Effect of a two-base insertion mutation of the TP53 gene on expression of p53 protein in canine histiocytic sarcoma cells

OBJECTIVE

To examine effects of a common mutation (2-base insertion in exon 5) of the TP53 gene on biological function of p53 protein in canine histiocytic sarcoma cells.

SAMPLE

Canine histiocytic tumor cell lines DH82 with deletion of TP53 and CHS-3 with the wild-type TP53 and canine wild-type and mutant TP53 fragments.

PROCEDURES

Wild-type or mutant TP53 with a polyprotein peptide tag at the N-terminus was transduced into DH82 and CHS-3 cells. Expression of p53 protein, changes in function as a transcription factor, and susceptibility to doxorubicin and nimustine were compared.

RESULTS

Transduced p53 protein was detected in wild-type TP53-transduced DH82 and CHS-3 cells, whereas expression was not detected in mutant TP53-transduced cells. There were significant increases in expression of target genes of p53 protein, including p21 and MDM2, in wild-type TP53-transduced cells, compared with results for native and mock-transfected cells, but not in mutant TP53-transduced cells. There was no significant difference in drug susceptibilities among native and derivative cells of CHS-3. However, cell viabilities of wild-type TP53-transduced DH82 cells incubated with doxorubicin were significantly lower than viabilities of native, mock-transfected, and AT insertion mutation-TP53-transduced DH82 cells; susceptibility to nimustine did not differ significantly among cells.

CONCLUSIONS AND CLINICAL RELEVANCE

Expression of p53 protein and its function as a transcription factor were lost after addition of a 2-base insertion in the TP53 gene in canine histiocytic tumor cells. Additional studies are needed to investigate the clinical relevance of this mutation in histiocytic sarcomas of dogs.

Molecular cloning and sequence variance analysis of the TEOSINTE BRANCHED1 (TB1) gene in bermudagrass [Cynodon dactylon (L.) Pers]

TEOSINTE BRANCHED1 (TB1) encodes a TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATING CELL FACTOR (TCP) transcription factor that represses axillary bud outgrowth and lateral branch formation in plants. Previous studies have elucidated the essential tillering regulatory roles of TB1 in many grasses, including maize and rice; however, the functions of TB1 in turf grasses remain unclear. In this study, we cloned the CdTB1 gene from bermudagrass, an important turfgrass species, and characterized the transactivation function of the CdTB1 protein. Sequencing the CdTB1 gene locus in a mini-core germplasm collection of Chinese bermudagrasses led to the successful identification of 66 SNP and 2 indel mutations in the protein-coding region as well as 28 SNP and 11 indel mutations in the promoter region. Interestingly, mutations in the C-terminal transactivation domain of the CdTB1 protein had no significant influence on the transactivation activity, whereas a novel 335-bp insertion mutation located in the promoter region could significantly increase the expression of the CdTB1 gene. Furthermore, wild accessions of bermudagrass harboring the novel insertion mutation were found to have significantly reduced tillers compared with other accessions, suggesting a negative correlation between the mutation and tillering. The results of this study not only expanded our knowledge of TB1 gene expression regulation but also provided possible molecular markers to breed cultivars of turf and forage grasses with specific architectural features.

Chicken β-globin insulators fail to shield the nkx2.5 promoter from integration site effects in zebrafish

Genetic lineage tracing and conditional mutagenesis are developmental genetics techniques reliant on precise tissue-specific expression of transgenes. In the mouse, high specificity is usually achieved by inserting the transgene into the locus of interest through homologous recombination in embryonic stem cells. In the zebrafish, DNA containing the transgenic construct is randomly integrated into the genome, usually through transposon-mediated transgenesis. Expression of such transgenes is affected by regulatory features surrounding the integration site from general accessibility of chromatin to tissue-specific enhancers. We tested if the 1.2 kb cHS4 insulators derived from the chicken β-globin locus can shield a transgene from chromosomal position effects in the zebrafish genome. As our test promoters, we used two different-length versions of the zebrafish nkx2.5. We found that flanking a transgenic construct by cHS4 insulation sequences leads to overall increase in the expression of nkx2.5:mRFP. However, we also observed a very high degree of variability of mRFP expression, indicating that cHS4 insulators fail to protect nkx2.5:mRFP from falling under the control of enhancers in the vicinity of integration site.

Quantitatively increased somatic transposition of transposable elements in Drosophila strains compromised for RNAi

In Drosophila melanogaster, small RNAs homologous to transposable elements (TEs) are of two types: piRNA (piwi-interacting RNA) with size 23-29nt and siRNA (small interfering RNA) with size 19-22nt. The siRNA pathway is suggested to silence TE activities in somatic tissues based on TE expression profiles, but direct evidence of transposition is lacking. Here we developed an efficient FISH (fluorescence in Situ hybridization) based method for polytene chromosomes from larval salivary glands to reveal new TE insertions. Analysis of the LTR-retrotransposon 297 and the non-LTR retroposon DOC shows that in the argonaut 2 (Ago2) and Dicer 2 (Dcr2) mutant strains, new transposition events are much more frequent than in heterozygous strains or wild type strains. The data demonstrate that the siRNA pathway represses TE transposition in somatic cells. Nevertheless, we found that loss of one functional copy of Ago2 or Dcr2 increases somatic transpositions of the elements at a lower level depending on the genetic background, suggesting a quantitative role for RNAi core components on mutation frequency.

Site-specific integration of foreign DNA into minimal bacterial and human target sequences mediated by a conjugative relaxase

BACKGROUND

Bacterial conjugation is a mechanism for horizontal DNA transfer between bacteria which requires cell to cell contact, usually mediated by self-transmissible plasmids. A protein known as relaxase is responsible for the processing of DNA during bacterial conjugation. TrwC, the relaxase of conjugative plasmid R388, is also able to catalyze site-specific integration of the transferred DNA into a copy of its target, the origin of transfer (oriT), present in a recipient plasmid. This reaction confers TrwC a high biotechnological potential as a tool for genomic engineering.

METHODOLOGY/PRINCIPAL FINDINGS

We have characterized this reaction by conjugal mobilization of a suicide plasmid to a recipient cell with an oriT-containing plasmid, selecting for the cointegrates. Proteins TrwA and IHF enhanced integration frequency. TrwC could also catalyze integration when it is expressed from the recipient cell. Both Y18 and Y26 catalytic tyrosil residues were essential to perform the reaction, while TrwC DNA helicase activity was dispensable. The target DNA could be reduced to 17 bp encompassing TrwC nicking and binding sites. Two human genomic sequences resembling the 17 bp segment were accepted as targets for TrwC-mediated site-specific integration. TrwC could also integrate the incoming DNA molecule into an oriT copy present in the recipient chromosome.

