Biology subjects

Thompson, K. M.

Publications and source records attributed to Thompson, K. M..

5 recordsLinked to original sources

bioRxiv2024

In-Flights of Outbreak Populations of Mountain Pine Beetle Alter the Local Genetic Structure of Established Populations a Decade After Range Expansion

Mountain pine beetles began to appear at epidemic levels in Alberta, Canada, in 2006, following six years of extensive outbreaks in neighboring British Columbia. We assessed the effect of genetic MPB in-flights from the peak of the outbreak on the genetic structure of established populations of MPB and the change over time in novel regions colonized by these inflights. We used five locations sampled during the peak of the outbreak (2005/2007) and re-sampled in 2016. We performed a ddRADseq protocol to generate a SNP dataset via single-end Illumina sequencing. We detected a northern and southern genetic cluster in both sampling sets (2005/2007 and 2016) and a demographic shift in cluster assignment after [~]10 generations from south to north in two of the sites in the path of the northern outbreak. Fst values were significantly different between most sites in the same years and between the same sites at different years, with some exceptions for northern sites established by inflights. Overall, sites in the spreading path of the MPB outbreak have taken on the genetic structure of the contiguous northern outbreak except for an isolated site in Golden, BC, and in Mount Robson Provincial Park where populations are admixed between north and south. Our results suggest that range expansion during insect outbreaks can alter the genetic structure of established populations and lead to interbreeding between populations.

genomics↗

bioRxiv2024

Post-transcriptional regulation of the MiaA prenyl transferase by CsrA and the small RNA CsrB in E. coli

To determine the role of small RNAs (sRNAs) in the regulation of miaA, we constructed a chromosomal miaA-lacZ translational fusion driven by the arabinose responsive PBAD promoter and used it to screen against an Escherichia coli small RNA library (containing small RNAs driven by the IPTG inducible PLac promoter). Our genetic screen and quantitative {beta}-galactosidase assays identified CsrB and its cognate protein CsrA as potential regulators of miaA expression in Escherichia coli. Consistent with our hypothesis that CsrA regulates MiaA post-transcriptional gene expression through binding to the MiaA mRNA 5 UTR, and CsrB binds and regulates MiaA post-transcriptional gene expression through sequestration of CsrA levels, a deletion of csrA significantly reduced expression of the reporter fusion as well as reducing miaA mRNA levels. These results suggest under conditions where CsrA is inhibited, MiaA translation and thus MiaA-dependent tRNA modification may be limiting. IMPORTANCEWe previously demonstrated a role for the i6A modification in the tuning of transcripts for several stress response genes in E. coli. The i6A tRNA modification is catalyzed by the tRNA prenyl transferase encoded by the miaA gene. We set out to identify posttranscriptional regulators of the enzyme necessary for the catalysis of i6A, MiaA, to further understand factors influencing i6A levels in the cell. We identified the CsrA RNA Binding Protein, the CsrB Small RNA, and RNA Degradosome enzymes: RNaseE and PNPase as regulators of miaA expressioin at the post-transcriptional level. Identifying these post-transcripitonal regulators of miaA will help us understand factors influencing i6A levels and may guide future investigations into RNA modifications with regulatory effects on the transcriptome.

microbiology↗

bioRxiv2022

Staphylococcus aureus SigS induces expression of a regulatory protein pair that modulate its mRNA stability

SigS is the sole extracytoplasmic function sigma in S. aureus and is necessary for virulence, immune evasion, as well as surviving exposure to toxic chemicals and environmental stressors. Despite the contribution of SigS to a myriad of critical phenotypes, the downstream effectors of the SigS-dependent S. aureus pathogenesis, immune evasion, and stress response remain elusive. To address this knowledge gap, we analyzed the S. aureus transcriptome following transient over-expression of SigS. We identified a bi-cistronic transcript, up-regulated by 1000-fold, containing two mid-sized genes each containing single domains of unknown function (DUF). We renamed these genes sroA (SigS regulated orfA) and sroB (SigS regulated orfB). We demonstrated that the SigS regulation of the sroAB operon is direct using in vitro transcription analysis. Using northern blot analysis, we also demonstrated that SroA and SroB have opposing auto- regulatory functions on the transcriptional architecture of the sigS locus; with SroA stimulated SigS mRNA levels and SroB stimulating s750 (SigS antisense) levels. We hypothesized that these this opposing regulatory effects were due to a direct interaction. We demonstrated an interaction between SroA and SroB using an in-vivo surrogate genetics approach via Bacterial Two Hybrid. We demonstrated that the SroA effect on SigS is at the post-transcriptional level of mRNA stability, highlighting a mechanism likely used by S. aureus to tightly control SigS levels. Finally, we demonstrate that the sroAB locus promotes virulence in a female murine pneumonia model of infection.

microbiology↗

bioRxiv2022

Host use does not drive genetic structure of mountain pine beetles in western North America

The mountain pine beetle (MPB) is one component of an intensively studied co-evolved host-pest system. We investigated the spatial genetic structure of MPB within its historic and recent geographic range expansion as it relates to host use in western North America using 13 pre-selected microsatellite loci. AMOVA shows that genetic structure is not correlated with the host tree species, arguing against the formation of host-race within this species. STRUCTURE analysis shows 4 main clusters in western North America: Northern - Northern British Columbia/Alberta; Central - Southern British Columbia/Alberta/Washington/Idaho/Montana; Southwest - Oregon/California/Nevada and; Southeast - Utah/Wyoming/Arizona/Colorado/South Dakota. Heterozygosity, allelic richness, and number of private alleles is greatest in the Southwest cluster. This cluster correlates with one of the three refugia hypothesized from a recent analysis of neo-Y haplotypes by Dowle and colleagues and represents an important reservoir of MPB genetic diversity.

genetics↗

bioRxiv2019

Autumn shifts in cold tolerance metabolites in overwintering adult mountain pine beetles

The mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae) is a major forest pest of pines in western North America. Beetles typically undergo a one-year life cycle with larval cold hardening in preparation for overwintering. Two-year life cycle beetles have been observed but not closely studied. This study tracks cold-hardening and preparation for overwintering by adult MPB in their natal galleries. Adults were collected in situ between September and December (2016) for a total of nine time points during 91 days. Concentrations of 41 metabolites in these pooled samples were assessed using quantitative NMR. Levels of glycerol and proline increased significantly with lowering temperature during the autumn. Newly eclosed mountain pine beetles prepare for winter by generating the same cold-tolerance compounds found in larvae, but high on-site mortality suggested that two-year life cycle adults have a less efficacious acclimation process. This is the first documentation of cold acclimation metabolite production in overwintering new adult beetles and is evidence of physiological plasticity that would allow evolution by natural selection of alternate life cycles (shortened or lengthened) under a changing climate or during expansion into new geoclimatic areas.

ecology↗