and specific biotypes, such as miRNA, tRNA, rRNA, and Y RNA. Results: We found that EV extraction methods varied in their reproducibility in isolating small RNAs, with effects on small RNA composition. Comparing proportional abundances of RNA biotypes between EVs and matched donor cells, we discovered that rRNA and tRNA fragments were relatively enriched, but miRNAs and snoRNA were depleted in EVs. Except for the export of eight miRNAs being context-independent, the selective release of most miRNAs into EVs was study-specific. Conclusion: This work guides quality control and the selection of EV isolation methods and enhances the interpretation of small RNA contents and preferential loading in EVs.

Human follicular fluid (hFF), as an extra oocyte microenvironment, is essential to the biological processes of oocyte development. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 426 proteins as consistently present in hFF from different participants. According to our gene chip data, the granulosa cells in the follicle locally produce 235 of these proteins. These data suggest that the granulosa cells actively participate in the follicular development by synthesizing important molecules to support the activity of pathways that are essential to oocyte development and genomic preservation. The computational Ingenuity Pathway Analysis (IPA) suggests that the identified proteins have well-established functions in the pathways of steroidogenesis, cell-to-cell signaling and interaction, molecular transport, the antioxidative system, interleukin 1 (IL-1) and IL-6 signaling, liver X receptor/retinoid X receptor (LXR/RXR) activation, and the interconnective insulin-like growth factor and lipid metabolism networks. The hFF peptide composition is likely to serve not only the inflammatory follicular state as has been previously suggested; rather, it is a highly diverse and multifunctional environment with several interconnected pathways. These results provide us with important knowledge related to the environment in which the oocyte develops as well as the molecular basis for controlling the process independently of blood supply.

While intercellular communication systems in Gram-negative bacteria are often based on homoserine lactones as signalling molecules, it has been shown that autoinducing peptides are involved in intercellular communication in Gram-positive bacteria. Many of these peptides are exported by dedicated systems, posttranslationally modified in various ways, and finally sensed by other cells via membrane-located receptors that are part of two-component regulatory systems. In this way the expression of a variety of functions including virulence, genetic competence and the production of antimicrobial compounds can be modulated in a co-ordinated and cell density- and growth phase-dependent manner. Occasionally the autoinducing peptide has a dual function, such as in the case of nisin that is both a signalling pheromone involved in quorum sensing and an antimicrobial peptide. Moreover, biochemical, genetic and genomic studies have shown that bacteria may contain multiple quorum sensing systems, underlining the importance of intercellular communication. Finally, in some cases different peptides may be recognised by the same receptor, while also hybrid receptors have been constructed that respond to new peptides or show novel responses. This paper provides an overview of the characteristics of autoinducing peptide-based quorum sensing systems, their application in various gram-positive bacteria, and the discovery of new systems in natural and engineered ecosystems.

An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis

Growth and development of multi-cellular organisms require mechanisms that allow for extensive cell-to-cell communication. In some incidences communication is established by signaling molecules that are directly transported from one cell to the other. These mobile signals in plants have been found in forms of proteins, RNAs, and small molecules. They are transmitted through the vascular system in a long distance (between organs), or through plasmodesmata in a short distance (between cell types). A growing number of studies show that transcription factors contribute as important mobile signals in plants. Transcription factors move in a short or long distance in forms of proteins and RNAs. Such transport activities are very important for patterning and growth of plant organs and tissues. In this chapter, we will comprehensively review transcription factors as mobile signals: factors that have been discovered, mechanisms of their mobility, new tools that will lead to the discovery of mobile transcription factors, and putative mobile transcription factors inferred from cell-type specific RNA profiling data.

Upon floral induction, the primary shoot meristem of an Arabidopsis plant begins to produce flower meristems rather than leaf primordia on its flanks. Assignment of floral fate to lateral meristems is primarily due to the cooperative activity of the flower meristem identity genes LEAFY (LFY), APETALA1 (AP1), and CAULIFLOWER. We present evidence here that AP1 expression in lateral meristems is activated by at least two independent pathways, one of which is regulated by LFY. In lfy mutants, the onset of AP1 expression is delayed, indicating that LFY is formally a positive regulator of AP1. We have found that AP1, in turn, can positively regulate LFY, because LFY is expressed prematurely in the converted floral meristems of plants constitutively expressing AP1. Shoot meristems maintain an identity distinct from that of flower meristems, in part through the action of genes such as TERMINAL FLOWER1 (TFL1), which bars AP1 and LFY expression from the influorescence shoot meristem. We show here that this negative regulation can be mutual because TFL1 expression is downregulated in plants constitutively expressing AP1. Therefore, the normally sharp phase transition between the production of leaves with associated shoots and formation of the flowers, which occurs upon floral induction, is promoted by positive feedback interactions between LFY and AP1, together with negative interactions of these two genes with TFL1.

Intergenic Transcripts Regulate the Epigenetic State of rRNA Genes

Overlapping Roles and Collective Requirement for the Coreceptors GAS1, CDO, and BOC in SHH Pathway Function

Small RNAs as plant morphogens

Canonical small RNAs in plants, including microRNAs and small interfering RNAs, are key triggers of RNA interference and regulate nearly every major biological process in plants. To establish systemic silencing, small RNAs undergo both short-distance intracellular trafficking or intercellular communication and long-distance transport from one organ to another, even across parasites or pathogens. This enables the delivery of effector molecules throughout the plant, promoting the spread of gene silencing. Biologically, the spatiotemporal regulation of small RNAs results in gradient distributions within cells or along the direction of organogenesis. Furthermore, the spreading capacity of small RNAs, generated in somatic or nurse cells, can guide target gene silencing in germlines in plants. In this review, we summarize recent advances in understanding the regulation and functional roles of local trafficking and long-distance transport of plant small RNAs in developmental polarity, the maintenance of cell identity, and with a particular focus, the mechanisms of small RNA movement and delivery between companion cells and gametes in plants. Additionally, we discuss the methods and challenges of monitoring small RNA transport in vivo through live imaging, as well as the potential applications of small RNA transport and delivery in the development of RNA-based pesticides.

Growth, development, and response to diverse environmental cues in all organisms rely on extra-, inter-, and intracellular communication mediated by complex signaling networks. In plants, there are several ways to achieve this, which include a wide array of receptors, secondary messengers, cascading kinases, reactive oxygen species, phytohormones, mobile transcription factors, noncoding RNAs, and secreted signaling peptides. Plant stability under stress is also vested with the concerted performance of the nuclear, mitochondrial, and chloroplast genomes, the relationship among which is not well defined. However, the signaling pathways that aid in the communication between various organelles of a plant cell are complex and interdependent. Among the various abiotic stresses, giving more focus to unravel the diverse signaling networks associated with drought stress response would be more rewarding in the wake of the increasing threat of acute water shortages in conjunction with the highly unpredictable climate scenario. A comprehensive understanding of the intricate drought stress response signaling networks will help in identifying key strategic candidates which when pathway engineered could help in achieving realizable levels of drought tolerance. This is very critical in the context of the polygenic nature of drought tolerance. Hence in this chapter we aim to address diverse plant stress signaling pathways and their overlapping roles in imparting tolerance to drought stress.

Mobile protein signals in plant development

Gene Expression Patterns Identify Novel Biologically Relevant Signaling and Transcriptional Pathways Involved in Terminal Erythroid Differentiation and Polycythemia Vera.

Molecular Tools: Biology, Prognosis, and Therapeutic Triage