CONCLUSIONS/SIGNIFICANCE

The results support a model for TrwC-mediated site-specific integration. This reaction may allow R388 to integrate into the genome of non-permissive hosts upon conjugative transfer. Also, the ability to act on target sequences present in the human genome underscores the biotechnological potential of conjugative relaxase TrwC as a site-specific integrase for genomic modification of human cells.

Recurrent insertion of 5'-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs

A survey of sequence databases revealed 10 instances of subgroup IIB1 mitochondrial ribosomal introns with 1 to 33 additional nucleotides inserted between the 5' exon and the consensus sequence at the intron 5' end. These 10 introns depart further from the IIB1 consensus in their predicted domain VI structure: In contrast to its basal helix and distal GNRA terminal loop, the middle part of domain VI is highly variable and lacks the bulging A that serves as the branchpoint in lariat formation. In vitro experiments using two closely related IIB1 members inserted at the same ribosomal RNA site in the basidiomycete fungi Grifola frondosa and Pycnoporellus fulgens revealed that both ribozymes are capable of efficient self-splicing. However, whereas the Grifola intron was excised predominantly as a lariat, the Pycnoporellus intron, which possesses six additional nucleotides at the 5' end, yielded only linear products, consistent with its predicted domain VI structure. Strikingly, all of the introns with 5' terminal insertions lack the EBS2 exon-binding site. Moreover, several of them are part of the small subset of group II introns that encode potentially functional homing endonucleases of the LAGLIDADG family rather than reverse transcriptases. Such coincidences suggest causal relationships between the shift to DNA-based mobility, the loss of one of the two ribozyme sites for binding the 5' exon, and the exclusive use of hydrolysis to initiate splicing.

Successful targeting and disruption of an integrated reporter lentivirus using the engineered homing endonuclease Y2 I-AniI

Current antiviral therapy does not cure HIV-infected individuals because the virus establishes lifelong latent infection within long-lived memory T cells as integrated HIV proviral DNA. Here, we report a new therapeutic approach that aims to cure cells of latent HIV infection by rendering latent virus incapable of replication and pathogenesis via targeted cellular mutagenesis of essential viral genes. This is achieved by using a homing endonuclease to introduce DNA double-stranded breaks (dsb) within the integrated proviral DNA, which is followed by triggering of the cellular DNA damage response and error-prone repair. To evaluate this concept, we developed an in vitro culture model of viral latency, consisting of an integrated lentiviral vector with an easily evaluated reporter system to detect targeted mutagenesis events. Using this system, we demonstrate that homing endonucleases can efficiently and selectively target an integrated reporter lentivirus within the cellular genome, leading to mutation in the proviral DNA and loss of reporter gene expression. This new technology offers the possibility of selectively disabling integrated HIV provirus within latently infected cells.

Mutation of a degS homologue in Enterobacter cloacae decreases colonization and biological control of damping-off on cucumber

We have been using mutagenesis to determine how biocontrol bacteria such as Enterobacter cloacae 501R3 deal with complex nutritional environments found in association with plants. E. cloacae C10, a mutant of 501R3 with a transposon insertion in degS, was diminished in growth on synthetic cucumber root exudate (SRE), colonization of cucumber seed and roots, and control of damping-off of cucumber caused by Pythium ultimum. DegS, a periplasmic serine protease in the closely related bacterium Escherichia coli K12, is required for the RpoE-mediated stress response. C10 containing wild-type degS from 501R3 or from E. coli K12 on pBeloBAC11 was significantly increased in growth on SRE, colonization of cucumber roots, and control of P. ultimum relative to C10 containing pBeloBAC11 alone. C10 and 501R3 were similar in sensitivity to acidic conditions, plant-derived phenolic compounds, oxidative stress caused by hydrogen peroxide, dessication, and high osmoticum; stress conditions potentially associated with plants. This study demonstrates a role for degS in the spermosphere and rhizosphere during colonization and disease control by Enterobacter cloacae. This study implicates, for the first time, the involvement of DegS and, by extension, the RpoE-mediated stress response, in reducing stress on E. cloacae resulting from the complex nutritional environments in the spermosphere and rhizosphere.

Disruption of Rac1 signaling reduces ischemia-reperfusion injury in the diabetic heart by inhibiting calpain

Diabetes increases myocardial ischemia/reperfusion (I/R) injury. However, the underlying mechanisms remain incompletely understood. This study investigated the role of Rac1 signaling and calpain in exacerbated I/R injury in diabetic hearts. Mice with cardiac-specific deletion of Rac1 (Rac1-ko) and transgenic mice with cardiac-specific superoxide dismutase-2 (SOD2) or calpastatin overexpression were rendered diabetic with streptozotocin. Isolated perfused hearts were subjected to global I/R. After I/R, Rac1 activity was significantly enhanced in diabetic compared with nondiabetic hearts. Diabetic hearts displayed more severe I/R injury than nondiabetic hearts, as evidenced by more lactate dehydrogenase release and apoptosis and decreased cardiac function. These adverse impacts of diabetes were abrogated in Rac1-ko hearts or by perfusion with the Rac1 inhibitor NSC23766. In an in vivo I/R mouse model, infarct size was much smaller in diabetic Rac1-ko compared with wild-type mice. Inhibition of Rac1 signaling prevented NADPH oxidase activation, reactive oxygen species production, and protein carbonyl accumulation, leading to inhibition of calpain activation. Furthermore, SOD2 or calpastatin overexpression significantly reduced I/R injury in diabetic hearts and improved cardiac function after I/R. In summary, Rac1 activation increases I/R injury in diabetic hearts and the role of Rac1 signaling is mediated, at least in part, through calpain activation.

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression.

The influence of rigid or flexible linkage between two ligands on the effective affinity and avidity for reversible interactions with bivalent receptors

Bivalent or polyvalent cooperative binding between ligand and receptor is much tighter and more efficient than monovalent binding of the same counterparts. Because of this, many biological processes involve polyvalent binding for realization of regulatory mechanisms. For this reason it is necessary to develop a general formalism for prediction of the relationship between the binding affinities of each ligand subunits, the length of the flexible linker between them and avidity of the interaction. Here, we consider an approach that is based on the description of the state of equilibrium for the reaction of mono- and multivalent ligand-receptor binding of algebraic equation systems. This approach allows the evaluation of the avidity of bivalent binding and to determine the concentrations of ligand-receptor complexes, which will be obtained at the equilibrium state. The analysis presented here may be useful in analysing the binding behaviour of a bivalent receptor and a ligand consisting of two subunits covalently connected with a rigid or flexible linker.

