Sc2.0 project hits new milestone: 5 additional chromosomes completed!

The global Sc2.0 team has built five new synthetic yeast chromosomes, meaning that 30 percent of S.cerevisiae’s genetic material has now been swapped out for engineered replacements. This is one of several findings of a package of seven papers published March 10 as the cover story for Science.

An international team of more than 200 authors produced the latest work from the Synthetic Yeast Project (Sc2.0). By the end of this year, this international consortium hopes to have designed and built synthetic versions all 16 chromosomes – the structures that contain DNA – for S. cerevisiae.

Like computer programmers, scientists add swaths of synthetic DNA to – or remove stretches from – human, plant, bacterial or yeast chromosomes in hopes of averting disease, manufacturing medicines, or making food more nutritious. Yeast has long served as an important research model because their cells share many features with human cells, but are simpler and easier to study.

“This work sets the stage for completion of designer, synthetic genomes to address unmet needs in medicine and industry,” says Jef Boeke, the Sc2.0 project director.  “Beyond any one application, the papers confirm that newly created systems and software can answer basic questions about the nature of genetic machinery by reprogramming chromosomes in living cells.”

In March 2014, Sc2.0 successfully assembled the first synthetic yeast chromosome (synthetic chromosome 3 or synIII) comprising 272,871 base pairs, the chemical units that make up the DNA code. The new round of papers consists of an overview and five papers describing the first assembly of synthetic yeast chromosomes synII, synV, synVI, synX, and synXII. A seventh paper provides a first look at the 3D structures of synthetic chromosomes in the cell nucleus which mimic their native counterparts with remarkable fidelity.

Many technologies developed in Sc2.0 serve as the foundation for GP–write, a related initiative aiming to synthesize complete sets of human and plant chromosomes (genomes) in the next ten years. GP-write will hold its next meeting in New York City on May 9-10, 2017; please visit this site for more information.  

Global Production

To begin synthesizing a yeast chromosome, researchers must first plan thousands of changes, some of which empower them to move around pieces of chromosomes in a kind of fast, high-powered evolution. Other changes remove stretches of DNA code found to be unlikely to have a functional role by past efforts. The BioStudio software as developed by a team at Johns Hopkins led by Joel Bader.

With the edits made, the team starts to assemble edited, synthetic DNA sequences into ever larger chunks, which are finally introduced into yeast cells, where cellular machinery finishes building the chromosome. A major innovation captured in the current round of papers involves this last step.

Previously, researchers were required to finish building one piece of a chromosome before they could start work on the next. Sequential requirements are bottlenecks, says Boeke, which slow processes and increase cost. The current round of papers features several efforts to “parallelize” the assembly of synthetic chromosomes.

Labs around the globe each synthesized different pieces in strains of yeast that were then mated (crossed) to quickly yield thriving yeast, not just with an entire synthetic chromosome, but in some instances with more than one. Specifically, a paper led by author Leslie Mitchell, PhD, a post-doctoral fellow from Boeke’s lab at NYU Langone, described the construction of a strain containing three synthetic chromosomes.

“Steps can be accomplished at the same time in many locales and then assembled at the end, like networking laptops to create a global super computer,” says Mitchell.

Along the way, the global team honed a number of innovations and came to understand yeast biology better. A team at Tsinghua University, for instance, led an effort where six teams built in pieces synthetic chromosome XII (synXII), which was then assembled into a final molecule more than a million base pairs (a megabase) in length. This largest synthetic chromosome to date is still 1/3,000 of what would be needed to build a human genome molecule, so new techniques will be needed.

In addition, experiments demonstrated that drastic changes can be made to the genomes of yeast without killing them, says Boeke. Yeast strains, for instance, survived experiments where sections of DNA code were moved from one chromosome to another, or even swapped between yeast species, with little effect. Genetically pliable (plastic) organisms make good platforms for the dramatic engineering that may be needed for future applications. The search for differences between the wild type and synthetic chromosomes was taken to new heights by the BGI/Edinburgh effort on synII, which used a “Transomic” approach to deeply profile the DNA, RNA protein and even metabolomics and phenomics, and confirm the “yeastiness” of the altered strain and its chromosomes.

