A German and French team explores features found in Bacillus subtilis bacteria engineered to have minimized genomes — genomes more than one-third smaller than those of wild-type strains. Using a combination of genome sequencing, metabolite and proteome profiling, expression analyses, and physiological assessments, the researchers characterized B. subtilis strains in which large sets of deletions were introduced to reduce the genome size. Their results revealed discrepancies in the resources afforded for translation of certain genes, for example, with the small collection of essential genes commanding more than half of this translation capacity. "Our results emphasize the key relevance of essential genes for the biology of the cell, and they provide important clues for further steps in genome reduction and molecular analysis of B. subtilis," the authors note.
Researchers from the UK and Canada report on efforts to come up with new computational methods for storing and analyzing massive sets of population genome data. In particular, they focused on approach that builds on Burrows-Wheeler transform (BWT) methods for compressed, reference-free sequence read indexing, combined with FM-index based sequence searches. The team applied its approach — known as population BWT — to low coverage whole-genome sequences and/or exome sequences for 2,705 of individuals from more than two dozen populations profiled for the 1000 Genomes Project, identifying SNPs, small insertions and deletions, and non-human reads stemming from viruses, in a subset of samples.
Finally, a team from Israel and the US consider conserved and divergent features involved in transcription initiation site patterns for mitochondrial DNA genes across human cell lines and in other vertebrate and invertebrate animals. Using a combination of Global Run-On sequencing (GRO-seq) and Precision Global Run-On sequencing (PRO-seq) assays, the researchers profiled mtDNA transcription start, pausing, and stop sites in 11 human cell types, along with cells from seven other species ranging from non-human primates, rats, and mice to fruit flies and Caenorhabditis elegans worms. Their analysis pointed to conserved transcription pausing sites, for example, while highlighting distinct mtDNA transcription profiles in the vertebrate and invertebrate animals.