Discovery and characterization of a novel splice variant of the GM-CSF receptor α subunit

OBJECTIVE

To characterize a novel splice variant of the alpha subunit of the granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor (GMRalpha), which we discovered in human neutrophils.

METHODS

We used reverse transcriptase polymerase chain reaction to identify, characterize, and examine the expression of a novel splice variant of the GMRalpha transcript. At the protein level, surface plasmon resonance was used to measure the affinity of a recombinant soluble form of the novel GMRalpha protein for GM-CSF ligand. The full-length novel GMRalpha protein was expressed in a recombinant cell culture system, and its expression and localization were examined using Western blotting, I(125) GM-CSF binding assays, flow cytometry, and a soluble GMRalpha enzyme-linked immunosorbent assay.

RESULTS

The novel GMRalpha transcript identified herein contains a previously undescribed exon of the GMRalpha gene; this exon derives from an Alu DNA repeat element, and is alternatively spliced in the novel GMRalpha transcript. Inclusion of this 102 nucleotide exon results in translation of a protein product, which we have named Alu-GMRalpha. Alu-GMRalpha is identical to cell surface GMRalpha, but additionally contains a 34 amino-acid insert in the juxtamembrane region of the extracellular domain of GMRalpha. Functionally, the Alu-GMRalpha-specific epitope does not modify the ability of the protein to bind GM-CSF, but rather appears to be preferentially targeted by ectodomain proteases to mediate the release of a third soluble GM-CSF receptor into the extracellular space.

CONCLUSIONS

This study provides the first example of a cytokine receptor system in which soluble receptors are produced by three distinct mechanisms. Our results highlight the importance of soluble GMRalpha proteins in regulation of GM-CSF signaling.

Molecular genetic basis of flower colour variegation inLinaria

To identify transposons that may be of use for mutagenesis we investigated the genetic molecular basis of a case of flower colour variegation inLinaria, a close relative of the model speciesAntirrhinum majus. We show that this variegation is attributable to an unstable mutant allele of the gene encoding dihydroflavonol-4-reductase, one of the enzymes required for anthocyanin biosynthesis. This allele carries an insertion of a transposon belonging to the CACTA family (Tl1, Transposon Linaria 1) which blocks its expression thus conferring an ivory flower colour phenotype. Tl1 is occasionally excised in dividing epidermal cells to produce clonal patches of red tissue on the ivory background, and in cells giving rise to gametes to generate reversion alleles conferring a fully coloured phenotype. This finding may open the way for targeted transposon-mutagenesis inLinaria, and hence for using this genus in comparative genetic studies.

Functional consequences of new exon acquisition in mammalian chromodomain Y-like (CDYL) genes

The origin of new exons is an important mechanism for proteome diversity. Here, we report the recurrent origination of new exons in mammalian chromodomain Y-like (CDYL) genes and the functional consequences associated with the acquisition of the new exons. Driven by positive selection, the newly evolved longer peptide exhibits weaker transcription repression activity and attenuates the repression activity of the old form, suggesting that the acquisition of the new exons is functionally significant.

Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives

We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences of TRIM elements, Br1 and Br2. TRIM display using genomic DNA produced 50-70 bands ranging from 100 to 700 bp in all the species of the family Brassicaceae. TRIM display using B. rapa cDNA produced about 20 bands. Sequences of 11 randomly selected bands, 7 from genomic DNA and 4 from cDNA, begin with about 104 bp of the terminal repeat sequences of TRIM elements Br1 or Br2 and end with unique sequences indicating that all bands are derived from unique insertion sites of TRIM elements. Furthermore, 7 of the 11 unique sequences showed significant similarity with expressed gene. Most of the TRIM display bands were polymorphic between genera and about 55% (132 of 239 bands) are polymorphic among 19 commercial F1 hybrid cultivars. Analysis of phylogenetic relationships shows clear-cut lineage among the 19 cultivars. Furthermore, a combination of 11 polymorphic bands derived from only one primer combination can clearly distinguish one cultivar from the others. TRIM display bands were reproducible and inheritable through successive generations that is revealed by genetic mapping of 6 out of 27 polymorphic TRIM markers on the genetic map of Brassica napus. Collective data provide evidence that TRIM display can provide useful DNA markers in Brassica relatives because these markers are distributed in gene-rich regions, and are sometimes involved in the restructuring of genes.

Infertile Finnish Yorkshire boars carry a full-length LINE-1 retrotransposon within the KPL2 gene

The KPL2 gene is expressed predominantly in cells with cilia or flagella. We have previously demonstrated that a large intronic insertion in KPL2 is associated with immotile sperm cells and infertility in the domesticated pig (Sus scrofa). To fully characterize the structure of the mutation, we have now cloned and sequenced the insertion. The data identified the presence of a long interspersed nuclear element-1 (LINE-1) encoding all activities required for retrotransposition, including a 5'-untranslated region (UTR) with an internal RNA polymerase II promoter, two open reading frames (ORF1 and ORF2) separated by an intergenic region and a 3' UTR containing a polyadenylation signal. Characterization of the junctions between the LINE-1 and the genomic target revealed the presence of direct repeats of 14 bp at both ends, showing that integration occurred by target-primed reverse transcription. Furthermore, sequence analysis suggested that the aberrant splicing pattern of KPL2 transcripts induced by the LINE-1 element is caused by interference with putative intronic splice signals and activation of a cryptic splice site. These data demonstrate that integration of a transposition-competent L1 element into KPL2 is responsible for the defective spermatozoa, which accentuates the role of mobile DNA elements as insertional mutagens in mammalian genomes.

Molecular analysis of Agrobacterium T-DNA integration in tomato reveals a role for left border sequence homology in most integration events

Studies in several plants have shown that Agrobacterium tumefaciens T-DNA can integrate into plant chromosomal DNA by different mechanisms involving single-stranded (ss) or double-stranded (ds) forms. One mechanism requires sequence homology between plant target and ssT-DNA border sequences and another double-strand-break repair in which preexisting chromosomal DSBs "capture" dsT-DNAs. To learn more about T-DNA integration in Solanum lycopersicum we characterised 98 T-DNA/plant DNA junction sequences and show that T-DNA left border (LB) and right border transfer is much more variable than previously reported in Arabidopsis thaliana and Populus tremula. The analysis of seven plant target sequences showed that regions of homology between the T-DNA LB and plant chromosomal DNA plays an important role in T-DNA integration. One T-DNA insertion generated a target sequence duplication that resulted from nucleolytic processing of a LB/plant DNA heteroduplex that generated a DSB in plant chromosomal DNA. One broken end contained a captured T-DNA that served as a template for DNA repair synthesis. We propose that most T-DNA integrations in tomato require sequence homology between the ssT-DNA LB and plant target DNA which results in the generation of DSBs in plant chromosomal DNA.