The package of seven newly published had authors from ten universities in several countries, including the US (NYU Langone, Johns Hopkins), China (Tsinghua, Tianjin), France (Institut Pasteur, Sorbonne Universités), and Scotland (Edinburgh); along with authors from key industry partners: BGI, the leading Chinese genomics company, and US/China-based Genscript.

Led by the School of Chemical Engineering and Technology at Tianjin University in China, the paper describing the synthesis of SynV is noteworthy in that is was done by undergraduate students as part of “Build-a-Genome China”, a class first taught in the United States at Johns Hopkins, where Boeke worked before coming to NYU Langone. This is part of an emerging global network of “chromosome foundries,” says Boeke, “which is building the next generation of synthetic biologists along with chromosomes.” The Tianjin group also notably completed two chromosomes, and developed powerful methods for “debugging” errors found in synthetic chromosomes.

In addition to Boeke and Mitchell, lead organizers for the current studies included Ying-Jin Yuan of Tianjin and Junbiao Dai of Tsinghua University, Joel Bader from Johns Hopkins, Romain Koszul at the Institut Pasteur, Yizhi Cai at the University of Edinburgh, and Huanming Yang at BGI. The US studies were supported principally by the National Science Foundation. Other key funding sources were the China National High Technology Research and Development Program, the National Science Foundation of China, the Chinese Ministry of Science and Technology, the UK Biotechnology and Biological Sciences Research Council, and ERASynBio.

Links to seven papers:

5th Annual Sc2.0 and Synthetic Genomes Conference, Edinburgh, UK on July 8-9, 2016

smallyeast

On July 8th-9th 2016 scientists from around the world will convene in Edinburgh at Dynamic Earth to discuss the progress of the international synthetic yeast genome project as well as other advances in genome engineering including genome assembly methodologies, mammalian synthetic biology, lab automation and software development for synthetic biology (for more details, go to conference website: http://syngenomesconf.cailab.org).

For the past four years, the conference has focused on the ongoing Synthetic Yeast Genome Project (Sc2.0). As the world’s first synthetic, designer eukaryotic genome project, the Synthetic Yeast Genome Project has garnered global attention. The Sc2.0 international consortium is building 16 designer synthetic chromosomes encompassing ~12 million base pairs of DNA, and we are around halfway through this very exciting project.

The conference has been expanded to include a focus on Synthetic Genomes and Engineering Biology. This is a hot topic and we are thrilled to announce that this year’s program will include at least one new panel discussion as well as Keynotes from leaders in the field including Jasper Rine (UC-Berkeley), Pam Silver (Harvard), Maitreya Dunham (University of Washington) and Jim Collins (MIT). The meeting will also feature panel speakers, demonstrations of the latest in lab automation, updates from the DNA synthesis industry and an exciting poster session.

Finally, delegates will be able to experience at first hand some local yeast strains in action with a glass or two of the local craft beers. During the event delegates will also get to enjoy many of the premiere foods for which Scotland has an international reputation.

There will be plenty of opportunity to burn off any additional calories at a lively traditional Ceilidh after the conference dinner and by strolling around the beautiful old city of Edinburgh during the long midsummer days! This meeting is being sponsored by LabCyte, BBSRC, Twist Bioscience, Autodesk, Gen9, Thermo Fisher Scientific, Synthetic Genomics, SULSA, the US National Science Foundation, the University of Edinburgh, New York University, and the UK Centre for Mammalian Synthetic Biology.

