Plant Physiology 132:726-727 (2003)
© 2003 American Society of Plant Biologists
THE HOT AND THE CLASSIC
HIGHLY CITED ARABIDOPSIS PAPERS PUBLISHED IN PLANT PHYSIOLOGY
Many people have asked what criteria are used in selecting the articles that are featured in the monthly column On the Inside. Foremost, of course, is what we judge to be the importance of the science presented. However, in each On the Inside we also try to provide a sampling of the many diverse areas of research that are covered in our journal. Thus, there have been instances when exceptionally good papers have not been covered because they had the misfortune of being included in an issue that had other exceptionally fine articles in the same field. In other cases, with the benefit of hindsight, we were just wrong in our selections. (One is reminded of the poor president of the Linnean Society who a few months after Darwin and Wallace's presentation to that society, declared that in reviewing the events of the year 1858, he could find no memorable scientific progress to record!). In an attempt to rectify past wrongs, this month's column highlights some of our journal's more highly cited Arabidopsis articles of late that were not covered in On the Inside.
Mitochondrial Proteomics
Mitochondria synthesize only 2% to 5% of the proteins required for their function: The remaining mitochondrial proteins are encoded by the nuclear genome and are targeted to the mitochondria as protein precursors. Prior analyses of the presequences that direct proteins to mitochondria in plants show substantial differences to the consensus sequences present in yeast (Saccharomyces cerevisiae). This means that the identification of mitochondria-targeted, nuclear-encoded proteins in plants cannot rely simply on existing bioinformatic tools. Indeed, bioinformatic analyses have been uncharacteristically unsuccessful in estimating the number of nuclear genes that code for mitochondrial proteins (estimates range from 349–2,897). Millar et al. (2001 ) took another approach to the question of the number of nuclear-encoded proteins in mitochondria. Using 2D gel separations of Arabidopsis cell culture mitochondrial proteins, they determined the presence of 100 abundant proteins and 250 low-abundance proteins. MALDI-ToF mass spectrometry spectra were obtained for 170 proteins. Using this dataset, 91 of the proteins were identified by searching translated Arabidopsis genomic databases. Of this set, 81 have defined functions based on sequence comparison. These functions include respiratory electron transport, tricarboxylic acid cycle metabolism, amino acid metabolism, protein import, processing and assembly, transcription, membrane transport, and antioxidant defense. Analysis of full-length putative protein sequences using bioinformatic tools to predict subcellular targeting revealed significant variation in predictions, and also a lack of mitochondrial targeting prediction for several characterized mitochondrial proteins.
Kruft et al. (2001) also presented a comprehensive data set concerning the mitochondrial proteome of Arabidopsis. Analyzing the Arabidopsis mitochondrial proteome by 2D gel electrophoresis and silver staining revealed about 650 different protein spots. The authors point out, however, that this number may be an underestimate for several reasons: very hydrophobic proteins are known to absent from gels after isoelectric focusing; very basic proteins were not analyzed; the inability to detect low-abundance proteins by means of silver staining; the possibility that the expression of some proteins may be tissue- or environment-specific; and the possibility that proteins may have yielded exactly overlapping spots.
Genomics of Lipid Biosynthesis
Mekhedov et al. (2000) uncovered sequences corresponding to 65 plant polypeptides involved in lipid metabolism. Several previously undescribed genes in Arabidopsis were tentatively identified. For example, two genomic sequences were identified as candidates for the palmitate-specific monogalactosyldiacylglycerol desaturase (FAD5). A candidate genomic sequence for 3-ketoacyl-acyl-carrier protein (ACP) synthase involved in mitochondrial fatty acid biosynthesis was also identified. The large number (>165,000) of plant expressed sequence tags (ESTs) also provided the authors with the opportunity to perform "digital northern" comparisons of gene expression levels across many genes. EST abundance in general correlated with biochemical and flux characteristics of the enzymes in Arabidopsis leaf tissue. In a few cases, however, statistically significant differences in EST abundance levels were observed for enzymes that catalyze similar reactions in fatty acid metabolism, providing clues concerning previously undescribed regulatory phenomena.