The role and aims of the FYSSION project

FYSSION is a resource for researchers working on the fission yeast Schizosaccharomyces pombe. It currently comprises libraries of temperature-sensitive mutants in essential genes, and insertional mutants in non-essential genes, available for screening by visiting workers. Here we outline methods for constructing and using the libraries, and describe future prospects for functional genomics of this organism, here and elsewhere.

Somatic microindels: analysis in mouse soma and comparison with the human germline

Microindels, defined as mutations that result in a colocalized microinsertion and microdeletion with a net gain or loss of between 1 and 50 nucleotides, may be an important contributor to cancer. We report the first comprehensive analysis of somatic microindels. Our large database of mutations in the lacI transgene of Big Blue((R)) mice contains 0.5% microindels, 2.8% pure microinsertions, and 11.5% pure microdeletions. There appears to be no age, gender, or tissue-type specificity in the frequency of microindels. Of the independent somatic mutations that result in a net in-frame insertion or deletion, microindels are responsible for 13% of protein expansions and 6% of protein contractions. These in-frame microindels may play a crucial role in oncogenesis and evolution via "protein tinkering" (i.e., modest expansion or contraction of proteins). Four characteristics suggest that microindels are caused by unique mechanisms, not just simple combinations of the same mechanisms that cause pure microinsertions and pure microdeletions. First, microinsertions and microdeletions commonly occur at hotspots, but none of the 30 microindels are recurrent. Second, the sizes of the deletions and insertions in microindels are larger and more varied than in pure microdeletions and pure microinsertions. Third, microinsertions overwhelmingly repeat the adjacent base (97%) while the insertions in microindels do so only infrequently (17%). Fourth, analysis of the sequence contexts of microindels is consistent with unique mechanisms including recruitment of translesion DNA synthesis polymerases. The mouse somatic microindels have characteristics similar to those of human germline microindels, consistent with similar causative mechanisms in mouse and human, and in soma and germline.

Agrobacterium-mediated insertional mutagenesis of the ochratoxigenic fungus Aspergillus westerdijkiae

Aspergillus westerdijkiae is a potent ochratoxin A (OTA) producer that has been found in coffee beans. OTA is known to have nephrotoxic effects and carcinogenic potential in animal species. Here we report for the first time the Agrobacterium-mediated transformation for Aspergillus westerdijkiae and the generation of ochratoxin-defective mutants. Conidia were transformed to hygromycin B resistance using strain AGL-1 of Agrobacterium tumefaciens. The obtained transformation frequency was up to 47 transformants per 106 target conidia. Among 600 transformants, approximately 5% showed morphological variations. Eight transformants with consistently reduced OTA production were obtained. Two of these transformants did not produce OTA (detection limit: 0.1 µg/kg); the other six mutants produced lower amounts of OTA (1%–32%) compared with the wild-type strain. By using thermal asymmetric interlaced polymerase chain reaction, we successfully identified a putative flavin adenine dinucleotide monooxygenase gene.Key words: Aspergillus ochraceus, Aspergillus westerdijkiae, Agrobacterium-mediated transformation, Agrobacterium-mediated insertional mutagenesis, ochratoxin A.

The insertion of a full-length Bos taurus LINE element is responsible for a transcriptional deregulation of the Normande Agouti gene

Mammalian pigmentation is controlled by the concerted action of Tyr, Tyrp1 and Dct producing eumelanin and/or pheomelanin in melanocytes. The ratio of these two pigments is determined by the agonist alpha-melanocyte stimulating hormone and the antagonist Agouti protein acting on the Mc1r. Here we show that the Agouti gene is over-expressed in Normande breed compared with Prim'Holstein breed. The Normande cattle have a characteristic coat color phenotype with a variable presence of black (eumelanin) hair over a red/brown background. We have found a previously undescribed full-length L1-BT element inserted in the 5'-genomic sequence of the Agouti gene in Normande cattle which promotes the over-expression of alternative transcripts. The variable expression of the alternative transcript directed by the long interspersed nuclear element promoter may be the origin of the brindle coat color pattern of the Normande breed. This new bovine Agouti allele isolated in Normande breed has been named Abr. Finally, as ectopic over-expression of Agouti in Ay mice is responsible for the obesity syndrome, we discuss the possible consequences of Abr for meat and milk production in cattle.

Tracking ancient polyploids: a retroposon insertion reveals an extinct diploid ancestor in the polyploid origin of belladonna

Polyploidy is a prominent process in plant evolution and adaptation, but molecular phylogenetic studies of polyploids based on DNA sequences have often been confounded by their complex gene and genome histories. We report here a retroposon insertion in the nuclear gene granule-bound starch synthase I (GBSSI or "waxy") that clearly reveals the ancient hybrid history of the medically important polyploid species belladonna (Atropa belladonna) and resolves the controversy over the taxonomic group to which it belongs, the tribe Hyoscyameae (Solanaceae). Our inferences based on the pattern of presence or absence of the retroposon insertion are corroborated by phylogenetic analyses of the GBSSI gene sequences. This case may suggest that retroposons are promising molecular markers to study polyploid evolution.

A diversity of serine phage integrases mediate site-specific recombination in mammalian cells

This study evaluated the ability of five serine phage integrases, from phages A118, U153, Bxb1, phiFC1, and phiRV1, to mediate recombination in mammalian cells. Two types of recombination were investigated, including the ability of an integrase to mediate recombination between its own phage att sites in the context of a mammalian cell and the ability of an integrase to perform genomic integration pairing a phage att site with an endogenous mammalian sequence. We demonstrated that the A118 integrase mediated precise intra-molecular recombination of a plasmid containing its attB and attP sites at a frequency of approximately 50% in human cells. The closely related U153 integrase also performed efficient recombination in human cells on a plasmid containing the attB and attP sites of A118. The integrases from phages Bxb1, phiFC1, and phiRV1 carried out such recombination at their attB and attP sites at frequencies ranging from 11 to 75%. Furthermore, the A118 integrase mediated recombination between its attP site on a plasmid and pseudo attB sites in the human genome, i.e. native sequences with partial identity to attB. Fifteen such A118 pseudo att sites were analyzed, and a consensus recognition site was identified. The other integrases did not mediate integration at genomic sequences at a frequency above background. These site-specific integrases represent valuable new tools for manipulating eukaryotic genomes.