New York Genome Center (NYGC) hosts 4th International Sc2.0 and synthetic Genomes meeting

sc2-meeting-2015The fourth international meeting of our group was held at the NYGC in lower Manhattan on July 16-17, 2015, and organized by Jef Boeke, Nancy J. Kelley and Leslie Mitchell. At the last meeting, our group decided to expand to a two day meeting and also to expand the topic area to include discussion and presentations on other synthetic genomes. Jef Boeke kicked off the meeting with an overview of the Sc2 project, and there were two nuts and bolts workshops where each team explained progress and challenges. Highlights included panel discussions on synthetic genomes and society and discussions of what is the next multicellular genome that should be synthesized. Sessions highlighting the relationship of yeast genomes to the flavors and behaviors of certain alcoholic beverages were discussed by Daniel Johnson and Sakkie Pretorius of the Australian Wine Research Institute and by Troels Prahl of White Labs with his colleague Toby Richardson of Synthetic Genomics Inc. Representatives of DNA synthesis and robotics and instrument companies were also in attendance. A very exciting meeting all around! We hope to see you in Edinburgh next year:

5th International Sc2.0 and Synthetic Genomes meeting, Dynamic Earth, Edinburgh, July 8-9, 2016, Main Organizer: Patrick Cai. Keynote speakers are Jasper Rine and Jim Collins.

Build-a-Genome Network Workshop, Aug 14-16 Loyola University Maryland, Baltimore MD

The Build-a-Genome (BAG) course offers undergraduate students an exceptional opportunity to participate in the cutting-edge research of the Synthetic Yeast Project. BAG offers students an authentic laboratory experience where they perform fundamental techniques in synthetic genomics, present and critique their data, and troubleshoot experiments until successful. By completion of the course, students who worked on synthetic chromosome III became so fluent in molecular and synthetic biology techniques that they produced numerous synthetic chromosome “building blocks” and earned authorship on that milestone research paper. After being established at Johns Hopkins University, BAG franchises were established at Loyola University Maryland and Tianjin University in China. Thanks to funding from the National Science Foundation RCN-UBE program, the Build-a-Genome Network has now been established with the goal of broadening the number of colleges and universities that offer the BAG course.

A national workshop for the Build-a-Genome Network will be held from August 14th to 16th at Loyola University Maryland in Baltimore. This meeting will:

(1) Introduce new members to the Synthetic Yeast Project and the BAG workflow through a series of talks, hands-on bioinformatics exercises, and wet-lab activities.
(2) Discuss strategies for adapting the BAG course to diverse undergraduate institutions. We seek to preserve the most attractive features of the BAG course while confronting the logistical hurdles that may arise when implementing research-intensive courses at undergraduate institutions.
(3) Develop course learning objectives and assessment tools for different variations of the BAG course.

These activities will create a network of expertise and “ready-to-implement” frameworks, both of which will allow network participants to implement the BAG curriculum (or similar synthetic genomics projects) at a broad range of academic institutions. For more information please contact Rob Newman (rhnewman@ncat.edu), Eric Cooper (ecooper@hartwick.edu), or Lisa Scheifele (lzscheifele@loyola.edu).

First SAVI-sponsored joint US-China paper on Sc2.0 published

Two graduate students from Tianjin University, Qiuhui Lin and Jia Bin, from the laboratory of Yingjin Yuan at Tianjin University traveled to Johns Hopkins University where they worked in the lab of Jef Boeke for several months, in an effort to exchange scientific information, and develop new methods.  Working with postdoctoral fellow Leslie Mitchell and graduate students Jingchuan Luo and Zhuwei Xu they developed efficient and standardized methods for assembling “Minichunks” of 2.5-4 kb, stringing together Building Blocks previously made by JHU “Build A Genome” students. Then the “RADOM” method, which produces up to 10 kb fragments “in yeasto”, used the Build A Genome Class, led by Karen Zeller, as a testbed, and the workflow was implemented in BioStudioDb by Kun Yang.  The work is published in ACS SynBio and sponsored by the NSF SAVI program..
The RADOM method

The RADOM method

3d International Synthetic Yeast Genome (Sc2.0) Consortium Meeting, Taormina, Italy on June 20, 2014 – sponsored by NSF SAVI

We are pleased to announce that this summer on June 20th, we will be hosting the 3d International Synthetic Yeast Genome (Sc2.0) Consortium Meeting at the Hotel Villa Diodoro, Sicily, Italy. This day-long meeting is now open for registration.  Notably it will be held the day after the International Synthetic and Systems Biology Summer School, so it will be easy to attend both activities.

