Lamelza, Piero et al. (2015) International Worm Meeting "Hybrid Incompatibility in Caenorhabditis nouraguensis."

Ailion, Michael, Young, Janet, Malik, Harmit, Lamelza, Piero

[International Worm Meeting, 2015]

Understanding the cause of reproductive barriers that demarcate species (e.g. hybrid lethality and sterility), is essential for understanding the process of speciation. We have recently discovered a lethal incompatibility between two distinct wild-isolates (JU1825 and NIC59) of Caenorhabditis nouraguensis. Embryonic death seems to be the result of a maternally inherited cytoplasmic factor from each strain being incompatible with a recessive nuclear gene from the other. To preclude the possibility that maternally inherited endosymbiotic bacteria cause the incompatibility, we have treated both strains with tetracycline for nine generations and shown that hybrid death is unaffected. We hypothesize that the maternally inherited factor is the mitochondrial genome and that mitochondrial dysfunction underlies hybrid death. We performed Illumina sequencing on these two strains and have generated the first genomic assemblies of C. nouraguensis. We have mapped the nuclear incompatibility loci to single chromosomes by bulk sequencing of viable F2 hybrids. We are currently genotyping introgression lines to more finely resolve these loci. Additionally, the NIC59 and JU1825 mitochondrial genomes differ by 95 SNPs and a 1 bp indel, with strong candidate polymorphisms in the cysteine tRNA gene, 16s rRNA gene and non-synonymous changes in the nd-1 and cox-1 genes (subunits of complex I and IV of the electron transport chain). Interestingly, NIC59 has a heteroplasmic 184 bp deletion that is predicted to result in a 122 a.a. C-terminal truncation of the nd-5 gene (subunit of complex I), reminiscent of a heteroplasmic deletion in the same gene seen in C. briggsae. We are also characterizing the mechanism of hybrid embryonic lethality. Incompatible hybrid embryos exhibit gross defects during the lima-bean stage and fail to undergo proper epidermal enclosure, resulting in ventral explosion and death. This phenotype is similar to C. elegans mutants with deficiencies in actin cytoskeletal regulation and cell-cell adhesion. Therefore, we will assay these cellular processes in inviable hybrids. .

Lamelza, Piero et al. (2013) International Worm Meeting "If we have children together, will they be less fit? Hybrid incompatibilities in Caenorhabditis species."

Lamelza, Piero, Cattin, Jerome, Ailion, Michael, Wilson, Vanessa, Topalidou, Irini

[International Worm Meeting, 2013]

Speciation often occurs by the accumulation of genetic incompatibilities between populations. We are studying the genetic basis of hybrid incompatibility in several Caenorhabditis species. In C. elegans, hybrid incompatibility between the Bristol and Hawaiian strains is mediated by the peel-1/zeel-1 genetic element. peel-1 encodes a sperm-expressed toxin and zeel-1 encodes its zygotically-expressed antidote. We are interested in determining the cellular mechanism of PEEL-1 toxicity. To identify other factors required for PEEL-1 toxicity, we conducted a screen for suppressors of ectopic PEEL-1 driven by a heat-shock promoter. Thus far, we have isolated five suppressors. The strongest suppressor fully suppresses PEEL-1 toxicity and is not allelic to the heat-shock transcription factor gene hsf-1. We have also expressed GFP-tagged PEEL-1 under a galactose-inducible promoter in yeast. Preliminary data suggest that PEEL-1 strongly inhibits growth of the yeast when induced. We have also begun a search for hybrid incompatibility genes in other Caenorhabditis species. We performed crosses between two recently isolated Caenorhabditis species, C. sp. 17 and C. sp. 29. When C. sp. 17 males were crossed to C. sp. 29 females, all F1 progeny arrested as embryos. However, when C. sp. 29 males were crossed to C. sp. 17 females, a very small percentage of F1 progeny did not arrest as embryos, but instead grew to the adult stage. Thus, as with peel-1, a parental effect contributes to the hybrid incompatibility. Almost all of the viable hybrids were female, indicating that the cross obeys Haldane's rule. The few F1 hybrid males are sterile. F1 hybrid females did not give viable progeny when crossed to C. sp. 29 males, but gave large numbers of viable F2 progeny and some arrested embryos when crossed to C. sp. 17 males. Among the surviving F2, there are more females than males, indicating that this cross also obeys Haldane's rule. There is significant variability in the relative proportion of males, females, and arrested embryos in the F2 generation from cross to cross, suggesting that particular combinations of genes in the rare surviving F1 females determine the proportions seen in the F2 crosses.

Lamelza, Piero et al. (2011) International Worm Meeting "Determining Whether Autosomes and the X Chromosome have Distinct Genetic Requirements for Synapsis Checkpoint Activation in C. elegans."

Bhalla, Needhi, Lamelza, Piero

[International Worm Meeting, 2011]

Meiosis is a specialized cell division in which diploid cells give rise to haploid gametes by undertaking a single round of replication and two rounds of chromosome segregation. During meiosis, chromosomes pair, synapse and recombine to generate the chiasmata necessary for proper chromosome segregation. Pairing Centers (PCs), cis-acting sites toward the end of each chromosome, promote pairing and synapsis. Checkpoints monitor proper prophase I progression, curbing the production of aneuploid oocytes by inducing apoptosis of nuclei with meiotic defects. We study the synapsis checkpoint, which is activated by unsynapsed chromosomes bearing a PC and results in increased germline apoptosis. Checkpoint activation occurs when the X-chromosome is unsynapsed (meDf2 heterozygotes) or when all chromosomes are unsynapsed (syp-1 mutants). MES-4, a histone methyl-transferase (HMT) which lays down active H3K36me3 marks, localizes on autosomes and the PC of the X-chromosome. Mutation of mes-4 abolishes the checkpoint when the X is unsynapsed. In contrast, syp-1 mutants require the mutation of another H3K36me3 HMT, MET-1, in conjunction with mes-4 for decreased levels of apoptosis. My project aims to determine whether autosomes and the X-chromosome have different genetic requirements for synapsis checkpoint activation. The model predicts MES-4 is needed for checkpoint activation if the X is unsynapsed while MET-1 is needed for checkpoint activation if the autosomes are unsynapsed. We predict that the active methyl marks laid down by MES-4 and MET-1 are required at PCs to maintain active chromatin on unsynapsed chromosomes which would normally be silenced by meiotic silencing of unpaired chromatin (MSUC).