Heterogeneity in synaptic transmission along a Drosophila larval motor axon

At the Drosophila melanogaster larval neuromuscular junction (NMJ), a motor neuron releases glutamate from 30-100 boutons onto the muscle it innervates. How transmission strength is distributed among the boutons of the NMJ is unknown. To address this, we created synapcam, a version of the Ca2+ reporter Cameleon. Synapcam localizes to the postsynaptic terminal and selectively reports Ca2+ influx through glutamate receptors (GluRs) with single-impulse and single-bouton resolution. GluR-based Ca2+ signals were uniform within a given connection (that is, a given bouton/postsynaptic terminal pair) but differed considerably among connections of an NMJ. A steep gradient of transmission strength was observed along axonal branches, from weak proximal connections to strong distal ones. Presynaptic imaging showed a matching axonal gradient, with higher Ca2+ influx and exocytosis at distal boutons. The results suggest that transmission strength is mainly determined presynaptically at the level of individual boutons, possibly by one or more factors existing in a gradient.

Gene therapy for lympho-hematopoietic disorders

Inherited lympho-hematopoietic disorders are considered to be some of the most amenable targets for development of gene therapy because of their defined molecular biology and pathophysiology and the potential for corrected cells to exhibit profound growth and survival advantages. Recently, several clinical studies have shown that conventional gene transfer technology can produce major beneficial therapeutic effects.

A mutation in the Icsbp1 gene causes susceptibility to infection and a chronic myeloid leukemia-like syndrome in BXH-2 mice

BXH-2 mice develop a fatal myeloid leukemia by a two-step mutagenic process. First, a BXH-2-specific recessive mutation causes a myeloproliferative syndrome. Second, retroviral insertions alter oncogenes or tumor suppressors, resulting in clonal expansion of leukemic cells. We have identified a recessive locus on chromosome 8 (Myls) that is responsible for myeloproliferation in BXH-2. This Myls interval has been narrowed down to 2 Mb and found to contain several positional candidates, including the interferon consensus sequence-binding protein 1 gene (Icsbp, also known as interferon regulatory factor 8 [IRF8]). We show that BXH-2 mice carry a mutation (915 C to T) resulting in an arginine-to-cysteine substitution at position 294 within the predicted IRF association domain of the protein. Although expression of Icsbp1 mRNA transcripts is normal in BXH-2 splenocytes, these cells are unable to produce interleukin 12 and interferon-gamma in response to activating stimuli, confirming that R294C behaves as a loss-of-function mutation. Myeloproliferation in BXH-2 mice is concomitant to increased susceptibility to Mycobacterium bovis (BCG) despite the presence of resistance alleles at the Nramp1 locus. These results suggest a two-step model for chronic myeloid leukemia in BXH-2, in which inactivation of Icsbp1 predisposes to myeloproliferation and immunodeficiency. This event is required for retroviral replication, and subsequent insertional mutagenesis that causes leukemia in BXH-2 mice.

Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase, due to 4-bp insertions in the gene

Bright blue or red flowers in the Japanese morning glory (Ipomoea nil) contain anthocyanidin 3-O-sophoroside derivatives, whereas the reddish-brown or purplish-gray petals in its dusky mutants accumulate anthocyanidin 3-O-glucoside derivatives. The Dusky gene was found to encode a novel glucosyltransferase, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase (3GGT), which mediates the glucosylation of anthocyanidin 3-O-glucosides to yield anthocyanidin 3-O-sophorosides. Ipomoea nil carries one copy of the 3GGT gene that contains no intron and produces 1.6-kbp transcripts mainly in the petals and tubes of flower buds at around 24 h before flower opening. The gene products of both In3GGT in I. nil and Ip3GGT in the common morning glory (Ipomoea purpurea) comprise 459 amino acids and showed a close relationship to the petunia UDP-rhamnose:anthocyanidin 3-O-glucoside-6''-O-rhamnosyltransferase (3RT), which controls the addition of a rhamnose molecule to anthocyanidin 3-O-glucosides for conversion into anthocyanidin 3-O-rutinosides. All of the 30 dusky mutants tested were found to carry the 4-bp insertion mutations GGAT or CGAT at an identical position near the 3' end of the gene, and the insertions caused frameshift mutations. The expected 3GGT enzymatic activities were found in the crude extracts of Escherichia coli, in which the 3GGT cDNA of I. nil or I. purpurea was expressed, while no such activity was detected in the extracts expressed with the dusky mutant cDNAs containing 4-bp insertions. Moreover, the introduced Ip3GGT cDNA efficiently produced 3GGT that converted cyanidin 3-O-glucoside into cyanidin 3-O-sophoroside in transgenic petunia plants.

Pinocchio, a novel protein expressed in the antenna, contributes to olfactory behavior inDrosophila melanogaster

Most organisms depend on chemoreception for survival and reproduction. In Drosophila melanogaster multigene families of chemosensory receptors and putative odorant binding proteins have been identified. Here, we introduce an additional distinct protein, encoded by the CG4710 gene, that contributes to olfactory behavior. Previously, we identified through P[lArB]-element mutagenesis a smell impaired (smi) mutant, smi21F, with odorant-specific defects in avoidance responses. Here, we show that the smi21F mutant also exhibits reduced attractant responses to some, but not all, of a select group of odorants. Furthermore, electroantennogram amplitudes are increased in smi21F flies. Characterization of flanking sequences of the P[lArB] insertion site, complementation mapping, phenotypic reversion through P-element excision, and expression analysis implicate a predicted gene, CG4710, as the candidate smi gene. CG4710 produces two transcripts that encode proteins that contain conserved cysteines and which are reduced in the smi21F mutant. Furthermore, in situ hybridization reveals CG4710 expression in the third antennal segment. We have named this gene of previously unknown function and its product "Pinocchio (Pino)".

Retroviral DNA integration--mechanism and consequences

Integration of retroviral cDNA into the host cell chromosome is an essential step in its replication. This process is catalyzed by the retroviral integrase protein, which is conserved among retroviruses and retrotransposons. Integrase binds viral and host DNA in a complex, called the preintegration complex (PIC), with other viral and cellular proteins. While the PIC is capable of directing integration of the viral DNA into any chromosomal location, different retroviruses have clear preferences for integration in or near particular chromosomal features. The determinants of integration site selection are under investigation but may include retrovirus-specific interactions between integrase and tethering factors bound to the host cell chromosomes. Research into the mechanisms of retroviral integration site selection has shed light on the phenomena of insertional mutagenesis and viral latency.

