Tale

Jumping Genes

Orsolya Barabas

European Molecular Biology Laboratory, Heidelberg

Published June 27, 2018

Thickly forested slopes define the environs around Heidelberg, Germany, the headquarters of the European Molecular Biology Laboratory. In her hillside EMBL laboratory, Orsolya Barabas probes the small pieces of moveable DNA that define the landscape of modern genomes.

Surprisingly few people have heard of transposons. These “jumping genes” have been flitting around genomes for millions of years, changing locations or introducing new copies of themselves all over the place in plants and animals. They escaped notice until the 1940s, when Barbara McClintock observed them in maize, where they dominate the DNA, eventually earning her a Nobel Prize in 1983.

At the last best guess, about half of the human genome is composed of mostly dormant remnants of transposons. Bacteria, on the other hand, rely on highly active transposons to share genes to help them adapt and survive, such as those that confer antibiotic resistance.

“Transposons are very simple DNA vehicles that can help integrate genetic cargo into the genome,” says Barabas, who works both sides of the potential medical applications, starting from the atomic details. Her group studies transposons used in genetic engineering, seeking to make their gene delivery more efficient. On the flip side, she also scrutinizes transposons that spread antibiotic resistance genes among bacteria, hoping to limit that activity.

The scientific world has been buzzing about CRISPR/Cas9 for targeting and editing a specific location on DNA, but transposons have the edge when it comes to the step of inserting a gene, Barabas says. Transposons also have some advantages over viral vectors, a more established way to insert genes efficiently.

“Transposons are the first line of non-viral gene delivery tools,” she says. “Their applicability is greatest for ex vivo cell engineering.” The early use of transposons has mostly been in personalized immunotherapy clinical trials, in which a patient’s immune cells are withdrawn, genetically altered to recognize and kill cancer cells, and then injected back into the patient.

Barabas and her colleagues have found a way to improve the first and most popular such tool. Called Sleeping Beauty, the transposon was synthesized about two decades ago by Hungarian researchers. The awakened transposon was reconstructed from ancient DNA sequences estimated to be more than 10 million years old, which had been fished out of the genomes of trout and salmon. In their lab in Germany, these same researchers have since modified Sleeping Beauty to be 100 times more efficient, a version called SB100X.

The first structure of the transposase protein of the Sleeping Beauty transposon is modeled into full transposition machinery. Image Franka Voigt & Irma Querques. Courtesy Nature.

“The coolness of this transposon is that there is no active copy in any genome,” says Barabas, who set up a collaboration with the original Sleeping Beauty team. “It’s a rational reconstitution of an evolutionary pathway. From an application point of view, this is cool because you can use the tool in any genome without unwanted mobilization of genomic DNA.”

In a 2016 paper in Nature Communications, Barabas and her co-authors reported the first crystal structure of the key piece, the SB100X transposase enzyme. Transposases are the workhorses of transposons, clamping, cleaving, and rejoining the DNA.

Using the new structure, the team tweaked some amino acids on the surface of the enzyme to make versions that could bind even better to the DNA where genetic integration occurs.

“They were the first rationally designed hyperactive transposon variants,” she says. The new design has a 30 percent efficiency boost. These variants are not yet in cancer trials, but for patients waiting for cancer treatment, Barabas estimates they may shave as much as a week off a month-long wait for SB100X to supercharge their immune cells.

“As well adapted parasites, transposase enzymes are not naturally optimized to work efficiently,” she adds. “This leaves a lot of room for optimizing their activities for human use or genome manufacturing at will.”

One limitation of transposons for genetic engineering is that they insert cargo in many different places on the DNA. In contrast, the CRISPR/Cas9 system can target a specific DNA site, but then it relies on the host’s DNA repair mechanism to insert a gene, which isn’t good enough for a medical setting, she says.

“Ideally, it would be nice to combine these things: Site specificity and integration,” Barabas says. Until that vision becomes reality, her lab continues to develop more hyperactive variants and seek ways to target them better.

A different project in the lab has the opposite goal: To derail transposon activity—at least those that spread antibiotic resistance among bacteria. The numbers of microbes resistant to multiple antibiotics has been increasing globally, causing concern among scientists and doctors about the threat to public health.

“The fact is that resistance genes already exist for all antibiotics we use,” she says. “There is not a single antibiotic for which a resistance mechanism does not exist.”

Transposons largely drive the spread of antibiotic resistant genes among bacteria, even within the resident microbes in our gut. Stress—such as antibiotic treatment—can trigger bacterial transposons to amplify.

The Barabas lab started with conjugative transposons, which move between the single-cell microbes during the process scientists jokingly refer to as bacterial sex. Normally, two single-celled microbes meet and form a membrane tube to swap DNA and proteins, including transposons carrying genes that confer drug-resistance.

