Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for .

Although an established model organism, remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst.

The Rab7 subfamily across species; evidence of high conservation in sequence and function.

We examined sequence conservation and signatures of selection in Rab7 proteins across 11 species, and determined the localization patterns of two Rab7 paralogs when expressed as GFP fusions in live cells. We found that, while there is a variable number of Rab7 paralogs per genome, Rab7 genes are highly conserved in sequence and appear to be under strong purifying selection across . Additionally, and surprisingly based on earlier studies, we found that two Rab7 proteins have virtually identical localization patterns.

Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies in species.

New gene functions arise within existing gene families as a result of gene duplication and subsequent diversification. To gain insight into the steps that led to the functional diversification of paralogues, we tracked duplicate retention patterns, expression-level divergence, and subcellular markers of functional diversification in the Rab GTPase gene family in three species. After whole-genome duplication, Rab GTPase duplicates are more highly retained than other genes in the genome but appear to be diverging more rapidly in expression levels, consistent with early steps in functional diversification.

One genome's junk is another's garbage.

Experiments on a single-celled ciliate reveal how mobile genetic elements can shape a genome, even one which is not transcriptionally active.

Conservation and innovation in Tetrahymena membrane traffic: proteins, lipids, and compartments.

The past decade has seen a significant expansion in our understanding of membrane traffic in Tetrahymena thermophila, facilitated by the development of new experimental tools and by the availability of the macronuclear genome sequence. Here we review studies on multiple pathways of uptake and secretion, as well as work on metabolism of membrane lipids. We discuss evidence for conservation versus innovation in the mechanisms used in ciliates compared with those in other eukaryotic lineages, and raise the possibility that existing gene expression databases can be exploited to analyze specific pathways of membrane traffic in these cells.

A Rab-based view of membrane traffic in the ciliate Tetrahymena thermophila.

Biologists have long recognized that some single-celled organisms show striking morphological and behavioral complexity, and details of the genetic underpinnings can be mined from the trove of newly-sequenced genomes. Ciliates, among which Tetrahymena thermophila and Paramecium tetraurelia have received most attention, provide clear examples of a lineage in which, as in animal cells, the core pathways of membrane traffic have undergone dramatic expansion and elaboration to facilitate multiple modes of exocytosis and endocytosis. Recent surveys of the Rab GTPases in T.

Comprehensive analysis reveals dynamic and evolutionary plasticity of Rab GTPases and membrane traffic in Tetrahymena thermophila.

Cellular sophistication is not exclusive to multicellular organisms, and unicellular eukaryotes can resemble differentiated animal cells in their complex network of membrane-bound structures. These comparisons can be illuminated by genome-wide surveys of key gene families. We report a systematic analysis of Rabs in a complex unicellular Ciliate, including gene prediction and phylogenetic clustering, expression profiling based on public data, and Green Fluorescent Protein (GFP) tagging.

The LATD gene of Medicago truncatula is required for both nodule and root development.

The evolutionary origins of legume root nodules are largely unknown. We have identified a gene, LATD, of the model legume Medicago truncatula, that is required for both nodule and root development, suggesting that these two developmental processes may share a common evolutionary origin. The latd mutant plants initiate nodule formation but do not complete it, resulting in immature, non-nitrogen-fixing nodules.