Histidine 518 in the S6-CNBD linker controls pH dependence and gating of HCN channel from sea-urchin sperm

Sperm motility is a tightly regulated process. One of the crucial factors determining the swimming of the sea-urchin sperm is an elevation of intracellular pH (pH(i)). The possibility that its hyperpolarisation-activated cyclic nucleotide-gated channel (SpHCN) is modulated directly by pH is addressed here. Site-directed mutagenesis showed that histidine 518 from the linker connecting the S6 helix with the cyclic nucleotide binding domain is responsible for the pH modulation of current kinetics and voltage dependence of activation. The effect of mutating histidine 518 to serine (H518S) on the time constant of activation was maximal at pH 6.4: 180+/-20 ms in the wild-type (wt) but only 56+/-10 ms in the H518S mutant channel. Furthermore, histidine 518 accounted for 31% of the shift in the voltage of half activation ( V(1/2)) in wt following a pH change from 6.4 to 8.4. The mutation H518S also shifted V(1/2) by 19 mV at pH 7.4 (-50.2+/-0.2 and -69+/-2 mV for H518S and wt, respectively). This indicates that histidine 518 couples voltage sensing to gating. The wt and H518S channels had a different affinity for cyclic adenosine monophosphate (cAMP) (IC(50) 1.0+/-0.02 and 2.5+/-0.06 microM, respectively). Changes in pH(i) also modulated channel selectivity.

Regulation of icaR gene expression in Staphylococcus epidermidis

LightCycler and conventional reverse transcription-polymerase chain reaction (RT-PCR) were used to examine regulation of icaR, which encodes a repressor of the Staphylococcus epidermidis ica operon. Varying concentrations of NaCl and ethanol activated ica but only high levels of both compounds repressed icaR transcription. Activation of ica by subinhibitory concentrations of tetracycline, which was strain-dependent, was also associated with icaR repression. In an ICAR::Em mutant, NaCl but not ethanol activated ica whereas both compounds repressed icaR expression indicating that environmental regulation of the icaR gene is IcaR-independent. Apparently ethanol signals exclusively through IcaR to activate ica and regulates IcaR at the transcriptional and posttranscriptional levels. NaCl also regulates icaR expression but in addition can activate ica via an icaR-independent pathway.

Targeted insertion results in a rhombomere 2-specific Hoxa2 knockdown and ectopic activation of Hoxa1 expression

Recent studies indicated that retention of selectable marker cassettes in targeted Hox loci may cause unexpected phenotypes in mutant mice, due to neighborhood effects. However, the molecular mechanisms have been poorly investigated. Here, we analysed the effects of the targeted insertion of a PGK-neo cassette in the 3' untranslated region of Hoxa2. Even at this 3' position, the insertion resulted in homozygous mutants that unexpectedly did not survive beyond 3 weeks of age. Molecular analysis of the targeted allele revealed a selective "knockdown" of Hoxa2 expression in rhombomere 2 and associated patterning abnormalities. Moreover, Hoxa1 was ectopically expressed in the hindbrain and branchial arches of mutant embryos. Of interest, we demonstrated that the ectopic expression was due to the generation of neo-Hoxa1 fusion transcripts, resulting from aberrant alternative splicing. These defects could be rescued after removal of the PGK-neo cassette by Flp-mediated recombination. These results underscore the complexity of transcriptional regulation at Hox loci and provide insights into the in vivo regulation of Hoxa2 segmental expression. They also provide a molecular basis for the interpretation of unexpected Hox knockout phenotypes in which the targeted selectable marker is retained in the locus.

Microarray transcription profiling of a Shewanella oneidensis etrA mutant

DNA microarrays were used to examine the effect of an insertional mutation in the Shewanella oneidensis etrA (electron transport regulator) locus on gene expression under anaerobic conditions. The mRNA levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an etrA-mutant genetic background. This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1.

icaR encodes a transcriptional repressor involved in environmental regulation of ica operon expression and biofilm formation in Staphylococcus epidermidis

Biofilm formation in Staphylococcus epidermidis is dependent upon the ica operon-encoded polysaccharide intercellular adhesin, which is subject to phase-variable and environmental regulation. The icaR gene, located adjacent to the ica operon, appears to be a member of the tetR family of transcriptional regulators. In the reference strain RP62A, reversible inactivation of the ica operon by IS256 accounts for 25 to 33% of phase variants. In this study, icaA and icaR regulation were compared in RP62A and a biofilm-forming clinical isolate, CSF41498, in which IS256 is absent. Predictably, ica operon expression was detected only in wild-type CSF41498 and RP62A but not in non-IS256-generated phase variants. In contrast, the icaR gene was not expressed in RP62A phase variants but was expressed in CSF41498 variants. An icaR::Em(r) insertion mutation in CSF41498 resulted in an at least a 5.8-fold increase in ica operon expression but did not significantly alter regulation of the icaR gene itself. Activation of ica operon transcription by ethanol in CSF41498 was icaR dependent. In contrast, a small but significant induction of ica by NaCl and glucose (NaCl-glucose) was observed in the icaR::Em(r) mutant. In addition, transcription of the icaR gene itself was not significantly affected by NaCl-glucose but was repressed by ethanol. Expression of the ica operon was induced by ethanol or NaCl-glucose in phase variants of CSF41498 (icaR+) but not in RP62A variants (icaR deficient). These data indicate that icaR encodes a repressor of ica operon transcription required for ethanol but not NaCl-glucose activation of ica operon expression and biofilm formation.

The malate dehydrogenase of Ralstonia eutropha and functionality of the C(3)/C(4) metabolism in a Tn5-induced mdh mutant

The Tn5-induced mutant VG12 of Ralstonia eutropha HF39, which was isolated in this study, revealed an interesting phenotype: it grew on fructose and pyruvate as well as autotrophically like the wild-type, whereas growth on tricarboxylic acid intermediates and glyoxylic acid was reduced, and no growth occurred if acetate, propionate or levulinate were provided as carbon source. Tn5 was mapped in a gene encoding an NAD(H)-dependent malate dehydrogenase (MDH), and MDH activity was strongly diminished in VG12. Furthermore, the mdh gene was cloned, sequenced and heterologously expressed in Escherichia coli, conferring significantly higher specific MDH activity to the recombinant strain. The phenotype of VG12 sheds light on the C(3)/C(4) metabolism of R. eutropha, which mediates between the Entner-Doudoroff pathway and the tricarboxylic acid cycle (TCC), demonstrating that enzymes catalyzing the conversion of C(3) and C(4) metabolites can circumvent the metabolic disruption of the TCC in VG12 and that the phosphoenolpyruvate carboxykinase serves a dual and important function.