They solved the first structure of a transposon of this class. A 2018 Cell paper reported the transposon DNA in conjunction with the protein machinery that plucks out resistance genes. The structure shows how the enzyme can peel open the DNA double helix in two parts. A single stranded segment forms a bubble that can touch down almost anywhere else without needing to match a specific sequence.

This structure captures a pair of transposases (two shades of blue) with their DNA cargo (red and black) after the transposon jumped out of one genome. The pink protein segments are poised to unpeel the DNA when the transposon lands on another target genome. This conformation reveals an unexpected stability that may help develop new strategies to prevent the spread of antibiotic resistance. Courtesy O. Barabas. Courtesy Cell.

Based on the structure, Barabas and her colleagues predicted two types of molecular inhibitors. One peptide blocks the transposase protein from moving to its activated conformation. The second is a small DNA and binds to the open site within the transposon, blocking the DNA strand replacement needed for resistance transfer.

She envisions potential inhibitors may be used in combination with a course of antibiotics, to prevent resistance spreading.

Barabas grew up in Hungary, the daughter of two chemical engineers. She remembers being fascinated by how things in everyday life could be explained by chemistry and other phenomena people can’t normally see. When it came time to train for a career, Barabas decided to direct her imagination and creativity toward chemistry and basic research. Her father was concerned, reasoning that the country could not support many basic researchers.

At Eötvös Loránd University in Budapest, Barabas studied structural chemistry. For her masters, she crystalized small molecules used in drugs and pills, learning how their structure influences their actions and effects. Then she moved on to enzymes, looking at their effect on nucleic acid metabolism and maintenance. When she finished her PhD in 2005, she was riveted by how proteins juggle with DNA.

She crossed the Atlantic Ocean for a postdoctoral position at the National Institutes of Health in Bethesda, Maryland, USA and was introduced to transposons in the lab of Frederick Dyda. “I had no idea what transposons were, but they sounded fascinating—dedicated elements in the genome that fancy to hop around, shaping us into who we are,” Barabas says. She became a group leader at EMBL in 2009. Over time, Barabas has become increasingly intent on connecting basic structural knowledge to applications.

“It’s important that we really use the structure to understand its function, and also develop it into something useful for society,” she says. “For me, the applicability of the acquired knowledge is critically important. Taxpayers pay us to have the most thrilling job, and I need to pay them back.” To help push past the basic discoveries, the Barabas lab does biochemistry, biophysics, structures, cell biology and other methods.

Collaborations abound. To explore how the antibiotic slaughter of gut bacteria affects their susceptibility to antibiotic resistance genes, she has teamed up with computational geneticists and a mouse biology lab, as well as with a clinician for human stool samples. This will allow investigating how transposons spread in microbial communities in the gut and what triggers induce the movements. More structures are on the menu to compare mechanisms among the many different transposons.

-Carol Cruzan Morton

Probing Microbes

Gira Bhabha

Published 30 September 2025

Drawn to the Light

Emina Stojković

Published 30 July 2025
The Final Phase

George Phillips

Published 31 May 2025

Mind and Muscle

Ryan Hibbs

Published 28 March 2025
The Shapes of Energy

Luke Chao

Published 12 December 2024

Predicting Proteins

Jens Meiler

Published 25 November 2024
Death Metal

Steven Damo

Published 28 April 2024

Context Matters

Bing Chen

Published 30 January 2024
The Crystal Whisperer

Sarah Bowman

Published 29 November 2023

Data in Motion

Nozomi Ando

Published 29 September 2023
The Monstrous Maw

André Hoelz

Published 28 June 2023

Second Takes

Andrea Thorn

Published 28 February 2023
Radical reactions

Yvain Nicolet

Published 31 January 2023

Floppy Physics

Eva Nogales

Published 30 November 2022
Structure of Equity

Jamaine Davis

Published 28 September 2022

Life and Death of a Cell

Evris Gavathiotis

Published 28 July 2022
Follow the glow

Kurt Krause

Published 29 April 2022

Resolution solutions

Willy Wriggers

Published 25 February 2022
Of enzymes and membranes

Ming Zhou

Published 28 October 2021

Step-by-step

Gabrielle Rudenko

Published 26 September 2021
Moving muscle

Montserrat Samso

Published 26 July 2021

Particle catcher

Stefan Raunser

Published 28 June 2021
Designer drugs

Ho Leung Ng

Published 25 February 2021

Right place, right time

Ernesto Fuentes

Published 29 January 2021
Shape-shifting secrets of membranes

James Hurley

Published 27 November 2020

Enzymatic action

Cynthia Wolberger

Published 28 September 2020
Rules of motion

Priyamvada Acharya

Published 31 July 2020

Cosmic Squared

Michael Cianfrocco

Published 27 June 2020
Kaps are Cool

Yuh Min Chook

Published 28 April 2020

Spiraling into focus

Carsten Sachse

Published 29 March 2020
Seeing cilia

Alan Brown

Published 27 February 2020

For the Love of EM

Guy Schoehn

Published 27 January 2020
Protein Puddles

Michael Rosen

Published 16 December 2019

Changing channels

Daniel Minor Jr.

