Inter-individual competition for resources and variability of the environment
Experimental studies of the biological evolution encounter two major limitations: a long time needed to observe these gradual changes and a large size of the population necessary for beneficial mutations to get fixed. Computational modeling allows us to overcome those limitations for the price of taking some simplifying assumptions. I am investigating can the inter-individual competition for resources and variability of the environment influence the size of the free-living bacteria genomes either by forcing streamlining or expansion of genome's size? The model, an agent-based simulation of individual cell having unique genomes, shows that under stable environmental conditions competition for the resource forces bacteria to do extreme energetic savings including decreasing the number of genes (as their expression cost). When environment is unpredictable the genomes become larger to prepare the individual for a wider span of the environmental conditions.
Gene networks in diatoms that are involved in acclimation to the changing climate
There is an urgent need to understand how important global primary producers such as diatoms perceive environmental changes to make predictions of how global change might influence life in the ocean. I plan to address this challenge using chromatin immunoprecipitation (ChIP) in combination with pyrosequencing (ChIPSeq) to globally identify genomic binding sites of different transcription factors in the sequenced diatom Thalassiosira pseudonana. Over the course of my project I will develop ChIP Seq methods to use with T. Pseudonana, and once established we plan to investigate transcription factors involved in response to biogeochemical stresses. We will establish which genes are upregulated under different environmental stresses. This project will provide an insight into genes which are co regulated and also identify new genes previously unidentified, with important consequences for understanding of important biogeochemical processes. These studies will also allow us to associate “unknown genes” with developmental pathways defined by these regulons and thus begin to infer potential functions for these gene products.
Whole genome expression profiling of the polar diatom Fragilariopsis cylindrus
Phytoplankton is involved in various biogeochemical cycles and plays key roles in maintaining the ecological balance of the earth. Global change will affect phytoplankton all over the world but especially threatens polar species by dramatic changes of their environment like the retreat of sea ice. Polar phytoplankton is highly adapted to extreme conditions. However, little is known about the effects of a rapidly changing environment on these organisms that serve as the basis for the polar food chain. The polar phytoplankton community is often dominated by diatoms and among them is the species Fragilariopsis cylindrus. F. cylindrus is a key species for polar primary production, because it is abundant both in sea ice and in open waters. Its genome was recently sequenced by the Joint Genome Institute (JGI), providing the first polar eukaryotic genome sequence. Highlights from the genome include a rhodopsin-like protein, which is not present in the sequenced genomes of the temperate model diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. The physiological role of a proton-pumping rhodopsin in the presence of the proton gradient-generating chlorophyll-based photosynthetic apparatus remains puzzling. To elucidate its function I am using functional genetic approaches. Furthermore, I am investigating the transcriptome under different environmental conditions accompanying climate change in order to identify the molecular underpinnings of adaptation and to identify novel genes that are involved in polar adaptation.
The Eukaryotic Meta-Transcriptome of the Upper Ocean
Ginger Armbrust, Micaela S. Parker, Adrian Marchetti (University of Washington, Seattle, USA)
Andreas Krell, Klaus Valentin (Alfred-Wegener Institute for Polar and Marine Research, Bremerhaven, Germany)
The microbial genetic inventory of the ocean is not known yet but we know that marine microbes are present at billions of cells per liter sea water and that they have a long evolutionary history that extends backwards further than other live forms on earth (Irigoien et al. 2004, Nature, 429:863-867).
Whole-genome analysis to identify nuclear-encoded plastid proteins in diatoms.
Ansgar Gruber, Peter Kroth (University of Konstanz, Germany)
Diatoms belong to Stremanopiles, which evolved based on secondary endosymbiosis (see figure). This led to a mixture of several genomes with significant gene transfer into the host nucleus. One consequence of this event includes a complex targeting mechanism to allow nuclear-encoded proteins to be imported into the plastid. The complete genome sequences of the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum have allowed to identifying these nuclear-encoded plastid proteins. We have taken a two step approach to identify diatom plastid targeted proteins. First, for anabolic pathways known to be localized to the plastids of green algae/higher plants we manually searched upstream of the predicted genes for a signal peptide and plastid transit sequence, both of which are required for plastid localization in diatoms. We identified a set of 118 proteins in both diatoms considered to be highly likely to be plastid targeted. Transit peptides from these 118 proteins were used to determine relative frequency of amino acids and the information content of each position in the transit peptide sequence for each diatom. Based on these “rules” the complete proteome of each diatom was screened to identify proteins with both signal and transit peptide sequences. We have identified over 400 genes in each genome that are putatively targeted to the plastid. This work allows the reconstruction of know plastid pathways and the identification of differences to green algae and higher plants and it furthermore is able to identify new and diatom specific plastid proteins. Current work includes expression analysis of the plastome and transformation experiments to verify predicted targeting.