Deshong, Alison J. et al. (2013) International Worm Meeting "A Quality Control Mechanism Coordinates Meiotic Prophase Events."

Deshong, Alison J., Bhalla, Needhi, Lamelza, Piero, Ye, Alice L.

[International Worm Meeting, 2013]

To achieve proper meiotic chromosome segregation, homologous chromosomes are physically linked by chiasmata so that they can effectively biorient on the meiosis I spindle. These linkages are established during meiotic prophase through a series of progressively intimate interactions between homologs (pairing and synapsis) to culminate in meiotic recombination. However, how pairing, synapsis and recombination are coordinated during meiotic prophase is poorly understood. The pch-2 gene has been implicated in various organisms in a wide array of meiotic functions including checkpoint signaling, chromosome axis structure, crossover control and interhomolog bias. Despite these findings, a common conserved function for PCH-2 has remained elusive. We present data that suggests PCH-2 restrains meiotic prophase events. In pch-2 mutants, pairing, synapsis and recombination all occur more rapidly than wildtype. We speculate that PCH-2 inhibits these events to coordinate them and maintain quality control of meiotic products.

Blaxter, Mark et al. (2015) International Worm Meeting "The Caenorhabditis Genomes Project."

Koutsovoulos, Georgios, Chandrasekar, Sinduja, Stevens, Lewis, Blaxter, Mark

[International Worm Meeting, 2015]

The sequencing of the genome of Caenorhabditis elegans remains one of the milestones of modern biology, and this genome sequence is the essential backdrop to a vast body of work on this key model organism. "Nothing in biology makes sense except in the light of evolution" (Dobzhansky) and thus it is clear that complete understanding of C. elegans will only be achieved when it is placed in an evolutionary context. While several additional Caenorhabditis genomes have been published or made available, a recent surge in the number of available species in culture makes the determination of the genomes of all the species in the genus a timely and rewarding project.We have initiated the Caenorhabditis Genomes Project. From material supplied by collaborators we have so far generated raw Illumina short-insert data for sixteen species. Where possible we have also generated mixed stage stranded RNASeq data for annotation. The data are being made publicly available as early as possible (warts-and-all) through a dedicated genome website at htttp://caenorhabditis.bio.ed.ac.uk, and completed genomes and annotations will be deposited in WormBase as mature assemblies emerge. We welcome additional collaborators to the CGP, whether to assemble new genomes or to delve into the evolutionary history of favourite gene sets and systems.Species sequenced thus far in Edinburgh: Caenorhabditis afra, Caenorhabditis castelli, Caenorhabditis doughertyi, Caenorhabditis guadeloupensis, Caenorhabditis macrosperma, Caenorhabditis nouraguensis, Caenorhabditis plicata, Caenorhabditis virilis, Caenorhabditis wallacei, Caenorhabditis sp. 1, Caenorhabditis sp. 5, Caenorhabditis sp. 21, Caenorhabditis sp. 26, Caenorhabditis sp. 31, Caenorhabditis sp. 32, Caenorhabditis sp. 38, Caenorhabditis sp. 39, Caenorhabditis sp. 40, Caenorhabditis sp. 43.[Samples have been supplied by Aurelien Richaud, Marie-Anne Felix, Christian Braendle, Michael Alion, Piero Lamelza].

Pierleoni A et al. (2006) Bioinformatics "BaCelLo: a balanced subcellular localization predictor."

Casadio R, Martelli PL, Fariselli P, Pierleoni A

[Bioinformatics, 2006]

Motivation. The knowledge of the subcellular localization of a protein is fundamental for elucidating its function. It is difficult to determine the subcellular location for eukaryotic cells with experimental high-throughput procedures. Computational procedures are then needed for annotating the subcellular location of proteins in large scale genomic projects. Results. BaCelLo is a predictor for five classes of subcellular localization (secretory pathway, cytoplasm, nucleus, mitochondrion and chloroplast) and it is based on different SVMs organized in a decision tree. The system exploits the information derived from the residue sequence and from the evolutionary information contained in alignment profiles. It analyzes the whole sequence composition and the compositions of both the N- and C-termini. The training set is curated in order to avoid redundancy. For the first time a balancing procedure is introduced in order to mitigate the effect of biased training sets. Three kingdom-specific predictors are implemented: for animals, plants and fungi, respectively. When distributing the proteins from animals and fungi into four classes, accuracy of BaCelLo reach 74% and 76%, respectively; a score of 67% is obtained when proteins from plants are distributed into five classes. BaCelLo outperforms the other presently available methods for the same task and gives more balanced accuracy and coverage values for each class. We also predict the subcellular localization of five whole proteomes, Homo sapiens, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae and Arabidopsis thaliana, comparing the protein content in each different compartment. Availability. BaCelLo can be accessed at http://www.biocomp.unibo.it/bacello/ Contact. casadio@alma.unibo.it, andrea@biocomp.unibo.it, gigi@biocomp.unibo.it, piero@biocomp.unibo.it.