In the terrestrial ecosystem, higher plants live through specific relationships, i.e., pathogenic, parasitic, or symbiotic interactions with diverse kinds of microorganisms. Among them, root nodule symbiosis in leguminous plants and arbuscular mycorrhization in many plant species have critical importance in agriculture in respect to utilization of atmospheric nitrogen and uptake of phosphate from the soil, respectively. Understanding of these interactions will open the door for sustainable food production with conservation of global environment. We put together the feature story on two representative plant-microbe endosymbioses, root nodule symbiosis with Rhizobial bacteria and arbuscular mycorrhizal symbiosis with Glomus fungi. In the following articles in this issue, we summarize recent progress in understanding the molecular mechanisms by which host plants accommodate their micro-symbiotic partners.

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Over the last couple of decades, rapid progress has been made in understanding the molecular mechanism of legume-microbe endosymbiotic interactions. Forward and reverse genetic approaches, using model legumes Lotus japonicus and Medicago truncatula, allowed the identification of host plant genes, especially responsible for the early stage of infections by micro-symbionts. In the case of root nodule symbiosis, rhizobia release symbiotic signal molecules, Nod factors (NFs). Host-specific recognition of NFs leads to the activation of symbiotic Ca^<2+> spiking. In response to compatible rhizobia, root hair curling and the formation of intracellular tubular structure, infection threads (ITs) occur. In accordance with rhizobial infection through ITs, cortical cell division is triggered and root nodules are developed. In this chapter, we introduce host symbiotic genes classified into three steps of rhizobial infection, i.e., (1) Perception of host-specific NFs by LysM receptor kinases, (2) Induction of Ca^<2+> spiking and transduction of Ca^<2+> signals through common symbiosis pathway, and (3) Rhizobial infection via intracellular root hair ITs.

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Legume plants establish symbiosis with rhizobia to obtain nitrogen from atmosphere by nitrogen-fixing ability of endosymbiotic rhizobia. Most terrestrial plants including legumes make symbiosis with arbuscular mycorrhizal (AM) fungi, which help the host plants in nutrient uptake, especially in phosphate uptake through the hyphae developed in soil. These two symbiotic systems are thought to be highly valuable for establishing sustainable agriculture. In both symbioses, microsymbionts endow these valuable functions under the strict control by the host plants. Genetic defects in the host plant mechanisms required for these functions cause incompetence in symbiotic association itself. Model legumes have allowed us to identify host plant genes essential for those functional symbioses. Here we describe recent advances in understanding host plant gene functions involved in symbiotic nitrogen fixation and mycorrhizal symbiosis.

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Several phytohormones have been reported to positively or negatively regulate formation of a nitrogen-fixing nodule. Auxin transport system is important for root nodulation and affects the number of nodules. Ethylene, gibberellin and abscisic acid inhibit the cortical cell divisions induced by cytokinin. Abscisic acid affects the nitrogen fixation activity through the control of nitric oxide level. Though jasmonic acid is known as a negative regulator for nodulation, recent data suggest that it functions as a positive regulator at the adequate range of concentration. Defense responses induced by salicylic acid is avoided for the successful infection of compatible symbionts.

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In the endosymbiosis with nitrogen-fixing bacteria, rhizobia, legume plants form lateral organs called nodules on their roots. Although this symbiosis gives legumes an advantage in surviving on the land with limited nitrogen, nodule development associated with cell division and nitrogen-fixation cost appreciable amounts of morphological and metabolic energy. To keep the balance of symbiosis and homeostasis, the number of nodules is regulated by host plants. Nodules developed at early stage suppress nodule formation at later stage. This systemic negative regulation of nodule formation has been termed autoregulation of nodulation (AON). One of most important mechanisms of AON involves long-distance signaling via shoot-functioning receptor-like kinases and proteins (RLKs and RLPs) such as HAR1, KLV and LjCLV2 in Lotus japonicus, SUNN in Medicago truncatula, NARK in Glycine max, and SYM29, PsCLV2 in Pea sativum. These RLKs and RLPs have high homologies with other RLKs that regulate stem cell proliferation in shoot apical meristem in non-legume plants, indicating similarity and functional divergence of molecular mechanisms between the regulation of nodulation in legumes and the regulation of shoot apical meristem in non-legume plants. Based on recent studies, the following model is proposed to explain AON. First, several CLE peptides are induced by rhizobial infection or nitrogen compounds and function as root-derived signals (RDS). RDSs are transported to shoot and perceived by shoot-functioning RLKs and RLPs. Then the signals are converted into shoot-derived signals (SDS) and SDSs are in turn transported to root to suppress further nodulation.

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Stomata are composed of a pair of guard cells and a pore between them. The stomatal guard cells control gas exchange by changing the pore size, so that plants balance CO_2 uptake needed for photosynthesis vs. the loss of water. The density of stomata also affects gas-exchange rate, and is controlled by genetic and environmental factors. During the leaf development, epidermal cells of leaf primordia are multipotent. A proper number of cells are selected to undergo asymmetric cell division, which produces two types of cells, the meristemoid and its sister cell. The meristemoid becomes the guard mother cell, which symmetrically divides producing two guard cells. The sister cell may differentiate into the pavement cell or may undergo asymmetric cell division creating a meristemoid and the sister cell. Recent studies on stomatal formation revealed that the Epidermal Patterning Factor (EPF) family peptides, named EPF1, EPF2 and stomagen, play pivotal roles in these developmental steps. In this review, we will introduce recent findings in the mechanisms underlying the stomatal development, especially focusing on the cell-to-cell communication via peptide ligands and their receptors.

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In this report, I summarize physiological manipulation of plants by herbivorous insects, such as "green island formation" by a leaf-mining moth and other herbivores, gall induction by various insects, neoplasm formation by pea weevil, and the growth of cynipid-induced galls on shed leaves.

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Advancement of high-throughput sequencing technology has provided novel discoveries in plant science. Especially, "Epigenomics" is a novel noteworthy research area using this technology and has contributed greatly to further our understanding of epigenetic mechanisms, such as histone modifications and DNA methylations, involved in many biological phenomena in eukaryotes. Alterations of histone modifications and DNA methylation correlate with regulation of gene activity and genome maintenance. The sample preparation and computational analysis are the critical steps for precise identification of the epigenome information using the high-throughput sequencers. The quality of the histone modification data that are obtained by the high-throughput sequencing technology depends on the methods of Chromatin Immunoprecipitation (ChIP) and computational analysis. In this technical note, we refer to the the practical problems in the epigenome analysis and describe the methods that we have optimized for Arabidopsis ChIP analyses to identify site-specific and genome-wide histone modification status.

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