The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.

The protein coding regions of plastid mRNAs in higher plants are generally flanked by 3′ inverted repeat sequences. In spinach chloroplast mRNAs, these inverted repeat sequences can fold into stem‐loop structures and serve as signals for the correct processing of the mature mRNA 3′ ends. The inverted repeat sequences are also required to stabilize 5′ upstream mRNA segments, and interact with chloroplast protein in vitro. To dissect the molecular components involved in chloroplast mRNA 3′ end processing and stability, a spinach chloroplast protein extract containing mRNA 3′ end processing activity was fractionated by FPLC and RNA affinity chromatography. The purified fraction consisted of several proteins and was capable of processing the 3′ ends of the psbA, rbcL, petD and rps14 mRNAs. This protein fraction was enriched for a 28 kd RNA‐binding protein (28RNP) which interacts with both the precursor and mature 3′ ends of the four mRNAs. Using specific antibodies to this protein, the poly(A) RNA‐derived cDNA for the 28RNP was cloned and sequenced. The predicted amino acid sequence for the 28RNP reveals two conserved RNA‐binding domains, including the consensus sequences RNP‐CS1 and CS2, and a novel acidic and glycine‐rich N‐terminal domain. The accumulation of the nuclear‐encoded 28RNP mRNA and protein are developmentally regulated in spinach cotyledons, leaves, root and stem, and are enhanced during light‐dependent chloroplast development. The general correlation between accumulation of the 28RNP and plastid mRNA during development, together with the result that depletion of the 28RNP from the chloroplast protein extract interferes with the correct 3′ end processing of several chloroplast mRNAs, suggests that the 28RNP is required for plastid mRNA 3′ end processing and/or stability.

In the absence of efficient transcription termination correct 3′‐end processing is an essential step in the synthesis of stable chloroplast mRNAs in higher plants. We show here that 3′‐end processing in vitro involves endonucleolytic cleavage downstream from the mature terminus, followed by exonucleolytic processing to a stem‐loop within the 3′‐untranslated region. These processing steps require a high molecular weight complex that contains both endoribonucleases and an exoribonuclease. In the presence of ancillary RNA binding proteins the complex correctly processes the 3′‐end of precursor RNA. In the absence of these ancillary proteins 3′‐end maturation is prevented and plastid mRNAs are degraded. Based on these results we propose a novel mechanism for the regulation of mRNA 3′‐end processing and stability in chloroplasts.

Post-translational attachment of isoprenyl groups to conserved cysteine residues at the C-terminus of a number of regulatory proteins is important for their function and subcellular localization. We have identified a novel calmodulin, CaM53, with an extended C-terminal basic domain and a CTIL CaaX-box motif which are required for efficient prenylation of the protein in vitro and in vivo. Ectopic expression of wild-type CaM53 or a non-prenylated mutant protein in plants causes distinct morphological changes. Prenylated CaM53 associates with the plasma membrane, but the non-prenylated mutant protein localizes to the nucleus, indicating a dual role for the C-terminal domain. The subcellular localization of CaM53 can be altered by a block in isoprenoid biosynthesis or sugar depletion, suggesting that CaM53 activates different targets in response to metabolic changes. Thus, prenylation of CaM53 appears to be a novel mechanism by which plant cells can coordinate Ca2+ signaling with changes in metabolic activities.

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