The Synthetic Yeast Genome Project (Sc2.0) is synthesizing and constructing a modified version of the Saccharomyces cerevisiae genome to test biological questions and give new functions.

We will be bringing those around the world involved in the Sc2.0 project together to discuss progress on the synthetic genome, opportunities to use the strains and tools of the project, and related projects in synbio and sysbio. This meeting is open to all interested in Sc2.0 and we encourage you (and your colleagues) to register if you’d like to attend.

http://syntheticyeast3.eventbrite.com/

Please note the happy smiling faces of the participants at the 2d Sc2.0 meeting in London — this time we will sample some Sicilian beers and maybe even wines!

IMG_0159

NYU Langone Medical Center Press Release

Scientists Synthesize First Functional “Designer” Chromosome in Yeast

Study reports major advance in synthetic biology

March 27, 2014 (All day)

An international team of scientists led by Jef Boeke, PhD, director of NYU Langone Medical Center’s Institute for Systems Genetics, has synthesized the first functional chromosome in yeast, an important step in the emerging field of synthetic biology, designing microorganisms to produce novel medicines, raw materials for food, and biofuels.

Over the last five years, scientists have built bacterial chromosomes and viral DNA, but this is the first report of an entire eukaryotic chromosome, the threadlike structure that carries genes in the nucleus of all plant and animal cells, built from scratch. Researchers say their team’s global effort also marks one of the most significant advances in yeast genetics since 1996, when scientists initially mapped out yeast’s entire DNA code, or genetic blueprint.

“Our research moves the needle in synthetic biology from theory to reality,” says Dr. Boeke, a pioneer in synthetic biology who recently joined NYU Langone from Johns Hopkins University.

“This work represents the biggest step yet in an international effort to construct the full genome of synthetic yeast,” says Dr. Boeke. “It is the most extensively altered chromosome ever built. But the milestone that really counts is integrating it into a living yeast cell. We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot.”

In this week’s issue of Science online March 27, the team reports how, using computer-aided design, they built a fully functioning chromosome, which they call synIII, and successfully incorporated it into brewer’s yeast, known scientifically as Saccharomyces cerevisiae.

The seven-year effort to construct synIII tied together some 273, 871 base pairs of DNA, shorter than its native yeast counterpart, which has 316,667 base pairs. Dr. Boeke and his team made more than 500 alterations to its genetic base, removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins, and “jumping gene” segments known to randomly move around and introduce mutations. Other sets of base pairs were added or altered to enable researchers to tag DNA as synthetic or native, and to delete or move genes on synIII.

“When you change the genome you”re gambling. One wrong change can kill the cell,” says Dr. Boeke. “We have made over 50,000 changes to the DNA code in the chromosome and our yeast still live. That is remarkable. It shows that our synthetic chromosome is hardy, and it endows the yeast with new properties.”

The Herculean effort was aided by some 60 undergraduate students enrolled in the “Build a Genome” project, founded by Dr. Boeke at Johns Hopkins. The students pieced together short snippets of the synthetic DNA into stretches of 750 to 1,000 base pairs or more. These pieces were then assembled into larger ones, which were swapped for native yeast DNA, an effort led by Srinivasan Chandrasegaran, PhD, a professor at Johns Hopkins. Chandrasegaran is also the senior investigator of the team’s studies on synIII.

