Volume 24, Issue 11, November 2012

This work identifies 6480 long intergenic noncoding RNAs in Arabidopsis, many of which show organ-specific and stress-responsive expression. The biogenesis of a group of long intergenic noncoding RNAs is coregulated by the RNA processing proteins SERRATE, CBP20, and CBP80.

This study employs a high-throughput, sequencing-based, structure-mapping approach to investigate RNA secondary structure throughout the Arabidopsis transcriptome. By combining these structural insights with a number of other RNA sequencing–based approaches, it provides a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.

Alternative precursor mRNA splicing massively expands the transcriptome diversity in higher eukaryotes. In this report, we describe Arabidopsis Polypyrimidine tract binding protein homologs as critical components of the plant splicing code and provide links between regulated alternative splicing events and seed germination as well as flowering time control.

This work shows that poly(A) site choice is affected in 45% or more of all genes in an Arabidopsis thaliana mutant that lacks a core polyadenylation factor subunit and that a novel poly(A) signal exists that can function in the absence of the affected protein. These results provide new insight into mechanisms of alternative polyadenylation in plants.

A fundamental challenge in plant biology is to discover the unknown connections within and between pathways and to associate previously unknown genes with specific biological processes. MORPH is a computational method for predicting genes that function in or regulate a biological pathway. MORPH fills pathway gaps and defines complex biological networks as shown for Arabidopsis and tomato.

This work identifies an epi-allele of rice Fertilization Independent Endosperm1 (FIE1) with DNA hypomethylation, reduced H3 Lys 9 dimethylation, increased H3 Lys 4 trimethylation, ectopic FIE1 expression, and loss imprinting, plus altered H3 Lys 27 trimethylation and perturbed expression of hundreds of genes. This suggests a regulatory link among these epigenetic marks.

The authors developed a strategy to identify putative transposon insertions that are present in a resequenced soybean population but absent in the soybean reference genome. Comparison of the distribution patterns of these elements and the patterns in the reference genome revealed evolutionary processes that reshaped the landscape of transposons after their integration in the host genome.

Ripening of the tomato fruit is accompanied by an increase in ethylene production and involves color changes, altered sugar metabolism, tissue softening, and the synthesis of aroma volatiles. This study shows that the MADS domain transcription factors FUL1 and FUL2 play a role in the regulation of these ripening processes, but in an ethylene-independent manner.

Pollen grains are protected by beautiful and elaborate cell walls, exines. This work examines the formation of one distinct patterning element of pollen surfaces, apertures, or areas where exine is not deposited. It demonstrates that the formation of apertures depends on the novel plant protein INP1, which is directed to aperture areas and regulates aperture length in a dosage-dependent manner.

Analysis of the supramolecular organization of enzymes in the lignin pathway shows that cytochrome P450s oligomerize and move along with the very mobile plant endoplasmic reticulum. Their expression favors relocalization of their soluble partner proteins nearer the membrane and association of sequential enzymes in the pathway.

This work identifies three basic helix-loop-helix (bHLH) transcription factors that competitively regulate cell elongation. In this tri-antagonistic system, a negative regulatory bHLH interacts with and interferes with the function of an activator bHLH that activates genes for cell elongation. A third bHLH inactivates the negative bHLH; this double negative regulation activates cell elongation.

Medicago truncatula NOOT and Pisum sativum COCH were found to maintain nodule identity during symbiotic interactions with rhizobia and were identified as orthologs of Arabidopsis BLADE-ON-PETIOLE genes, which are involved in leaf and flower development.

A unique galacturonic acidic–containing xyloglucan was identified in Arabidopsis root hair cell walls and characterized using genetic, biochemical, and chemical methods. Plants with a null mutation in a gene encoding a GT47 glycosyltransferase synthesize xyloglucan that lacks galacturonic acid and have short root hairs. These findings highlight a key role for acidic xyloglucan in root hair growth.

The crystal structure of an indole-3-acetic acid amido synthetase from Vitis vinifera involved in auxin homeostasis is presented. Residues likely to be involved in acyl group, amino acid, and ATP substrate binding have been identified, and this information provides a tool for designing new, effective auxins.

Fimbrin family proteins have long been known as actin binding proteins that regulate the formation of higher-order actin filament structures. FIM1, a fimbrin homolog from Lilium longiflorum, is found to cross-link actin microfilaments into bundles in vitro and is demonstrated to play important roles in the maintenance of the actin fringe in pollen tubes.

