Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles.DOI: http://dx.doi.org/10.7554/eLife.00603.001

Several studies have found evidence for more positive selection on the chimpanzee lineage compared with the human lineage since the two species split. A potential concern, however, is that these findings may simply reflect artifacts of the data: inaccuracies in the underlying chimpanzee genome sequence, which is of lower quality than human. To test this hypothesis, we generated de novo genome assemblies of chimpanzee and macaque and aligned them with human. We also implemented a novel bioinformatic procedure for producing alignments of closely related species that uses synteny information to remove misassembled and misaligned regions, and sequence quality scores to remove nucleotides that are less reliable. We applied this procedure to re-examine 59 genes recently identified as candidates for positive selection in chimpanzees. The great majority of these signals disappear after application of our new bioinformatic procedure. We also carried out laboratory-based resequencing of 10 of the regions in multiple chimpanzees and humans, and found that our alignments were correct wherever there was a conflict with the published results. These findings throw into question previous findings that there has been more positive selection in chimpanzees than in humans since the two species diverged. Our study also highlights the challenges of searching the extreme tails of distributions for signals of natural selection. Inaccuracies in the genome sequence at even a tiny fraction of genes can produce false-positive signals, which make it difficult to identify loci that have genuinely been targets of selection.

Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity

Here we report a summary classification and the features of five anaerobic oral bacteria from the family Peptostreptococcaceae. Bacterial strains were isolated from human subgingival plaque. Strains ACC19a, CM2, CM5, and OBRC8 represent the first known cultivable members of “yet uncultured” human oral taxon 081; strain AS15 belongs to “cultivable” human oral taxon 377. Based on 16S rRNA gene sequence comparisons, strains ACC19a, CM2, CM5, and OBRC8 are distantly related to Eubacteriumyurii subs. yurii and Filifactor alocis, with 93.2 – 94.4 % and 85.5 % of sequence identity, respectively. The genomes of strains ACC19a, CM2, CM5, OBRC8 and AS15 are 2,541,543; 2,312,592; 2,594,242; 2,553,276; and 2,654,638 bp long. The genomes are comprised of 2277, 1973, 2325, 2277, and 2308 protein-coding genes and 54, 57, 54, 36, and 28 RNA genes, respectively. Based on the distinct characteristics presented here, we suggest that strains ACC19a, CM2, CM5, and OBRC8 represent a novel genus and species within the family Peptostreptococcaceae, for which we propose the name Peptoanaerobacter stomatis gen. nov., sp. nov. The type strain is strain ACC19aT (=HM-483T; =DSM 28705T; =ATCC BAA-2665T).Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-015-0027-8) contains supplementary material, which is available to authorized users.

Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1 T , ACB7 T and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1 T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7 T grew weakly on sucrose only. The growth temperature range was 30-42 6C with optimum growth at 37 6C. Major metabolic fermentation end products of strain ACB1 T were acetate and lactate; the only product of strains ACB7 T and ACB8 was acetate. Major fatty acids of strain ACB1 T were C 14 : 0 , C 16 : 0 , C 16 : 1 v7c dimethyl aldehyde (DMA) and C 18 : 1 v7c DMA. Major fatty acids of strain ACB7 T were C 12 : 0 , C 14 : 0 , C 16 : 0 , C 16 : 1 v7c and C 16 : 1 v7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1c. Genomic DNA G+C content varied from 42 to 43.3 % between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1 T , ACB8 and ACB7 T formed two separate branches within the genus Oribacterium, with 98.1-98.6 % sequence similarity to the type strain of the type species, Oribacterium sinus. Predicted DNA-DNA hybridization values between strains ACB1 T , ACB8, ACB7 T and O. sinus F0268 were ,70 %. Based on distinct genotypic and phenotypic characteristics, strains ACB1 T and ACB8, and strain ACB7 T are considered to represent two distinct species of the genus Oribacterium, for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1 T (5DSM

No abstract

9Acinetobacter baumannii, a Gram-negative opportunistic pathogen, is a leading cause of hospital-10 acquired infections. A. baumannii is difficult to eradicate from hospitals due to its propensity to 11 quickly gain antibiotic resistances and ability to robustly survive on dry surfaces. These strategies are 12 largely mediated by mutagenesis and biofilm development, respectively. Mutagenesis is partly 13 governed by the DNA damage response (DDR). Biofilms are multicellular communities, often 14 surface-attached, that are more difficult to eradicate than free-living planktonic cells. There is 15 increasing evidence that the DDR and biofilm development are linked processes. Here, we show that 16 upon DNA damage, the relative intracellular concentration of RecA, the key DDR protein, is lower 17 than those of Escherichia coli. Notably, we report that RecA negatively influences biofilm 18 development. Cells lacking RecA (∆recA), that are unable to upregulate the DDR, have increased 19 surface attachment and sugar content within the biofilm matrix. We further show that in A. 20 baumannii, a modest increase in RecA concentrations, akin to DDR induction, decreases surface-21 attachment. Importantly, biofilms formed by ∆ recA cells are more difficult to eradicate with 22 2 antibiotic treatment. The evidence suggests that the A. baumannii DDR influences survival 23 independent from mutagenesis. It also demonstrates the importance of understanding fundamental 24 biology to better appreciate the relationships between different bacterial survival strategies. 25 Introduction 26Acinetobacter baumannii is an emerging Gram-negative opportunistic pathogen and one of the 27 ESKAPE pathogens, a group of bacteria responsible for the majority of hospital-acquired infections 28 1 . Interest in these bacteria has stemmed from A. baumannii outbreaks in hospitals worldwide that are 29 difficult to eradicate, due to increased multi-drug resistance (MDR) 2 and resistance to desiccation 3 . 30A. baumannii is very dangerous to immunocompromised individuals, causing different illnesses, 31including pneumonia, septicemia, and wound infections 4 . 32One response pathway that underlies MDR is the DNA damage response (DDR). When gene 33 products involved in antibiotic binding or processing are mutated, resistance is acquired 5 . 34Mutagenesis can result from induction of error-prone DNA polymerase genes which are part of the 35 DDR regulon, a strategy used by different bacteria 6,7 . In Escherichia coli and many other bacteria, 36 the cells' main recombinase, RecA, and the global transcriptional repressor, LexA, manage the DDR, 37 also known as the SOS response 8 . In A. baumannii, however, there is no known LexA homologue, 38 making the A. baumannii DDR circuitry unique 9,10 . We have shown that in A. baumannii expression 39 of multiple error-prone polymerases and clinically-relevant antibiotic resistance acquisition are 40 dependent on RecA 11 . 41A. baumannii is notorious for its ability to robustly survive on surfaces. Under dry conditions, A....

Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles.