A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes. Because of the small format and high density of the arrays, hybridization volumes of 2 microliters could be used that enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA. Differential expression measurements of 45 Arabidopsis genes were made by means of simultaneous, two-color fluorescence hybridization.

https://science.sciencemag.org/content/sci/270/5235/467.full.pdf

Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

/pdf/analysis-of-the-genome-sequence-of-the-flowering-plant-3vizsb52m2.pdf

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Phenylpropanoid compounds encompass a wide range of structural classes and biological functions. Limiting discussion to stress-induced phenylpropanoids eliminates few of the structural classes, because many compounds thst are constitutive in one plant species or tissue can be induced by various stresses in another species or in another tissue of the same plant (Beggs et al., 1987; Christie et al., 1994).

/pdf/stress-induced-phenylpropanoid-metabolism-3mfsiitk82.pdf

Stress-Induced Phenylpropanoid Metabolism.

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

/pdf/the-genome-of-black-cottonwood-populus-trichocarpa-torr-gray-uje0c9fwz6.pdf

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

The 75th anniversary of Plant Physiology comes at a very exciting time in the history of plant biology. We are currently experiencing an unprecedented acceleration in the pace of scientific progress (as our Society's recent publication of the 1,400-page textbook Plant Biochemistry and Molecular

/pdf/plant-physiology-past-present-and-future-4y3590v67m.pdf

Plant Physiology: Past, Present, and Future

Chemical genomics (i.e., genomics-scale chemical genetics) approaches are based on the ability of low-molecular-mass molecules to modify biological processes. Such molecules are used to affect the activity of a protein or a pathway in a manner that is tunable and reversible. A major advantage of this approach compared to classical plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure activity relationships (SARs) and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms in which the results can be translated to plants. Here, we describe approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis. We will also discuss considerations for the characterization of bioactive compounds and genetic screens for target identification. This should provide those who are considering this approach some practical knowledge of how to design and establish a chemical genomics screen.

Chemical Genomics Approaches in Plant Biology

A polypeptide enabling sorting of proteins to vacuoles in plants, particularly tobacco is described. The polypeptide has the sequence VFAEAIAANSTLVAE. Without this sequence, the protein is not sorted to the vacuoles. The polypeptide is attached to the C-terminal region of the protein and is particularly useful for sorting of lectins to the vacuole which are insecticidal.

Polypeptides enabling sorting of proteins to vacuoles in plants

We used RNA gel-blot analysis, in-situ hybridization, and nuclear run-on transcription to examine the effects of exogenous abscisic acid (ABA) on the spatial distribution of mRNA for the lectin wheat-germ agglutinin (WGA) in developing wheat (Triticum aestivum L. cv. Marshall) embryos and seedlings. When analyzed by RNA gel blots, both developing embryos and seedlings exhibited higher steady-state levels of WGA mRNA after ABA treatment. As determined by in-situ hybridization, incubation of developing embryos in 0.1 mM ABA resulted in accumulation of WGA mRNA in the epidermal and subepidermal cell layers of the radicle and seminal roots and throughout the rootcap and coleorhiza. This spatial distribution was identical to that in control embryos. Nuclear run-on transcription assays indicated that at least part of this increase is attributable to transcriptional induction. Thus, exogenous ABA is capable of inducing increased WGA mRNA accumulation only in cells where it is expressed during normal embryogenesis. When seeds were germinated in the absence of ABA, WGA mRNA was detected only in the rootcap. In contrast, seeds imbibed and germinated in the presence of ABA for 3 d exhibited a spatial distribution of WGA mRNA similar to that observed in developing embryos treated with ABA. In contrast, when ABA was added to 3-d-old seedlings, WGA mRNA was not detected in regions of the root beyond the rootcap. We conclude that exogenous ABA, when applied continuously from imbibition, causes retention of the embryo-specific pattern of WGA mRNA distribution and that the spatial pattern of WGA mRNA expression in roots does not change when ABA is added after germination.

Abscisic acid enhances the transcription of wheat-germ agglutinin mRNA without altering its tissue-specific expression.

Several proteomic studies in Arabidopsis have shown the presence of heterogeneous ribosomal populations in different tissues. However, the phenotypic consequences of the imbalance of those ribosomal populations, and the regulatory mechanisms activated to control specific ratios between them, have yet to be evaluated. In our previous report, the phenotypic characterization of the Arabidopsis ribosomal L4 (RPL4) family suggests that the maintenance of proper auxin-regulated developmental responses requires the simultaneous presence of RPL4A- and RPL4D-containing ribosomes. Based on the analysis of the compensatory mechanisms within the RPL4 family proteins in the rpl4a and rpl4d backgrounds, we propose the Gene Dosage Balance Hypothesis (GDBH) as a regulatory mechanism for ribosomal complexes in Arabidopsis. By using the concepts of dosage compensation and hierarchy, GDBH is able to explain the severity and specificity of different ribosomal mutant phenotypes associated with the same ribosomal complex.

Natasha V. Raikhel

Papers

Plant Physiology: Past, Present, and Future

Chemical Genomics Approaches in Plant Biology

Polypeptides enabling sorting of proteins to vacuoles in plants

Abscisic acid enhances the transcription of wheat-germ agglutinin mRNA without altering its tissue-specific expression.

Application of the gene dosage balance hypothesis to auxin-related ribosomal mutants in Arabidopsis.