Consistent over-estimation of gene number in complex plant genomes

The first comprehensive comparison of gene content between higher plant species provided the unexpected conclusions that rice contained about twice as many genes as Arabidopsis, and that about half of the rice genes had no obvious homologs in any other organism. Our subsequent analyses indicate that most of these "extra, novel" rice genes are mis-annotated segments of transposable elements, especially retrotransposons. Aggressive annotation of a randomly selected subset of the rice genome suggests that the gene number is less than 40000. The five fantasies of automated plant gene discovery are described and a protocol is provided to minimize (or at least predict) the inaccuracy of future plant genome annotations.     

水稻扩展蛋白家族的生物信息学分析

扩展蛋白是植物细胞壁的重要组成部分,具有松驰细胞壁和增加细胞壁柔韧性的作用,在植物的生长发育及抗性等方面起到重要的作用。水稻的全基因组序列统计分析显示,水稻扩展蛋白基因家族包含58个成员,分属于A(34)、B(19)、LA(4)和LB(1)4个亚家族,分布在水稻10条染色体上的58个位点,且同一亚家族成员有成簇存在的现象。扩展蛋白基因长度范围为687~1128 bp,编码蛋白质具有保守的结构域,以及保守的半胱氨酸和色氨酸残基。多数情况下,亚家族成员之间的氨基酸一致率小于35%,而同一亚家族成员之间的氨基酸一致率大于35%。在内含子、外显子组成模式上,水稻扩展蛋白呈现明显的亚家族特异性,除个别基因以外,A类基因含有1或2个内含子,B类含有3个内含子,LA和LB类含有4个内含子。密码子使用统计显示,与其他物种相比,水稻中的扩展蛋白具有更多的密码子使用偏好性,有26个高频密码子存在。研究结果展示了水稻扩展蛋白基因家族的基本信息,为深入研究扩展蛋白基因的功能、探讨物种间的进化关系奠定基础。     

Properties of group I allergens from grass pollen and their relation to cathepsin B, a member of the C1 family of cysteine proteinases.

Expansins are a family of proteins that catalyze pH-dependent long-term extension of isolated plant cell walls. They are divided into two groups, alpha and beta, the latter consisting of the grass group I pollen allergens and their vegetative homologs. Expansins are suggested to mediate plant cell growth by interfering with either structural proteins or the polysaccharide network in the cell wall. Our group reported papain-like properties of beta-expansin of Timothy grass (Phleum pratense) pollen, Phl p 1, and suggested that cleavage of cell wall structural proteins may be the underlying mechanism of expansin-mediated wall extension. Here, we report additional data showing that beta-expansins resemble ancient and modern cathepsin B, which is a member of the papain (C1) family of cysteine proteinases. Using the Pichia pastoris expression system, we show that cleavage of inhibitory prosequences from the recombinant allergen is facilitated by its N-glycosylation and that the truncated, activated allergen shows proteolytic activity, resulting in very low stability of the protein. We also show that deglycosylated, full-length allergen is not activated efficiently and therefore is relatively stable. Motif and homology search tools detected significant similarity between beta-expansins and cathepsins of modern animals as well as the archezoa Giardia lamblia, confirming the presence of inhibitory prosequences, active site and other functional amino-acid residues, as well as a conserved location of these features within these molecules. Lastly, we demonstrate by site-directed mutagenesis that the conserved His104 residue is involved in the catalytic activity of beta-expansins. These results indicate a common origin of cathepsin B and beta-expansins, especially if taken together with their previously known biochemical properties.     

The growing world of expansins

Expansins are cell wall proteins that induce pH-dependent wall extension and stress relaxation in a characteristic and unique manner. Two families of expansins are known, named alpha- and beta-expansins, and they comprise large multigene families whose members show diverse organ-, tissue- and cell-specific expression patterns. Other genes that bear distant sequence similarity to expansins are also represented in the sequence databases, but their biological and biochemical functions have not yet been uncovered. Expansin appears to weaken glucan-glucan binding, but its detailed mechanism of action is not well established. The biological roles of expansins are diverse, but can be related to the action of expansins to loosen cell walls, for example during cell enlargement, fruit softening, pollen tube and root hair growth, and abscission. Expansin-like proteins have also been identified in bacteria and fungi, where they may aid microbial invasion of the plant body.     

Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.     

Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.     

Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice

Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation.     

A simple nomenclature for a complex proton pump: VHA genes encode the vacuolar H(+)-ATPase

The vacuolar-type H(+)-ATPase acidifies intracellular compartments and is essential for many processes, including cotransport, guard cell movement, development, and tolerance to environmental stress. We have identified at least 26 genes encoding subunits of the vacuolar-type H(+)-ATPase in the Arabidopsis thaliana genome, although inconsistent nomenclature of these genes is confusing. The pump consists of subunits A through H of the peripheral V(1) complex, and subunits a, c, c" and d of the V(o) membrane sector. Most V(1) subunits are encoded by a single gene, whereas V(o) subunits are encoded by multiple genes found in duplicated segments of the genome. We propose to name these genes VHA-x, where x represents the letter code for each subunit. Applying a consistent nomenclature will help us to understand how the expression, assembly and activity of this pump are integrated with plant growth, signaling, development and adaptation.     

Analysis of rice mitochondrial genome organization using pulsed-field gel electrophoresis

Most of the plant mitochondrial (mt) genomes that have been mapped are believed to be organized as master circle molecules from which sub-genomic molecules arise through homologous recombination. We have evidence to suggest that a major part of the rice mt genome is organized as independent, sub-genomic molecules or mt chromosomes, one of which has already been mapped. This study is aimed at the identification of the other molecular entities that comprise the genome. Pulsed-field gel electrophoresis of the native rice mt DNA and Southern analysis with different mt gene probes have shown that in addition to the 117 kb mt chromosome, at least four more such molecules of sizes 130 kb, 95 kb, 70 kb and 56 kb account for most of the rice mt genome. A majority of the rice mt genes that encode products involved in oxidative phosphorylation are distributed among these five chromosomes. Partial restriction map of the 95 kborf 25/cox 3 chromosome, indicating the sites for the enzymesBglII andHindIII has also been determined.     

The expression profile of genes in rice roots under low phosphorus stress

Phosphorus (P) is one of the most essential macronutrients required for plant growth. Although it is abundant in soil, P is often the limiting nutrient for crop yield potential because of the low concentration of soluble P that plants can absorb directly. The gene expression profile was investigated in rice roots at 6, 24 and 72 h under low P stress and compared with a control (normal P) profile, using a DNA chip of 60000 oligos (70 mer) that represented all putative genes of the rice genome. A total of 795 differentially expressed genes were identified in response to phosphate (Pi) starvation in at least one of the treatments. Based on the analysis, we found that: (i) The genes coding for the Pi transporter, acid phosphatase and RNase were up-regulated in rice roots; (ii) the genes involved in glycolysis were first up-regulated and then down-regulated; (iii) several genes involved in N metabolism and lipid metabolism changed their expression patterns; (iv) some genes involved in cell senescence and DNA or protein degradation were up-regulated; and (v) some transmembrane transporter genes were up-regulated. The results may provide useful information in the molecular process associated with Pi deficiency and thus facilitate research in improving Pi utilization in crop species.     

The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis

The GH3 gene family in Arabidopsis, implicated in hormonal homeostasis through the conjugation of indolacetic and jasmonic acids to amino acids, is involved in a broad range of plant growth and development processes. In this work, the analysis of the GH3 family in the genome of Oryza sativa identified 13 hypothetical ORFs. EST analysis and RT-PCR assays demonstrated that 12 of them were active genes. An extensive EST analysis of the GH3 family performed on 26 plant species was used to estimate the minimum number of GH3 genes en each one. The data indicated that the members of the GH3 family progressively increased in the different plant divisions from Chlorophyta (0), Bryophyta (3), and Coniferophyta (4), to Magnoliophyta (7-19). Phylogenetic analyses showed a high degree of conservation between Arabidopsis and rice GH3 proteins and, in general, in the plant kingdom. The data revealed a homology clustering consistent with the functional classification of the Arabidopsis proteins, since most of the 110 sequences analyzed grouped into 2 main clusters, corresponding to the Arabidopsis functional groups I (jasmonic acid adenylation) and II (indolacetic acid adenylation). And additional cluster including group III (non-adenylation ability) was exclusively composed of proteins from Arabidopsis thaliana, Brassica napus and Gossypium hirsutum.