Ammonia oxidation in soil was, until recently, thought to be dominated by autotrophic, chemolithotrophic proteobacteria. These organisms gain energy from oxidation of ammonia to nitrite and perform the first step in nitrification. All cultivated ammonia oxidising bacteria show no or very poor growth in liquid batch culture below pH 7. Paradoxically, nitrification occurs in acid soils at rates that are often faster than those in apparently more favourable neutral and alkaline soils. Understanding acidophilic ammonia oxidation is important globally and economically. Approximately 30% of the world’s soils are acidic (pH<5), including 50% of arable soils, and up to 70% of ammonia-based nitrogen fertiliser is lost through nitrification and leaching or denitrification of nitrate. Potential mechanisms for acidophilic ammonia oxidation include urea hydrolysis, protection in biofilms and aggregates and heterotrophic nitrification, but could also be due to acidophilic or acidotolerant ammonia oxidisers. Assessment of selection for such groups in acid soils was impossible…

The talk will cover results from three as yet unpublished projects. It will start with an introduction into protein sequence searching and to our software package HH-suite for very sensitive remote homology detection. I will show how we can significanlty boost the sensitivity of searches in HH-suite using a homology-enriched profile-HMM database. Second, I will present our new software package MMseqs (Many-against-Many sequence searching) for very fast batch protein sequence searches and clustering of huge protein sequence data sets, such as UniProt or sets of predicted open reading frames from large metagenomics experiments. MMseqs achieves a comparable sensitivity as protein BLAST (blastpgp) at 400x its speed. Third, I present a method for the discovery of regulatory motifs in nucleotide sequences that goes beyond the standard position weight matrix model by learning the dependence of binding affinities on neighboring nucleotides. Importantly, our method automatically learns the dependencies up to the optimum order (i.e.…

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Genome-wide measurements of transcriptional activity in bacteriaindicate that the transcription of successive genes is stronglycorrelated beyond the scale of operons. I will present an analysis ofhundreds of bacterial genomes to identify supra-operonic segments ofgenes that are proximal in a large number of genomes. The syntenysegments that it yields correspond to genomic units of strongtranscriptional co-expression. Structurally, the segments containoperons with specific relative orientations (co-directional ordivergent) and nucleoid-associated proteins are found to bind at theirboundaries. Functionally, operons inside a same segment are highlyco-expressed even in the absence of regulatory factors at theirpromoter regions. Remote operons along DNA can also be co-expressed iftheir segments share a transcriptional or sigma factor, withoutrequiring these factors to bind directly to the promoters of theoperons. As evidence that these results apply across the bacterialkingdom, I will demonstrate them both in the Gram-negative bacteriumEscherichia coli and in the Gram-positive bacterium Bacillus subtilis.The underlying process that we propose involves only…

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Meiotic recombination is initiated in diploid germline cells by the programmed introduction of hundreds of DNA double strand breaks (DSBs) along chromosomes. These DSBs are then repaired by homologous recombination, one of the outcomes being the crossovers, where homologous chromosome arms are exchanged. Meiotic crossing overs are necessary for gamete viability. Errors in meiotic crossover formation are the major source of aneuploidies leading to sterility and chromosomal diseases such as Trisomy 21. Meiotic recombination is also an important source of genetic diversity, generated through the crossovers that shuffle existing combination of alleles, but also through the unidirectional events called conversions that take place at all meiotic recombination sites. We have recently uncovered a new function of the poorly characterized mismatch repair complex, MutLbeta (Mlh1-Mlh2 in budding yeast), in meiotic recombination. We found that it interacts with recombination proteins to regulate their activity and limit the extent of genetic material exchanged between homologs…

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