A plant phospholipase D (PLDα1) is activated by salt stress, and the produced lipid phosphatidic acid (PA) binds to a microtubule-associated protein MAP65-1. The PA and MAP65-1 interaction is essential for the regulation of microtubule organization and salt tolerance. This finding couples lipid signaling to the cytoskeleton and reveals a lipid-mediated signaling pathway that responds to stress.

PAN2 functions with PAN1, a Leu-rich repeat–receptor-like kinase (LRR-RLK) to polarize the divisions that form stomatal subsidiary cells in maize. Quantitative proteomics was used to identify PAN2 as a second LRR-RLK. PAN2 functions upstream of PAN1, potentially perceiving extracellular cues that initiate or amplify premitotic subsidiary mother cell polarity.

In UV-B–induced photomorphogenesis in Arabidopsis, COP1 is a UV-B–inducible gene and FHY3 and HY5 directly activate COP1, dependent on UV-B, by binding to the COP1 promoter to ensure photomorphogenic UV-B signaling. The working mode of FHY3 and HY5 in UV-B–specific signaling is distinct from that in far-red light and circadian conditions.

The ARC1 E3 ubiquitin ligase was previously shown to be required for self-pollen rejection in Brassica, and this report shows that its function is conserved in other Brassicaceae species. ARC1 was found to be required for self-pollen rejection in Arabidopsis lyrata and was frequently deleted in genomes of Brassicaceae species that had lost this self-incompatibility trait.

This article highlights the role of hydrogen sulfide as a relevant signaling molecule in plants, of comparable importance as described in animals. This study shows the regulatory role of sulfide generated by the cytosolic l-Cys desulfhydrase 1 enzyme on autophagy in eukaryotes.

Upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), cells activate an ER stress response to enable plants to tolerate these conditions. This work shows that one facet of this response is the activation of the autophagy pathway for degradation of ER fragments in the vacuole, which is regulated by the IRE1b splicing factor.

The Kennedy pathway and the Lands cycle are two principal metabolic modules of glycerolipid metabolism. This work examines the crosstalk of these two pathways and shows that loss of Lands cycle activity leads to an enhanced de novo phosphatidylcholine PC synthesis through the Kennedy pathway and PC turnover in Arabidopsis developing seeds.

A mutant of Chlamydomonas reinhardtii with impaired oil accumulation is shown to be deficient in a lipase with specificity for newly assembled monogalactolipids. Passage of fatty acids synthesized in the chloroplast through a transient chloroplast membrane lipid pool into triacylglycerols is proposed. A role of oil biosynthesis for survival following nutrient deprivation is demonstrated.

This study shows that an eyespot is a dynamic organelle and that the blue light photoreceptor phototropin is involved in the regulation of eyespot size and level of channelrhodopsin 1, which is the primary photoreceptor for photo-movement responses. This work also describes that, in addition to the C-terminal kinase domain, the N-terminal photoreceptor domains have independent signaling functions.

Exo70B2, a subunit of the exocyst complex, which is involved in exocytosis, is targeted for degradation by the ubiquitin ligase PUB22 upon activation of the immune system. This work also reveals that Exo70B2 is required for the activation of PAMP-triggered responses.

The targeting of proteins to specific locations within a cell is a dynamic process that requires sophisticated sorting mechanisms. This work shows that Arabidopsis KEEP ON GOING plays a central role in regulating movement of proteins from the plasma membrane to the central vacuole and in the secretion of defense proteins to the extracellular space.

Hemicellulose can retain a large amount of Al. This study demonstrates that an important component of hemicellulose, xyloglucan, can bind Al, and knockout of XTH31 increases Al resistance in Arabidopsis by decreasing xyloglucan endotransglucosylase action and the accumulation of xyloglucan in hemicellulose, which in turn reduces the retention of Al in the cell wall, thus excluding Al from roots.

This work shows that the Magnaporthe oryzae effector AvrPiz-t enters into rice cells to target the RING E3 ubiquitin ligase APIP6 for suppression of PAMP-triggered immunity in rice. It also describes that APIP6 degrades AvrPiz-t in planta and positively regulates basal defense to M. oryzae.

The bacterial phytotoxin coronatine mimics a plant hormone, jasmonic acid, and thus antagonizes signaling by another plant hormone, salicylic acid, important for plant defense. This study demonstrates that coronatine also suppresses SA-independent host defense, including the production of defense-promoting indole glucosinolates and has a target other than the jasmonic acid receptor.