Whole genome sequencing of the polar diatom Fragilariopsis cylindrus
Chris Bowler (Ecole Normale Supérieure, Paris, France)
Klaus Valentin (Alfred-Wegener Institute for Polar and Marine Research, Bremerhaven, Germany)
Igor V Grigoriev, Alan Kuo, Erica Lindquist, Kerrie Barry (Joint Genome Institute (JGI), Walnut Creek, California, USA)
Diatoms are microscopic unicellular algae distributed throughout the world’s marine and freshwater ecosystems, including ice systems. Numerous estimates suggest that, as a group, these organisms are responsible for as much as 20% of global photosynthesis, which is comparable to the amount of primary productivity generated by all the terrestrial rainforests combined. In polar regions, where extensive permafrost and glaciers limit the amount of photosynthesis possible on land, diatoms are responsible for a huge fraction of primary productivity and therefore also for carbon sequestration. Polar diatoms are adapted to cold temperatures and high salinities and they live both within the seawater and the brine channels formed within sea ice. They serve as the base of the entire polar food web. Polar regions are displaying the greatest responses to climate change, with increased melting of sea ice and the potential disruption of this sensitive ecosystem. The whole genome sequencing of a representative polar diatom was proposed in order to gain insights into how these organisms have adapted to the extreme environments in which they thrive.
From genes to structures: How diatoms form their nano-structured silica shells
and Angela Falciatore (University Pierre and Marie Curie, Paris, France)
Diatoms are nature's nanotechnology masters, able to produce beautifully ornamented shells made of silica (hydrogenated silicon). The beauty of these shells even inspired artists and precise hand drawings of them were already published by Ernst Haeckel in his book: "Artforms in Nature" beginning of the last century. The architecture of these shells differs from species to species but is the consequence of an optimization process that went on for over about 300 million years of evolution. They are light-weight and porous to keep the cells afloat and to ensure exchange of nutrients and gases for growth but on the other side they are very stable to protect the cell. This combination of properties caused a huge interest by engineers because they want to understand how diatoms are able to lay down these complex structures of silica in high order at the sub-nanometer range exceeding any current capabilities of human nano-technology. Diatoms directly build in 3D, which is why they are so attractive for any lithographic approaches. The applications of this knowledge are evident. Silica is related to silicon which is the key element for the semiconductor industry and thus for computer chips. If engineers can genetically control that process of silicon fiber formation as diatoms already do, they would have an entire new way of performing the nanofabrication used to make computer chips. Meanwhile they already have begun to combine diatom shells with semiconductor technology. On application of an electric field, the shells of some diatoms emit light, which is explained by the geometry of shells latticework of pores. They hope that further combinations of semiconductor technology and biologically produced nanostructures may yield novel devices. Diatom shells also influence incoming light by changing its spectral composition. These optical properties on a nano-scale can offer several advantages over current technologies for optical devices. Thus, diatom shells are of broad interests for many different biotechnological application but even more if we understand how these nanostructures are formed. We will then be able to create entirely novel technology with the help of natures knowledge build on million years of evolution. We already have done the first step into this direction by identifying which genes are involved in shell formation. We were able to select about 150 genes out of ca. 14,000 that only responded (turned on or off) by the availability of silicon in a diatom for which the whole genome sequence is available (Thalassiosira pseudonana). Now we know which of the organism's 14,000 genes are most likely to be involved in making the shells. However, the majority of these genes don't have a known function because they display no similarities to known genes from other organisms. We therefore apply modern molecular techniques to shed more light on the function of these unknown genes and also on those genes were we only have vague ideas about their function. We try to elucidate their function by genomic transformations and gene knockdown using RNA silencing technology. These data will significantly improve our knowledge about the genetic underpinnings of diatom silica shells and thus provide a first step towards a genetically controlled process for many different bionanotechnological applications.
* Courtesy of: Nils Kröger, Nicole Poulsen (Georgia Tech, College of Engineering, Atlanta, USA)