Genes necessary for cell division in modern bacterial cells identified

LA JOLLA, Calif., March 29, 2021 /PRNewswire/ -- Scientists from the J. Craig Venter Institute (JCVI), Massachusetts Institute of Technology (MIT), and National Institute of Standards and Technology (NIST) have identified 5 genes of previously unknown function which are used in cell division by nearly all modern bacterial species. Identifying these genes is an extension of decades of synthetic biology advances at JCVI, expanding on our understanding of the first principles of life.

JCVI constructed the first cell with a synthetic genome (Mycoplasma mycoides JCVI-syn1.0) in 2010, which is nearly identical to the wild type Mycoplasma mycoides subspecies capri (with the addition of watermarks), a bacterial parasite commonly found in goats. Building on this work in 2016, the team constructed a bacterial cell that encoded only 473 genes—fewer than half the number of genes found in JCVI-syn1.0—needed for replication and other vital cell functions. This new, near minimal cell, which has the smallest genome of any known cell capable of growth in laboratory media, was dubbed JCVI-syn3.0.

At the time of the minimal cell discovery, scientists noted that while JCVI-syn1.0 cells looked identical to the wild type, JCVI-syn3.0 cells were notably larger and exhibited unusual behavior when dividing. Senior author Elizabeth Strychalski, Ph.D., group leader of the Cellular Engineering Group at NIST, and first author James Pelletier, Ph.D., then a graduate student in the MIT Center for Bits and Atoms, developed microfluidics experiments where it was possible to observe and compare cellular division of JCVI-syn1.0 and JCVI-syn3.0.

"James and Elizabeth's observations told us that we had removed genes from a naturally occurring organism that enabled it to divide like a normal cell. This sent our team on a seven-year journey to discover what genes were responsible for modern cell division," commented John Glass, Ph.D., senior author and leader of the synthetic biology group at JCVI.

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Video: https://youtu.be/BBaUM7AyoIs 
Caption: Time-lapse video showing cell division and growth of three organisms with synthetic genomes.
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Motivated by the striking differences between the normal cell division exhibited by JCVI-syn1.0 and the lack of cell division shown in time-lapse videos of the minimal cell growing in microfluidic chambers, the JCVI team began a long series of experiments to determine which genes would be necessary to restore normal cell division to JCVI-syn3.0.

Fortunately, the JCVI team found a mutant made during the construction of the minimal cell that had an additional 19 genes beyond JCVI-syn3.0. This mutant, JCVI-syn3A, both looked and divided like the wild type and JCVI-syn1.0. Armed with the knowledge that one or more of the additional 19 genes in JCVI-syn3A enabled that organism to divide normally, the JCVI team set out to determine which gene or genes were involved.

JCVI scientist Lijie Sun, Ph.D., co-lead author on the paper, undertook the laborious task of constructing dozens of mutants in which individual genes and then groups of genes were added back to JCVI-syn3.0. After years of effort, she discovered to her and the project team's astonishment that only a specific set of seven otherwise non-essential genes were responsible for allowing JCVI-syn3A to divide and look like a modern bacterial cell. That set included two known cell division genes, ftsZ and sepF, plus 5 genes whose roles in the cell were completely unknown before this work.

Dr. Strychalski stated, "Designing whole genomes to achieve desired phenotypes stands as a grand challenge in synthetic biology. But our capacity to synthesize and modify genomes has rapidly outpaced our ability to predict phenotype from genotype for large-scale genome design. Our work uses reverse genetics to understand the function of genes of unknown function involved in the basic cell processes of controlling cell size and shape, and cell division. Every gene we are able to pair with its function gets us closer to realizing the goal of designing genomes for engineering cells."

JCVI-syn3.0 and JCVI-syn3A now provide a robust platform for investigating how modern cell division and cell size evolved. The synthetic cell and minimal cell are being used by over 40 labs worldwide. Among those research studies there are adapted laboratory evolution experiments being done by Bernhard Palsson's lab at University of California, San Diego and Jay Lennon's lab at the University of Indiana, research into membrane composition work being done in James Saenz's lab at the Technische Universität Dresden, and whole cell computational modeling being done by Zan Luthey-Schulten's group at the University of Illinois Urbana-Champaign. The cells are even being explored for commercial application.

The National Center for Imaging and Microscopy Research at the University of California, San Diego also contributed critical scanning electron micrographs of the cells being studied in this project.

The complete study, "Genetic requirements for cell division in a genomically minimal cell," may be found in the journal Cell.

About J. Craig Venter Institute

The J. Craig Venter Institute (JCVI) is a not-for-profit research institute in Rockville, Maryland and La Jolla, California. dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 150 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The JCVI is a 501(c)(3) organization. For additional information, please visit www.JCVI.org.

SOURCE J. Craig Venter Institute

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