Biology subjects

Dunn, M.

Publications and source records attributed to Dunn, M..

5 recordsLinked to original sources

bioRxiv2018

Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase

Rhizobium etli CE3 grown in succinate-ammonium minimal medium (MM) excreted outer membrane vesicles (OMVs) with diameters of 40 to 100 nm. Proteins from the OMVs and the periplasmic space were isolated from 6 and 24 h cultures and identified by proteome analysis. A total 770 proteins were identified: 73.8 and 21.3 % of these proteins occurred only in the periplasm and OMVs, respectively, and only 4.9 % were found in both locations. The majority of proteins found in either location were present only at 6 or 24 h: in the periplasm and OMVs, only 24 and 9 % of proteins, respectively, were present at both sampling times, indicating a time-dependent differential sorting of proteins into the two compartments. The OMVs contained proteins with physiologically varied roles, including Rhizobium adhering proteins (Rap), polysaccharidases, polysaccharide export proteins, autoaggregation and adherence proteins, glycosyl transferases, peptidoglycan binding and cross-linking enzymes, potential cell wall modifying enzymes, porins, multidrug efflux RND family proteins, ABC transporter proteins, and heat shock proteins. As expected, proteins with known periplasmic localizations (phosphatases, phosphodiesterases, pyrophosphatases) were found only in the periplasm, along with numerous proteins involved in amino acid and carbohydrate metabolism and transport. Nearly one-quarter of the proteins present in the OMVs were also found in our previous analysis of the R. etli total exproteome of MM-grown cells, indicating that these nanoparticles are an important mechanism for protein excretion in this species.\n\nIMPORTANCEThe reduction of atmospheric nitrogen to ammonia by rhizobia symbiotically associated with legumes is of major importance in sustainable agricultural. Rhizobia excrete a variety of symbiotically important proteins using canonical secretion systems. In this work, we show that Rhizobium etli grown in culture also excretes proteins in membrane-enclosed structures called outer membrane vesicles (OMVs). This study reports OMV production by rhizobia. Proteins identified in the OMVs included Rhizobium adhering (Rap) and autoaggregation proteins, polysaccharidases, RTX toxins, porins and multidrug efflux proteins. Some of these proteins have important roles in the R. etli-common bean symbiosis, and their packaging into OMVs could deliver them to the environment in a concentrated yet diffusible form protected from degradation. The work described here provides a basis for future studies on the function of rhizobial OMVs in free life and symbiosis.

microbiology↗

bioRxiv2018

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

The most commonly employed mammalian model organism is the laboratory mouse. A wide variety of genetically diverse inbred mouse strains, representing distinct physiological states, disease susceptibilities, and biological mechanisms have been developed over the last century. We report full length draft de novo genome assemblies for 16 of the most widely used inbred strains and reveal for the first time extensive strain-specific haplotype variation. We identify and characterise 2,567 regions on the current Genome Reference Consortium mouse reference genome exhibiting the greatest sequence diversity between strains. These regions are enriched for genes involved in defence and immunity, and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. Several immune related loci, some in previously identified QTLs for disease response have novel haplotypes not present in the reference that may explain the phenotype. We used these genomes to improve the mouse reference genome resulting in the completion of 10 new gene structures, and 62 new coding loci were added to the reference genome annotation. Notably this high quality collection of genomes revealed a previously unannotated gene (Efcab3-like) encoding 5,874 amino acids, one of the largest known in the rodent lineage. Interestingly, Efcab3-like-/- mice exhibit severe size anomalies in four regions of the brain suggesting a mechanism of Efcab3-like regulating brain development.

genomics↗

bioRxiv2018

Candida albicans dispersed cells signify a developmental state distinct from biofilm and planktonic phases

Candida albicans surface-attached biofilms are sites of amplification of an infection through continuous discharge of cells capable of initiating new infectious foci. Yeast cells released from biofilms on intravenous catheters have direct access to the bloodstream. We previously reported that dispersed cells are largely lateral yeast cells that originate from the hyphal layers of the biofilm. Compared to their planktonic counterparts, these biofilm-dispersed yeast cells displayed enhanced virulence-associated gene expression and drug resistance. Little is known about the molecular properties of dispersed cells. We found that the inducer of dispersal, PES1, genetically interacts with the repressor of filamentation, NRG1, in a manner that supports a genetic definition of dispersed cells as yeast. We combined a flow biofilm model with RNA sequencing technology, to identify transcriptomic characteristics of freshly dispersed yeast cells versus biofilms or age-matched planktonic yeast cells growing in glucose-rich medium. Dispersed cells largely inherited a biofilm-like mRNA profile but with one stark difference: dispersed cells were transcriptionally reprogrammed to metabolize alternative carbon sources, while their sessile parents expressed glycolytic genes, despite exposure to the same nutritional signals. Our studies hence define dispersal cell production as an intrinsic step of biofilm development which generates propagules capable of colonizing distant host sites. This developmental step anticipates the need for virulence-associated gene expression before experiencing the associated external signals.

microbiology↗

bioRxiv2017

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

genomics↗

bioRxiv2016

Chromosome assembly of large and complex genomes using multiple references

Despite the rapid development of sequencing technologies, assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout, a reference-assisted assembly tool that now works for large and complex genomes. Taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. Using Ragout, we transformed NGS assemblies of 15 different Mus musculus and one Mus spretus genomes into sets of complete chromosomes, leaving less than 5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long PacBio reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. Additionally, we applied Ragout to Mus caroli and Mus pahari genomes, which exhibit karyotype-scale variations compared to other genomes from the Muridae family. Chromosome color maps confirmed most large-scale rearrangements that Ragout detected.

bioinformatics↗