Hello everyone. My name is Priscilla handheld. I'm a PhD candidate in the bioinformatics data science program. And I'll be speaking about my transcriptome analysis of non phototrophic actinobacteria with enhanced growth. So well served by introducing you to the microbes I work with and their surface freshwater environment. We'll then discuss the methods we use to understand how these microbes respond to light. And then I'll end by showing some of the results from our data analyses. Good art like your bacteria, our lineage of bacteria that are distributed ubiquitously in freshwater and are highly abundant. This lineages of particular interest in freshwater because they've been shown to be inversely correlated and abundance with cyanobacteria. Cyanobacteria are primary producers that can cause irreversible damage to freshwater ecosystems. While primary producers convert light to chemical energy, usually via photosynthesis, some freshwater actinobacteria are non phototrophic. A non phototrophic bacteria don't converts light to chemical energy. But we do know many species and still sense light. And we think that some species, namely wrote a Luna Lisa cola and around microbiome by one shown here, use light as information that ultimately increases their growth. However, we don't know how this happens in these species. So part of my work is to characterize the effects of light on the species. And this will help us understand which biological processes that are correlated with light exposure. A non phototrophic carbon uptake in freshwater actinobacteria. Split off the gate this week, bioinformatics approach, where our goal is to merge and interpret layers of data to identify potential mechanisms that characterize this response to light. And one question we asked was, which biological processes are changing in response to the presence and absence of light. And how are they changing? So we sample to the RNA of these two species through a 24 hour light-dark cycle to capture gene expression changes. And then we identify groups of genes with similar expression patterns. What we found was that the gene expression patterns shown at the top of the heatmap figures here are very different between the two species. Additionally, we found that the biological processes significantly represented in these groups of genes is also different. The monarch has seemingly cyclical response where transcription of genes involved in mediating oxidative damage, iron-sulfur assembly and transcription or decreased in the light and increased in the dark. While transcripts of growth-related genes involved in gluconeogenesis, DNA replication, and amino acid uptake are increased in the late and decrease in the dark. In a run-through microbium mu1 porphyrin synthesis transcript, or increased in the light and decreased in the dark. Then ribosome biogenesis, translation, protein folding and transport change expression in the dark. So although light inhibits growth and the ability to respond to light and dark is white bread and freshwater actinobacteria. The genetic networks controlled by light and dark very significantly even between two closely related species. This may be because species from different freshwater environments are uniquely poised to use light as a signal to time their carbon uptake with maximum production from their primary producer neighbors. So to wrap up, non phototrophic light enhance growth. Even more complicated than we previously thought while wrote a lunar Lisa cola and around some microbium, mu1 are phenotypically, morphologically and genetically similar. Their gene expression changes in response to light and dark cycling is very different. And the biological processes affected by light dark cycling vary greatly between the two species. So with that, I'd like to think my advisor there, Julie more ESCA, my committee, all the contributing researchers and members of the Mosque, a lab for their support. And now I'll take any questions.

Transcriptome of non-phototrophic Actinobacteria that display light-enhanced growth, Priscilla Hempel

From Lauren Mosesso April 13, 2021

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Freshwater lakes play a critical role in the global carbon budget. Given that microbes are at the center of the carbon cycle in freshwater, understanding how their metabolic processes are affected by their environment is of interest. In surface freshwater, sunlight is both an environmental cue and source of energy for primary producers and other bacteria. Within freshwater bacterial communities, the Actinobacteria are highly abundant. Multiple species within the Microbacteriaceae family of the Actinobacteria phylum have putative proteins that capture light energy, and while light mediated gene expression of phototrophs has been well characterized, in heterotrophs it is not as well understood. Here, we characterize transcription throughout a light/dark cycle of R. lacicola and Aurantimicrobium sp. strain MWH-Mo1, which are Microbacteriaceae strains that grow faster in light than in dark. Although both strains share a phenotype, their gene expression changes through a light/dark cycle are quite different. R. lacicola has a cyclical response, where transcripts of genes involved in mediating oxidative damage, iron-sulfur assembly, and transcription are downregulated in the light and upregulated in the dark, while transcripts of growth-related genes involved in gluconeogenesis, DNA replication, and amino acid uptake are upregulated in the light and down regulated in the dark. In Aurantimicrobium sp. strain MWH-Mo1, porphyrin synthesis is upregulated in the light and downregulated in the dark. Additionally, dark triggers downregulation of molecular chaperone genes. This indicates the light-enhanced growth phenotype and the ability to respond to light/dark may be widespread in freshwater Actinobacteria, but the genetic networks controlled by light/dark may vary significantly.

Department Name: Bioinformatics Data Science
Appears In: GSG presents 10th Annual Graduate Students’ Forum

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