TITAN Endosperm Mutants
The early development of endosperm in Arabidopsis is characterized by specialized patterns of nuclear division and migration, and by delayed cellularization. The titan (tnn) mutants of Arabidopsis exhibit striking defects in seed development, particularly a dramatic enlargement of endosperm nuclei. Several TTN genes encode for proteins (condensins and cohesins) involved in maintaining chromosomal structure during mitosis. Another TTN gene product (TTN5) is related to the ARL2 class of GTP-binding proteins. To establish a more complete picture of TTN functions in seed development, Tzafrir et al. (2002) performed a forward genetic screen for additional knockouts within a large collection of insertion lines. They identified four additional TTN genes and concluded that the titan phenotype can result from disruption of chromosome dynamics or microtubule function.
Auxin/IAA Proteins
Auxin rapidly activates the transcription of a select set of early response genes, including members of the Aux/IAA gene family. Aux/IAA proteins are transcription factors that also appear to participate in certain phytochrome responses such as hypocotyl elongation. Genetic studies suggest that the short hypocotyl mutants shy2–1D and shy2–2 bypass a phytochrome requirement for certain aspects of photomorphogenesis. Colon-Carmona et al. (2000) demonstrated that recombinant Aux/IAA proteins from Arabidopsis and pea (Pisum sativum) interact in vitro with recombinant phytochrome A from oat (Avena sativa), and that recombinant SHY2/IAA3, AXR3/IAA17, IAA1, IAA9, and Ps-IAA4 are phosphorylated by recombinant oat phytochrome A in vitro. They also demonstrated increased steady-state levels of mutant IAA3 in shy2–2 plants and phosphorylation of the SHY2–2 protein in vivo. Phytochrome-dependent phosphorylation of Aux/IAA proteins, therefore, is a key molecular mechanism for integrating auxin and light signaling in plant development.
In another development, Nagpal et al. (2000) cloned the AXR2 gene using a map-based approach, and found that it is identical to IAA7, a member of the IAA family of auxin-inducible genes. A null mutant was shown to have a slightly longer hypocotyl than wild-type plants, but had normal root growth. Conversely, a gain-of-function mutant had a short hypocotyl and made expanded leaves in the dark. These results indicate that AXR2/IAA7 contributes to shoot photomorphogenesis, but is not essential for root development. The collected results from mutations in six different IAA genes suggest that domain II plays a key role in the function of various AUX/IAA proteins, and that it may be a target for the regulatory action of auxin or some other signal.
SNARE Proteins
All eukaryotes control the traffic of proteins and lipids though the endo-membrane system. Many factors have been characterized as essential for vesicle trafficking, including a number of proteins commonly referred to as soluble N-ethylmaleimide-sensitive factor adaptor protein receptor (SNARE) components. Sanderfoot et al. (2000) revealed that the Arabidopsis genome contains a remarkable number of SNAREs. For example, Arabidopsis has twice as many syntaxins as Caenorhabditis elegans or Drosophila melanogaster. The authors speculate that some of these proteins may have specialized in the plant-specific method of cytokinesis.
Brassinosteroid (BR)-Insensitive Mutant
BR-resistant dwarf mutants exhibit a short, robust stature and dark-green leaves, and they develop abnormally under dark conditions. Some of these mutants are defective in BR biosynthesis, whereas others are effective in BR signaling. Screens for BR signaling mutants identified one locus, BRI1, which encodes a protein with homology to Leu-rich repeat receptor Ser (Ser)/Thr (Thr) kinases. Friedrichsen et al. (2000) elucidated the importance of certain domains for BRI1 function by identifying the molecular lesions of 14 recessive alleles that represent five new BRI1 mutations; BRI1 is expressed at high levels in the meristem, root, shoot, and hypocotyl of seedlings and at lower levels later in development. This finding is consistent with physiological data that showed that exogenously applied BRs promote growth only in younger tissues. Although the steroid receptors of animal cells are usually in the nucleus, confocal microscopy analysis of full-length BRI1 fused to green fluorescent protein indicates that BRI1 is localized in the plasma membrane in Arabidopsis. BRI1 appears, therefore, to be a ubiquitously expressed Leurich repeat receptor that plays a key role in BR signaling through Ser/Thr phosphorylation.
Peter V. Minorsky
Department of Natural Sciences Mercy College Dobbs Ferry, NY 10522
FOOTNOTES
www.plantphysiol.org/cgi/doi/10.1104/pp.900079.
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