Student participation kicked off what has become an international effort, called Sc2.0 for short, in which several academic researchers have partnered to reconstruct the entire yeast genome, including collaborators at universities in China, Australia, Singapore, the United Kingdom, and elsewhere in the U.S.

Yeast chromosome III was selected for synthesis because it is among the smallest of the 16 yeast chromosomes and controls how yeast cells mate and undergo genetic change. DNA comprises four letter-designated base macromolecules strung together in matching sets, or base pairs, in a pattern of repeating letters. “A” stands for adenine, paired with “T” for thymine; and “C” represents cysteine, paired with “G” for guanine. When stacked, these base pairs form a helical structure of DNA resembling a twisted ladder.

Yeast shares roughly a third of its 6,000 genes—functional units of chromosomal DNA for encoding proteins — with humans. The team was able to manipulate large sections of yeast DNA without compromising chromosomal viability and function using a so-called scrambling technique that allowed the scientists to shuffle genes like a deck of cards, where each gene is a card. “We can pull together any group of cards, shuffle the order and make millions and millions of different decks, all in one small tube of yeast,” Dr. Boeke says. “Now that we can shuffle the genomic deck, it will allow us to ask, can we make a deck of cards with a better hand for making yeast survive under any of a multitude of conditions, such as tolerating higher alcohol levels.”

Using the scrambling technique, researchers say they will be able to more quickly develop synthetic strains of yeast that could be used in the manufacture of rare medicines, such as artemisinin for malaria, or in the production of certain vaccines, including the vaccine for hepatitis B, which is derived from yeast. Synthetic yeast, they say, could also be used to bolster development of more efficient biofuels, such as alcohol, butanol, and biodiesel.

The study will also likely spur laboratory investigations into specific gene function and interactions between genes, adds Dr. Boeke, in an effort to understand how whole networks of genes specify individual biological behaviors.

Their initial success rebuilding a functioning chromosome will likely lead to the construction of other yeast chromosomes (yeast has a total of 16 chromosomes, compared to humans’ 23 pairs), and move genetic research one step closer to constructing the organism’s entire functioning genome, says Dr. Boeke.

Dr. Boeke says the international team’s next steps involve synthesizing larger yeast chromosomes, faster and cheaper. His team, with further support from Build a Genome students, is already working on assembling base pairs in chunks of more than 10,000 base pairs. They also plan studies of synIII where they scramble the chromosome, removing, duplicating, or changing gene order.

Detailing the Landmark Research Process

Before testing the scrambling technique, researchers first assessed synIII’s reproductive fitness,  comparing its growth and viability in its unscrambled from  — from a single cell to a colony of many cells — with that of native yeast III. Yeast proliferation was gauged under 19 different environmental conditions, including changes in temperature, acidity, and hydrogen peroxide, a DNA-damaging chemical. Growth rates remained the same for all but one condition.

Further tests of unscrambled synIII, involving some 30 different colonies after 125 cell divisions, showed that its genetic structure remained intact as it reproduced. According to Dr. Boeke, individual chromosome loss of one in a million cell divisions is normal as cells divide. Chromosome loss rates for synIII were only marginally higher than for native yeast III.

To test the scrambling technique, researchers successfully converted a non-mating cell with synIII to a cell that could mate by eliminating the gene that prevented it from mating.

Funding support for these experiments was provided by National Science Foundation, the National Institutes of Health, and Microsoft. Corresponding federal grant numbers are MCB-0718846 and GM-077291. Additional funding support was provided by fellowships from La Fondation pour la Recherche Médicale, Pasteur-Roux, National Sciences and Engineering Research Council of Canada, U.S. Department of Energy, and grants from the Exploratory Research Grant from the Maryland Stem Cell Research Fund and the Johns Hopkins University Applied Physics Laboratory.

Besides the teams at NYU Langone and Johns Hopkins, other scientific teams involved in the global Sc2.0 research effort are based at Loyola University in Baltimore, Md; BGI in Shenzhen, China; Tianjin University in China; Tsinghua University in China; MacQuarie University in Sydney, Australia; the Australian Wine Institute in Adelaide, Australia; the National University of Singapore; Imperial College, London, England; and the University of Edinburgh in Scotland.

