User:Jernej Turnsek

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Biology and Engineering of Phytoplankton Biominerals


The overarching ambition of my research is to understand molecular, cellular, and evolutionary underpinnings of phytoplankton biomineralization, and to ultimately turn this knowledge into medical, industrial, and environmental applications.


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I am a synthetic biologist-turned-phytoplankton molecular and cell biologist, currently a postdoctoral research scientist in Krishna K. Niyogi's laboratory in the Department of Plant & Microbial Biology at the University of California, Berkeley.


Research

Background and Motivation

Phytoplankton are photosynthetic microalgae and cyanobacteria living in marine and freshwater habitats worldwide. They form the base of aquatic food webs and account for ~50% of global primary production. Silicon cycle is linked to other major biogeochemical cycles (e.g., carbon, nitrogen, phosphorus, iron) through growth and activity of silicifying phytoplankton. These microorganisms produce intricate silica (glass) skeletons. How they orchestrate the assembly of these ornate biominerals at mild temperatures and pressures is a fascinating question, a bridge between nanoscale and planetary scale biological and geological processes. Additionally, the biocompatibility and hierarchical mesoporous structure of naturally produced silica represent a basis for medical and (bio)technological applications.


Diatom Biosilicification

Cleaned diatom frustules arranged by Klaus Kemp.


Diatoms are a widely distributed group of silicifying microalgae. They account for ~40% of marine primary production and are pivotal to exporting carbon to the deep ocean as part of the biological carbon pump. Ecological and evolutionary success of diatoms has been attributed to their silica-based cell wall called a frustule. There are tens of thousands of different diatom species collectively producing a dazzling variety of frustule shapes and patterns. This makes them a very good model system to study the genetic determinants of biomineral morphogenesis.


I aim to understand the molecular and cellular mechanisms of silica-based cell wall biogenesis and morphogenesis in diatoms. I am employing reverse genetics, imaging, omics, and bioinformatics to achieve these goals. My primary experimental model system is a centric marine diatom Thalassiosira pseudonana.


My current diatom research focuses on:

  • molecular links between nitrogen and silicon metabolism;
  • trafficking of frustule-associated proteins;
  • mechanism(s) of silicic acid sensing and signaling.


How Diatoms Build Their Beautiful Shells is a wonderfully narrated video about diatoms produced by the Journey to the Microcosmos.



Molecular Tools for Diatoms

Biological and technological breakthroughs in diatom research will depend on ease and scale with which these microalgae can be genetically engineered, manipulated, and programmed.

I have recently implemented a novel genome engineering approach in Thalassiosira pseudonana based on bacterial conjugation-mediated transformation method. 

Turnšek J et al. Multiplex genome editing in the model marine diatom Thalassiosira pseudonana (in preparation)

I pioneered the use of proximity-dependent proteomic mapping in a pennate model marine diatom Phaeodactylum tricornutum, which led to the discovery of a putative iron trafficking pathway. 

Turnšek J et al. 2021. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 10:e52770. DOI

I showed the utility of bacterial conjugation to express biosilica-targeted proteins in Thalassiosira pseudonana. 

Faktorová D et al. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 17:481–494. DOI
Revisited Thalassiosira pseudonana (Tp) conjugation protocol enables fusion protein delivery to Tp frustule (protocols.io, Feb 18, 2018)


New Phytoplankton Model Systems for Biosilicification Research

I am establishing a new biosilicification model system, a freshwater alga Synura petersenii. Synurophytes, including Synura petersenii, are heterokont algae related to diatoms. In contrast to diatoms, they don't require silicon for growth and can completely shed off their silica biomineral, which offers some unique research opportunities.


Establishment of uniformly scaleless Synura petersenii cell lines. (Left) Silica scales covering S. petersenii cell surface can be observed when cultures are supplemented with sodium metasilicate. (Right) Complete depletion of silicon in the medium leads to uniformly demineralized cells.


Mathematics of Biomineral Morphogenesis in Microalgae

I am interested in how knowledge of pattern formation in multicellular organisms can inform our description of biomineral growth and morphogenesis in microalgae like diatoms.


Past Work

Diatom Pyrenoid

Pyrenoids are subchloroplastic RuBisCO-rich proteinaceous compartments crucial for CO2 fixation in many algae and in a group of land plants called hornworths. I worked on an iron- and CO2-sensitive chloroplast-localized disordered protein in a pennate model marine diatom Phaeodactylum tricornutum. We hypothesize this protein, which undergoes a series of post-translational cleavage events, is involved in pyrenoid organization in P. tricornutum. More details about this work can be found in my Doctoral Dissertation.


Flavors and Fragrances Biotechnology

I spent a year at Ginkgo Bioworks engineering Escherichia coli to produce precursor molecules for the flavors and fragrances industry.


Metabolic Engineering

Inspired by natural examples of metabolic channeling in enzymes, enzyme complexes, and bacterial microcompartments, we showed that synthetic assemblies of biosynthetic pathways on DNA scaffolds lead to improved metabolite production in Escherichia coli. 

Conrado RJ et al. 2012. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40:1879–1889. DOI


2010 iGEM World Champion

I was a member and a copresenter of the Team Slovenia's Grand Prize-winning iGEM project at the Massachusetts Institute of Technology.


Funding

  • The Gordon and Betty Moore Foundation Grant GBMF4958 (August 2015–July 2018)


Contact Information

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Jernej Turnšek, PhD
Department of Plant & Microbial Biology, University of California, Berkeley, 431 Koshland Hall, Berkeley, CA 94720
turnsek@berkeley.edu


Linkedin.png LinkedIn 1.png ORCID Google-Scholar.png Google Scholar



Publications

  • Turnšek J et al. 2021. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 10:e52770. DOI
  • Faktorová D et al. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 17:481–494. DOI
  • Conrado RJ et al. 2012. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40:1879–1889. DOI


Protocols


Outreach

Creative Writing

Science Art

In the News


Education

  • PhD, Biological and Biomedical Sciences, Harvard University
  • MSc, Biotechnology, University of Ljubljana


Endurance Sports

I am an avid multisport athlete having competed in numerous open water swimming, running, cycling, and triathlon races including two marathons and three Half Ironman triathlons. I was a competitive basketball player prior to transitioning to endurance sports.

Personal Records

Triathlon Podiums

  • 1st place (age group), Alpha Win Napa Valley Half Ironman, Lake Berryessa, CA, 10/2021
  • 1st place (age group), Rock the Bay Triathlon, San Diego, CA, 09/2018
  • 3rd place (age group), Mission Bay Triathlon, San Diego, CA, 10/2017


Sci-fi Vignettes

I've become interested in flash science fiction after learning about postcard-sized stories by Arthur C. Clarke and his contemporaries. "Short Tales from the Mothership" event at the UCSD Geisel Library promotes this elegant genre.


Recently Read

  • The Cellist of Sarajevo ~ Steven Galloway
  • The Yugoslav Wars of the 1990s ~ Catherine Baker
  • Born on a Blue Day ~ Daniel Tammet
  • Hero ~ Rhonda Byrne
  • The Old Man and the Sea ~ Ernest Hemingway
  • Zen Mind, Beginner's Mind ~ Shunryu Suzuki
  • Indian running ~ Peter Nabokov
  • The Doors of Perception ~ Aldous Huxley
  • Deep Simplicity ~ John Gribbin
  • Pravica ~ Srečko Kosovel


Web

Advice to a Young Scientist

Phytoplankton

Slovenian Language and Culture

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