Functional role of the prokaryotic proline-tRNA synthetase insertion domain in amino acid editing

Aminoacyl-tRNA synthetases catalyze the attachment of specific amino acids to cognate tRNAs in a two-step process that is critical for the faithful translation of genetic information. During the first chemical step of tRNA aminoacylation, noncognate amino acids that are smaller than or isosteric with the cognate substrate can be misactivated. Thus, to maintain high accuracy during protein translation, some synthetases have evolved an editing mechanism. Previously, we showed that class II Escherichia coli proline-tRNA synthetase (ProRS) is capable of (1) weakly misactivating Ala, (2) hydrolyzing the misactivated Ala-AMP in a reaction known as pretransfer editing, and (3) deacylating a mischarged Ala-tRNA(Pro) variant via a post-transfer editing pathway. In contrast to most systems where an editing function has been established, pretransfer editing by E. coli ProRS occurs in a tRNA-independent fashion. However, neither the pre- nor the post-transfer editing active site(s) has been identified. Sequence analyses revealed that most prokaryotic ProRSs possess a large insertion domain (INS) between class II conserved motifs 2 and 3. The function of the approximately 180-amino acid INS in E. coli ProRS is the subject of this investigation. Alignment-guided Ala scanning mutagenesis was carried out to test conserved amino acid residues present in the INS for their role in pre- and post-transfer editing. Our biochemical data and modeling studies suggest that the prokaryotic INS plays a critical role in editing and that this activity resides in a domain that is functionally and structurally distinct from the aminoacylation active site.

Disruption of the alpha5 helix of transducin impairs rhodopsin-catalyzed nucleotide exchange

Photoactivated rhodopsin (R) catalyzes nucleotide exchange by transducin, the heterotrimeric G protein of the rod cell. Recently, we showed that certain alanine replacement mutants of the alpha5 helix of the alpha subunit of transducin (Galpha(t)) displayed very rapid nucleotide exchange rates even in the absence of R [Marin, E. P., Krishna, A. G., and Sakmar, T. P. (2001) J. Biol. Chem. 276, 27400-27405]. We suggested that R catalyzes nucleotide exchange by perturbing residues on the alpha5 helix. Here, we characterize deletion, insertion, and proline replacement mutants of amino acid residues in alpha5. In general, the proline mutants exhibited rates of uncatalyzed nucleotide exchange that were 4-8-fold greater than wild type. The proline mutants also generally displayed decreased rates of R-catalyzed activation. The degree of reduction of the activation rate correlated with the position of the residue replaced with proline. Mutants with replacement of residues at the amino terminus of alpha5 exhibited mild (<2-fold) decreases, whereas mutants with replacement of residues at the carboxyl terminus of alpha5 were completely resistant to R-catalyzed activation. In addition, insertion of a single helical turn in the form of four alanine residues following Ile339 at the carboxyl terminus of alpha5 prevented R-catalyzed activation. Together, the results provide evidence that alpha5 serves an important function in mediating R-catalyzed nucleotide exchange. In particular, the data suggest the importance of the connection between the alpha5 helix and the adjacent carboxyl-terminal region of Galpha(t).

The intraflagellar transport protein, IFT88, is essential for vertebrate photoreceptor assembly and maintenance

Approximately 10% of the photoreceptor outer segment (OS) is turned over each day, requiring large amounts of lipid and protein to be moved from the inner segment to the OS. Defects in intraphotoreceptor transport can lead to retinal degeneration and blindness. The transport mechanisms are unknown, but because the OS is a modified cilium, intraflagellar transport (IFT) is a candidate mechanism. IFT involves movement of large protein complexes along ciliary microtubules and is required for assembly and maintenance of cilia. We show that IFT particle proteins are localized to photoreceptor connecting cilia. We further find that mice with a mutation in the IFT particle protein gene, Tg737/IFT88, have abnormal OS development and retinal degeneration. Thus, IFT is important for assembly and maintenance of the vertebrate OS.

Calcium/calmodulin-dependent protein kinase IIbeta isoform is expressed in motor neurons during axon outgrowth and is part of slow axonal transport

Previously, we identified calcium/calmodulin-dependent protein kinase IIbeta (CaMKIIbeta) mRNA in spinal motor neurons with 372 bp inserted in what corresponds to the "association" domain of the protein. This was interesting because known additions and deletions to CaMKIIbeta mRNA are usually less than 100 bp in size and found in the "variable" region. Changes in the association domain of CaMKIIbeta could influence substrate specificity, activity or intracellular targeting. We show that three variations of this insert are found in CNS neurons or sciatic motor neurons of Sprague-Dawley rats. We used PCR and nucleic acid sequencing to identify inserts of 114, 243, or 372 bases. We also show that addition of the 372 bases is associated with outgrowth of the axon (the standard CaMKIIbeta downregulates when axon outgrowth occurs). Radiolabeling, immunoblots, and 2D PAGE identified this larger CaMKIIbeta as part of the group of soluble proteins moving at the slowest rate of axonal transport (SCa) in sciatic motor neurons (similar1 mm/day). This group is composed mainly of structural proteins (e.g., tubulin) used to assemble the cytoskeleton of regrowing axons.

Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes

We recently reported a novel transposition system in which two retroelements from Drosophila melanogaster, ZAM and Idefix, are highly mobilized and preferentially insert within intergenic regions. Among the loci where new copies are detected, a hot spot for their insertion was identified at the white locus, where up to three elements occurred within a 3-kb fragment upstream of the transcriptional start site of white. We have used these insertions as molecular entry points to throw light on the mutagenic effect exerted by multiple insertions of retrotransposons within intergenic regions of a genome. Analysis of the molecular mechanisms by which ZAM and Idefix elements interfere with the regulation of the white gene has shown that ZAM bears cis-acting regulatory sequences able to enhance transcription of the white gene in the eyes of the flies. This activation may be counteracted by Idefix, which acts as an insulator able to isolate the white gene from the upstream ZAM enhancer. In addition to revealing a novel insulator sequence with its own specific features, our data clearly illustrate how retroelements can act as epigenetic factors able to interfere with the transcriptional regulation of their host.

Mile-high view of plant biology

A report on Plant Biology 2002, the annual meeting of the American Society of Plant Biologists, Denver, USA, 3-7 August 2002.

In vitro adaptation of a ligase ribozyme for activity under a low-pH condition

A ligase ribozyme accelerating a ligation reaction with oligonucleotide under a low-pH condition was selected by in vitro adaptation. A ribozyme active at pH 7 was randomly mutated, and the resultant RNA library was subjected to in vitro adaptation under a low-pH reaction condition. At pH 4, the adapted RNAs reacted with the oligonucleotide substrates about 200 times faster than the original ribozyme. When the ribozyme was cloned and sequenced, 10 of the 30 clones sequenced had identical sequences. The differences in sequence from the original ribozyme were found at four positions in the middle region and at the 3' end. A few sequential differences dominated the activity of the ribozyme under the extreme condition. The adapted ribozyme had one repeating sequence that was critical for the activity.

