Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei , and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II–directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.

The three yeast A kinase catalytic subunit isoforms are redundant for viability. We demonstrate that they have dramatically different roles in pseudohyphal development: Tpk2 is essential, whereas Tpk3 inhibits. Tpk1 has no discernible effect. Two-hybrid analysis identified the transcription factor Sf l1 as a protein that interacts specifically with Tpk2, but not Tpk1 or Tpk3. Deletion of SFL1 enhances pseudohyphal and invasive growth. Flo11, a cell surface f locculin required for pseudohyphal development, is transcriptionally regulated by Tpk2 and Sf l1. Genetic evidence indicates that Tpk2 acts upstream of Sf l1 in the regulation of Flo11.

Tpk2, but not Tpk1 or Tpk3, is required for pseudohyphal growth. Genome-wide transcriptional profiling has revealed unique signatures for each of the three A kinases leading to the identification of additional functional diversity among these proteins. Tpk2 negatively regulates genes involved in iron uptake and positively regulates genes involved in trehalose degradation and water homeostasis. Tpk1 is required for the derepression of branched chain amino acid biosynthesis genes that seem to have a second role in the maintenance of iron levels and DNA stability within mitochondria. The fact that TPK2 mutants grow better than wild types on nonfermentable carbon sources and on media deficient in iron supports the unique role of Tpk2 in respiratory growth and carbon source use.I n yeast, cAMP acting through the A kinases (PKA) provides a key regulatory signal for growth on diverse carbon sources. Growth on fermentable carbon sources (e.g., glucose, fructose, and sucrose) requires a higher basal level of cAMP than does growth on nonfermentable carbon sources (e.g., ethanol, glycerol, and acetate). Therefore, the level of cAMP must decrease in order for cells to switch from growth on fermentable carbon sources to growth on nonfermentable carbon sources (the diauxic shift; ref. 1). Addition of glucose to yeast cells growing on a nonfermentable carbon source or starved for glucose results in a transient peak in intracellular cAMP levels. This transition to fermentation requires both the transient increase of cAMP and the cAMP-dependent PKA (2). Activated PKA shifts the metabolic flux away from gluconeogenesis and toward glycolysis by regulating key enzymes in these processes including fructose-1,6-bisphosphatase and phosphofructokinase-2 (3). Phosphorylation by PKA inactivates the transcription factor Adr1, a positive regulatory factor for the transcription of the respiratory enzyme Adh2 (4). In addition, PKA promotes the breakdown of glycogen and trehalose by inhibiting enzymes involved in synthesis (trehalose synthase and glycogen synthase) and activating enzymes involved in breakdown (trehalase and glycogen phosphorylase) of these storage carbohydrates.The transcriptional changes occurring in the transition from fermentative growth to respiratory growth have been monitored by genome expression arrays (5). As glucose is depleted, transcription of genes involved in respiration, the tricarboxylic acid cycle, the glyoxylate cycle, gluconeogenesis, and storage carbohydrate synthesis is induced, whereas transcription of genes involved in glycolysis and protein synthesis is repressed (5). Consistent with the shift to respiratory growth, cytoplasmic ribosomal protein genes are repressed, and mitochondrial ribosomal genes are induced. In view of the role of cAMP and the PKAs in the use of carbon sources, these results raise the question of whether the PKAs function in respiratory growth and whether they are redundant for this function.To elucidate more broadly the functional differences between the PKA catalytic subunits, we ...

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SummaryFilamentous fungi are model microorganisms for studying nuclear migration in eukaryotic cells. Two genes, apsA and apsB (¼ anucleate primary sterigmata), were identified in Aspergillus nidulans that affect nuclear distribution in hyphae and specifically block conidiophore development at the metula stage when mutant. Here we describe the cloning, sequencing and molecular analysis of apsB. The gene encodes a 121 kDa coiled-coil, hydrophilic protein that was localized in the cytoplasm. No protein-protein interaction was detected between ApsB and ApsA, a membrane-associated, previously identified protein. An apsB null mutant was characterized by video epifluorescence microscopy using strains that express green fluorescent protein (GFP) in nuclei. With this novel approach, we have discovered a new mutant phenotype and have found that nuclei display an increased chaotic movement in older hyphal compartments that results in clustering and an uneven distribution of these organelles. These results suggest a regulatory role of ApsB in nuclear migration.

The parr-smolt transformation in Atlantic salmon (Salmo salar) is a complex developmental process that culminates in the ability to migrate to and live in seawater. We used GRASP 16K cDNA microarrays to identify genes that are differentially expressed in the liver, gill, hypothalamus, pituitary, and olfactory rosettes of smolts compared to parr. Smolts had higher levels of gill Na + /K + -ATPase activity, plasma cortisol and plasma thyroid hormones relative to parr. Across all five tissues, stringent microarray analyses identified 48 features that were differentially expressed in smolts compared to parr. Using a less stringent method we found 477 features that were differentially expressed at least 1.2-fold in smolts, including 172 features in the gill. Smolts had higher mRNA levels of genes involved in transcription, protein biosynthesis and folding, electron transport, oxygen transport, and sensory perception and lower mRNA levels for genes involved in proteolysis. Quantitative RT-PCR was used to confirm differential expression in select genes identified by microarray analyses and to quantify expression of other genes known to be involved in smolting. This study expands our understanding of the molecular processes that underlie smolting in Atlantic salmon and identifies genes for further investigation.Published by Elsevier Inc.