Published 27 September 2019
Listening Tips

Marcos Sotomayor

Published 30 July 2019

Beyond Cool

Published 31 May 2019
Hao Wu

A Higher Order

Published 30 May 2019

Aye Aye Captain

Alexandre Bonvin

Published 29 April 2019
The PARP Family Family

John Pascal

Published 28 February 2019

Frame by frame

Nikolaus Grigorieff

Published 28 January 2019
Predicting Success

Bil Clemons

Published 18 December 2018

Curiouser and Curiouser

Ramaswamy Subramanian

Published 27 November 2018
Rely on This

Sjors Scheres

Published 26 October 2018

Proteins out of bounds

Gerhard Wagner

Published 27 September 2018
Hiding in plain sight

Gaya Amarasinghe

Published 27 July 2018

Jumping Genes

Orsolya Barabas

Published 27 June 2018
Data Whisperer

Karolin Luger

Published 30 May 2018

Flipping the Switch

Jacqueline Cherfils

Published 27 April 2018
Tooling Around

Andrew Kruse

Published 29 March 2018

Comings and Goings

Tom Rapoport, Ph.D.

Published 23 February 2018
Transcriptional Rhythm

Seth Darst

Published 27 January 2018

The Language of Gene Regulation

Daniel Panne

Published 21 November 2017
Not Your Average Protein

James Fraser

Published 23 October 2017

Message Received

Sebastien Granier

Published 24 August 2017
Resistance is Futile

Celia Schiffer

Published 28 July 2017

Twist of Fate

Leemor Joshua-Tor

Published 28 June 2017
Drug Designer

John Buolamwini

Published 30 May 2017

Mathematically Minded

James Holton

Published 28 April 2017
Garbage Out

Kay Diederichs

Published 30 March 2017

Fixer Upper

Brandt Eichman

Published 27 February 2017
Mobilizers

Phoebe Rice

Published 31 January 2017

Escape Artist

Katya Heldwein

Published 19 December 2016
Nature’s Confectioner

Jochen Zimmer

Published 29 November 2016

State of Fusion

Jason McLellan

Published 27 October 2016
Here Be Dragons

Brian Fox

Published 28 September 2016

SBGrid Assumes Ownership of PyMOLWiki

Published 15 September 2016
Pharm Team

Oleg Tsodikov

Published 24 August 2016

Spiro-Gyra

Alejandro Buschiazzo

Published 27 July 2016
Turning the DIALS

Nicholas Sauter

Published 29 June 2016

Pipeline Dreams

Bridget Carragher and Clint Potter

Published 26 April 2016
U-Store-It

The SBGrid Data Bank provides an affordable and sustainable way to preserve and share structural biology data

Published 28 March 2016

Big Questions, Big Answers

Jennifer Doudna

Published 22 February 2016
Not a Structural Biologist

Enrico Di Cera

Published 17 December 2015

Divide and Conquer

Kevin Corbett

Published 19 November 2015
Computing Cellular Clockworks

Klaus Schulten

Published 23 October 2015

Trans-Plant

Gang Dong

Published 26 September 2015
Keep on Moving

James Berger

Published 23 August 2015

Totally Tubular

Antonina Roll-Mecak

Published 27 July 2015
From Disorder, Function

Julie Forman-Kay

Published 29 June 2015

Into Alignment

Geoff Barton

Published 27 May 2015
Two Labs, Many Methods

Michael Sattler

Published 28 April 2015

Picture This

Georgios Skiniotis

Published 20 March 2015
Intron Intrigue

Navtej Toor

Published 20 February 2015

Cut and Paste

Martin Jinek

Published 28 January 2015
Basics and Beyond

Qing Fan

Published 18 December 2014

Bloodletting and Other Studies

Pedro José Barbosa Pereira

Published 25 November 2014
Wire Models, Wired

A brief history of UCSF Chimera

Published 29 October 2014

In Search of…New Drugs

Doug Daniels

Published 30 September 2014
An Affinity for Affinity…and Corals

John C. Williams

Published 29 August 2014

Pete Meyer, Ph.D.

Research Computing Specialist

Published 22 August 2014
Justin O'Connor

Sr. System Administrator

Published 20 August 2014

Carol Herre

Software Release Engineer

Published 15 August 2014
Elizabeth Dougherty

Science Writer

Published 13 August 2014

Andrew Morin, Ph.D.