£1 Million from BBSRC and EPSRC for Synthetic Yeast

David Willetts, Minister for Universities and Science, announced nearly £1M funding for synthetic yeast at the Sixth International Meeting on Synthetic Biology (SB6.0) at Imperial College London on Thursday (July 11). David Willetts said: Sc2.0 project “is truly groundbreaking and pushes the boundaries of synthetic biology. Thanks to this investment, UK scientists will be at the centre of an international effort using yeast – which gives us everything from beer to biofuels – to provide new research techniques and unparalleled insights into genetics. This will impact important industrial sectors like life sciences and agriculture.” Funding for the yeast project is part of a £60M package for synthetic biology.

Dr.Tom Ellis, Lecturer in Synthetic Biology at Imperial College London, said: “We are excited to be welcoming our new international consortium partners to London to discuss Sc2.0. Having recently secured funding for the UK to be part of this ground-breaking project, we are looking forward to getting started and being part of the action. It”s a perfect fit for our work in synthetic biology here at Imperial, where we really view yeast as a tiny factory that can be tooled-up to produce new molecules. A synthetic genome will allow us to reprogram yeast and our goal is to use it to produce new antibiotics as resistance arises to existing ones.”

When completed, synthetic yeast will be the first time scientists have built the whole genome of a eukaryotic organism – those organisms, like animals and plants, which store DNA within a nucleus. Scientists can then design different strains of synthetic yeast that contain genes to make commercially valuable products such as chemicals, vaccines or biofuels.

Professor Boeke, the overall head of the project at Johns Hopkins Medical School in Baltimore, said: “Sc2.0, once completed, will provide unparalleled opportunities for asking profound questions about biology in new and interesting ways, such as: How much genome scrambling generates a new species? How many genes can we delete from the genome and still have a healthy yeast? And how can an organism adapt its gene networks to cope with the loss of an important gene? Moreover, genome scrambling may find many uses in biotechnology, for example in the development of yeast that can tolerate higher ethanol levels.”

Alongside BBSRC and EPSRC, major funders for the Sc2.0 consortium members in their respective countries include the US National Science Foundation (NSF), the US Department of Energy, China”s Ministry of Science and Technology (MoST) and the Tsinghua University Initiative Scientific Research Program.

More related news:

http://www.guardian.co.uk/science/2013/jul/11/uk-project-synthetic-organism
http://www.epsrc.ac.uk/newsevents/news/2013/Pages/syntheticbiologyprogress.aspx
http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_10-7-2013-12-14-56
http://www.bbsrc.ac.uk/news/research-technologies/2013/130711-pr-funding-to-build-worldfirst-synthetic-yeast.aspx
https://www.gov.uk/government/news/over-60-million-for-synthetic-biology

2nd International Synthetic Yeast Genome (Sc2.0) Consortium Meeting, London, UK, July 12, 2013

We are pleased to announce that this summer on Friday 12th July, we will be hosting the 2nd International Synthetic Yeast Genome (Sc2.0) Consortium Meeting here in the UK at Imperial College London. This day-long meeting is now open for registration.  Notably it will be held the day after the SB6.0 meeting, so it will be easy to attend both.

The Synthetic Yeast Genome Project (Sc2.0) is synthesizing and constructing a modified version of the S. Cerevisiae genome to test biological questions and give new functions.

We will be bringing those around the world involved in the Sc2.0 project together to discuss progress on the synthetic S. cerevisiae genome and opportunities to use the strains and tools of the project. This meeting is open to all interested in Sc2.0 and we encourage you (and your colleagues) to register if you”d like to attend.

http://syntheticyeast.eventbrite.com/

Rumor has it microbrew beer samples will be available – as it should be for a yeast meeting. See you in London?