User:Jernej Turnsek

Welcome & Contact Information

Jernej Turnšek, PhD

Department of Plant and Microbial Biology, University of California, Berkeley, 431 Koshland Hall, Berkeley, CA 94720

[email protected]

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Research Overview

Diatom Biology and Biotechnology

My research program integrates diatom molecular and cell biology, molecular tool development, and biotechnology. We are advancing basic understanding of diatom biology and translating our findings to applications that will help alleviate the climate crisis.

Diatoms are widespread photosynthetic single-celled algae estimated to account for 20% of the oxygen we breathe. We have been pioneering the use of modern molecular tools, including proximity labeling and CRISPR, in diatoms over the past decade. Our specific research interests have been revolving around biosilicification and silicon metabolism in diatoms. These efforts are improving our molecular understanding of their vital role in global biogeochemical cycles. New insights into diatom biology carry potential for biotechnology innovations in carbon sequestration, materials science, biomedicine, and beyond.

Summary of my research directions. Created with Biorender.com.

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. I received this microscope slide as a gift early in my PhD.

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.

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

Our diatom biosilicification research focuses on:

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

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

We 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

We showed the utility of bacterial conjugation-mediated transformation method 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
Turnšek J Revisited Thalassiosira pseudonana (Tp) conjugation protocol enables fusion protein delivery to Tp frustule (protocols.io, Feb 18, 2018)

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. We 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)

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

• Revisited Thalassiosira pseudonana (Tp) conjugation protocol enables fusion protein delivery to Tp frustule (protocols.io, Feb 18, 2018)
• HA tag enables highly efficient detection of heterologous proteins in Phaeodactylum tricornutum (Pt) exconjugants (protocols.io, Oct 5, 2017)
• Guidelines for highly efficient construction of diatom episomes using Gibson Assembly (protocols.io, Sep 21, 2017)
• Pour plating of Thalassiosira pseudonana (Tp) (protocols.io, Aug 16, 2017)
• Simple & rapid genotyping of marine microeukaryotes (protocols.io, Aug 11, 2017)
• Conjugation of Thalassiosira pseudonana (protocols.io, Oct 19, 2016)

Outreach

Creative Writing

• Marine Microbes: Triathlete's Best Friends, January/February 2018

Science Art

• Diatoms: Nature's Nanotechnologists, May 2014

In the News

• Meta PHoDcast, January 2022 (interview)
• Scientists map how iron is processed by algae, March 2021 (eLife manuscript press release)
• A genetic toolbox for marine protists, April 2020 (Nature Methods manuscript commentary)
• VELIKI KORAKI, May 2019
• Prvih uspešnih sedem desetletij ljubljanske Biotehniške fakultete, February 2017
• Meta PHoDcast, January 2016 (interview)
• Tapping the marine microbiome, December 2015 (GBMF grant press release)
• Slovenec, ki na Harvardu secira alge, February 2015 (interview)
• Prava ideja!, October 2013 (TV show guest)

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, cycling, running, and triathlon races including two marathons and four Half Ironman triathlons. I was a competitive basketball player prior to transitioning to endurance sports.

Personal Bests

• Half Ironman triathlon ~ Ironman 70.3 Santa Cruz 09/2022: 5h 21' 12"
• Olympic distance triathlon ~ Mass State Triathlon 07/2016: 2h 17' 24"
• Sprint distance triathlon ~ Mission Bay Triathlon 10/2017: 58' 33"
• 26.2 ~ Baystate Marathon 10/2013: 3h 30' 55"
• 13.1 ~ Boston's Run to Remember 05/2013: 1h 26' 30"
• 10k ~ Mardi Gras 10K 02/2017: 38' 26"
• 5k ~ Triton 5K 04/2017: 18' 32"

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

Running Podiums

• 1st place, Mardi Gras 10K, San Diego, CA, 02/2017

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.

• Aarcteron
• Tahonts

Recently Read

• Wildsam Field Guides: California
• Kako so nastala živa bitja ~ Anton Polenec
• Jurij Vega ~ Jože Pavšič
• Pivovar Simon Kukec ~ ZKŠT Žalec
• 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

Web

Advice to a Young Scientist

• You and Your Research by Richard W. Hamming
• Night Science by Itai Yanai and Martin J. Lercher
• How To Choose a Good Scientific Problem by Uri Alon

Phytoplankton

• The Secret Life of Plankton ~ Five Reasons to Thank Plankton ~ Ocean Drifters ~ Planktomania ~ The Diatomist ~ Journey to the Microcosmos

Slovenian Language and Culture

• I grew up in Slovenia. My hometown Žalec is the capital of the Land of Green Gold.
• Izbor misli iz knjige Franceta Cokana "Eno življenje je premalo".