Molecular mycology: a genetic toolbox for Histoplasma capsulatum

Research in medical mycology has traditionally been a mix of exciting biology and frustrating genetics, although the excitement has been steadily increasing as genetic obstacles have been successfully overcome. Now, a variety of fungal pathogens can be studied using molecular techniques derived from classical bacterial and yeast genetics, but with selective and strategic adaptations. Histoplasma capsulatum is the best-studied of the primary pathogens known as 'dimorphic' fungi, and tailored molecular genetic strategies are beginning to reveal a repertoire of genes and gene products intimately associated with pathogenesis.

The bld1 mutation identifies the Chlamydomonas osm-6 homolog as a gene required for flagellar assembly

Insertional mutagenesis procedures in Chlamydomonas have facilitated the identification and characterization of dozens of genes required for the assembly and motility of flagella in Chlamydomonas. Many of these genes have been found to have homologs in animal systems. Here we describe a new gene required for flagellar assembly. Null mutants at the BLD1 locus assemble no flagella, and the flagellar membrane abuts the end of the transition zone distal to the basal body. Unlike mutants with basal body ultrastructural defects, such as bld2, bld1 mutants have normal basal bodies and cytoplasmic microtubule rootlets. The wild-type BLD1 gene was cloned by using DNA flanking the site of insertion of plasmid DNA in an insertional mutant; the cloned gene rescues the bld1 mutant phenotype upon transformation. The predicted BLD1 gene product is a 50.4 kDa protein with extensive regions of sequence similarity to the osm-6 gene of Caenorhabditis elegans whose product is necessary for the assembly of a set of sensory cilia. The protein product of the BLD1 gene corresponds to IFT52, a protein component of "raft" particles shown to undergo rapid transport up and down Chlamydomonas flagella between the flagellar membrane and the axoneme in a process known as intraflagellar transport (IFT). The BLD1 RNA transcript is upregulated upon flagellar amputation, as observed for many other genes encoding flagellar proteins. These results demonstrate that the function of the IFT52 protein in Chlamydomonas is essential for the assembly and/or maintenance of the flagella.

The transmembrane protein Off-track associates with Plexins and functions downstream of Semaphorin signaling during axon guidance

The Plexin family of transmembrane proteins appears to function as repulsive receptors for most if not all Semaphorins. Here, we use genetic and biochemical analysis in Drosophila to show that the transmembrane protein Off-track (OTK) associates with Plexin A, the receptor for Sema 1a, and that OTK is a component of the repulsive signaling response to Semaphorin ligands. In vitro, OTK associates with Plexins. In vivo, mutations in the otk gene lead to phenotypes resembling those of loss-of-function mutations of either Sema1a or PlexA. The otk gene displays strong genetic interactions with Sema1a and PlexA, suggesting that OTK and Plexin A function downstream of Sema 1a.

Within-intron correlation with base composition of adjacent exons in different genomes

Within-intron difference of correlation with base composition of the adjacent exons was studied in the genomes of 34 species. For this purpose, GC-percent was determined for segments of 50 bp in length taken at both intron margins and in the internal part of the intron. It was found that in certain genomes the coefficient of correlation with GC-percent of the adjacent exon was significantly higher for the intron margin than for the internal part of the intron (homeotherms, cereals). Only part of this difference can be explained by unequal probability of insertion of transposable elements. Those multicellular organisms which have a low or no within-intron difference in correlation with the adjacent exons (anamniotes, invertebrates, dicots) show a higher local compositional heterogeneity (a greater exon/intron contrast in the GC-content). These results are evidence against the mutational bias being a possible explanation for the compositional genome heterogeneity. Thus, in the genomes with a high global heterogeneity there seems to be a selective force for compliance of intron base composition with the adjacent exons. This force is stronger in those parts of the intron that are closer to exons. In addition, the previously found positive general correlation between the genome size and average intron length was confirmed with a much larger dataset. However, within separate phylogenetic groups this rule can be broken, as it occurs in the cereals (family Poaceae), where a negative correlation was found.

Functional analysis of the Saccharomyces cerevisiae YFR021w/YGR223c/YPL100w ORF family suggests relations to mitochondrial/peroxisomal functions and amino acid signalling pathways

Saccharomyces cerevisiae YFR021w, YGR223c and YPL100w are paralogous ORFs of unknown function. Phenotypic analysis of overexpression, single-, double- and triple-ORF deletion strains under various growth conditions indicated mitochondria-related functions for all three ORFs. Two-hybrid screens of a yeast genomic library identified potentially interacting proteins for the three ORFs. Among these, the transcriptional activator Rtg3p interacted with both Yfr021wp and Ypl100wp and both ORF single deletions reduced the constitutive expression of the RTG-regulated CIT2 and DLD3 genes and caused typical retrograde response of CIT2 and DLD3 under growth conditions requiring functional mitochondria, indicating that YFR021w and YPL100w are also involved in unidentified mitochondrial functions. Ptr3p, a component of the amino acid sensor Ssy1p/Ptr3p, was also found as a two-hybrid interactant of Yfr021wp. Of the three single-ORF deletions, ypl100w Delta exhibited ptr3 Delta-similar phenotypes. These findings, combined with the fact that RTG-dependent expression is modulated by specific amino acids, suggested possible relations of Yfr021wp and Ypl100wp to amino acid signalling pathways. Under most conditions examined, the effects of the single- and double-ORF deletions indicated that YFR021w, YPL100w and YGR223c are not parts of the same pathway. We found no unique phenotype attributed to the deletion of YGR223c. However, its function interferes with the function of the other two ORFs, as revealed by the effects of double- and triple-ORF deletions.

beta-Catenin controls hair follicle morphogenesis and stem cell differentiation in the skin

beta-Catenin is an essential molecule in Wnt/wingless signaling, which controls decisive steps in embryogenesis. To study the role of beta-catenin in skin development, we introduced a conditional mutation of the gene in the epidermis and hair follicles using Cre/loxP technology. When beta-catenin is mutated during embryogenesis, formation of placodes that generate hair follicles is blocked. We show that beta-catenin is required genetically downstream of tabby/downless and upstream of bmp and shh in placode formation. If beta-catenin is deleted after hair follicles have formed, hair is completely lost after the first hair cycle. Further analysis demonstrates that beta-catenin is essential for fate decisions of skin stem cells: in the absence of beta-catenin, stem cells fail to differentiate into follicular keratinocytes, but instead adopt an epidermal fate.