Policy Research Fellow

Published 11 August 2014
Jason Key, Ph.D.

Associate Director of Technology and Innovation

Published 8 August 2014

Piotr Sliz, Ph.D.

Principal Investigator, SBGrid

Published 1 August 2014
New Kid on the Block

James Chen

Published 29 July 2014

Membrane Master

Tamir Gonen

Published 30 June 2014
The Natural Bridge

Piotr Sliz

Published 13 June 2014

Surprise, Surprise

Catherine Drennan

Published 26 April 2014
Gone Viral

Olve Peersen

Published 20 March 2014

All Who Wander Are Not Lost

Frank Delaglio

Published 24 February 2014
The Raw and the Cooked

Graeme Winter

Published 24 January 2014

Vacc-elerator

Peter Kwong

Published 17 December 2013
Structural Storyteller

Karin Reinisch

Published 15 November 2013

The Fixer

Jane Richardson

Published 28 October 2013
Inside the Box

Mishtu Dey

Published 17 September 2013

Sensing a Change

Brian Crane

Published 16 August 2013
Towards Personalized Oncology

Mark Lemmon

Published 16 July 2013

Brush with Fame

Yizhi Jane Tao

Published 14 June 2013
Toxic Avenger

Borden Lacy

Published 21 May 2013

Pushing the Boundaries

Stephen Harrison

Published 22 April 2013
Strength in Numbers

Joseph Ho

Published 18 March 2013

One Lab, Many Methods

Wesley Sundquist

Published 12 February 2013
Unplanned Pioneer

Tim Stevens

Published 15 January 2013

From Actin to Action

Emil Pai

Published 11 January 2013
Unstructured

A Brief History of CCP4

Published 12 December 2012

Stop, Collaborate and Listen

Eleanor Dodson

Published 5 November 2012
X-PLORer

Axel Brunger

Published 1 October 2012

Share the Wealth

Zbyszek Otwinowski

Published 22 August 2012
Unraveling RNA

Anna Pyle

Published 18 July 2012

Sharper Image

Pawel Penczek and SPARX

Published 4 June 2012
Creative Copy Cat

Pamela Bjorkman

Published 25 April 2012

Charm and Diplomacy

Gerard Kleywegt

Published 7 March 2012
From Curiosity to Cure

Marc Kvansakul

Published 13 December 2011

The Lure of the Sandbox

Paul Emsley and Coot

Published 15 October 2011
Springsteen, Tolkien, Protein

Alwyn Jones and Frodo

Published 17 June 2011

Structures Solved Simply

Paul Adams and Tom Terwilliger on Phenix

Published 2 June 2011
Escape from the Darkroom

Wolfgang Kabsch and XDS

Published 19 May 2011

Playing the Odds

Randy Read and Phaser

Published 19 May 2011
Crystallography for Kids

Lynne Howell

Published 17 May 2011

Better, Faster, Stronger, More

Victor Lamzin and ARP/wARP

Published 17 May 2011

Probing Microbes

Drawn to the Light

The Final Phase

Mind and Muscle

The Shapes of Energy

Predicting Proteins

Death Metal

Context Matters

The Crystal Whisperer

Data in Motion

The Monstrous Maw

Second Takes

Radical reactions

Floppy Physics

Structure of Equity

Life and Death of a Cell

Follow the glow

Resolution solutions

Of enzymes and membranes

Step-by-step

Moving muscle

Particle catcher

Designer drugs

Right place, right time

Shape-shifting secrets of membranes

Enzymatic action

Rules of motion

Cosmic Squared

Kaps are Cool

Spiraling into focus

Seeing cilia

For the Love of EM

Protein Puddles

Changing channels

Listening Tips

Beyond Cool

Hao Wu

Aye Aye Captain

The PARP Family Family

Frame by frame

Predicting Success

Curiouser and Curiouser

Rely on This

Proteins out of bounds

Hiding in plain sight

Jumping Genes

Data Whisperer

Flipping the Switch

Tooling Around

Comings and Goings

Transcriptional Rhythm

The Language of Gene Regulation

Not Your Average Protein

Message Received

Resistance is Futile

Twist of Fate

Drug Designer

Mathematically Minded

Garbage Out

Fixer Upper

Mobilizers

Escape Artist

Nature’s Confectioner

State of Fusion

Here Be Dragons

SBGrid Assumes Ownership of PyMOLWiki

Pharm Team

Spiro-Gyra

Turning the DIALS

Pipeline Dreams

U-Store-It

Big Questions, Big Answers

Not a Structural Biologist

Divide and Conquer

Computing Cellular Clockworks

Trans-Plant

Keep on Moving

Totally Tubular

From Disorder, Function

Into Alignment