NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways

Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.

The ER body, a new organelle in Arabidopsis thaliana, requires NAI2 for its formation and accumulates specific beta-glucosidases

Plants develop various ER-derived structures with specific functions. The ER body found in Arabidopsis thaliana is a spindle-shaped structure. ER bodies accumulate in epidermal cells in seedlings or are induced by wounding. The molecular mechanisms underlying the formation of the ER body remained obscure. We isolated an ER body-deficient mutant in Arabidopsis seedlings, which we termed nai2. The NAI2 gene encodes a member of a unique protein family. NAI2 localizes to the ER body and the downregulation of NAI2 elongates ER bodies and reduces their number. ER bodies specifically accumulate high levels of PYK10/BGLU23, which is a beta-glucosidase that bears an ER retention signal. Additionally, in the nai2 mutant, PYK10 protein is diffuse throughout the ER and the PYK10 protein level is reduced. These observations indicate that NAI2 is a key factor for the formation of ER bodies and for the accumulation of PYK10 in the ER bodies of Arabidopsis. We also found that BGLU18, which encodes another beta-glucosidase with an ER retention signal, is induced at the site of wounding. Immunocytochemical analysis revealed that the BGLU18 protein is exclusively localized in ER bodies formed directly at the wounding site of cotyledons. These results suggest that BGLU18 is a component of the ER body in wounded leaves of Arabidopsis.

A mutant strain Arabidopsis thaliana that lacks vacuolar membrane zinc transporter MTP1 revealed the latent tolerance to excessive zinc

A mutant line of Arabidopsis thaliana that lacks a vacuolar membrane Zn(2+)/H(+) antiporter MTP1 is sensitive to zinc. We examined the physiological changes in this loss-of-function mutant under high-Zn conditions to gain an understanding of the mechanism of adaptation to Zn stress. When grown in excessive Zn and observed using energy-dispersive X-ray analysis, wild-type roots were found to accumulate Zn in vacuolar-like organelles but mutant roots did not. The Zn content of mutant roots, determined by chemical analysis, was one-third that of wild-type roots grown in high-Zn medium. Severe inhibition of root growth was observed in mtp1-1 seedlings in 500 muM ZnSO(4). Suppression of cell division and elongation by excessive Zn was reversible and the cells resumed growth in normal medium. In mutant roots, a marked formation of reactive oxygen species (ROS) appeared in the meristematic zone, where the MTP1 gene was highly expressed. Zn treatment enhanced the expression of several genes involved in Zn tolerance: namely, the plasma membrane Zn(2+)-export ATPase, HMA4, and plasma and vacuolar membrane proton pumps. CuZn-superoxide dismutases, involved in the detoxification of ROS, were also induced. The expression of plasma membrane Zn-uptake transporter, ZIP1, was suppressed. The up- or down-regulation of these genes might confer the resistance to Zn toxicity. These results indicate an essential role of MTP1 in detoxification of excessive Zn and provide novel information on the latent adaptation mechanism to Zn stress, which is hidden by MTP1.