Maybe the most famous one is Mycoplasma genitalium byt there are others, and notably with lower biosafety levels:
www.lgcstandards-atcc.org/products/all/49896.aspx:
- £355.00 in 2019
- biosafety level: 2
Size: 300 x 600 nm
Reproduction time: www.quora.com/unanswered/How-long-do-Mycoplasma-bacteria-take-to-reproduce-under-optimal-conditions
Has one of the smallest genomes known, and JCVI made a minimized strain with 473 genes: JCVI-syn3.0.
The reason why genitalium has such a small genome is that parasites tend to have smaller DNAs. So it must be highlighted that genitalium can only survive in highly enriched environments, it can't even make its own amino acids, which it normally obtains fromthe host cells! And because it cannot do cellular respiration, it very likely replicates slower than say E. Coli. It's easy to be small in such scenarios!
Power, Sex, Suicide by Nick Lane (2006) section "How to lose the cell wall without dying" page 184 has some related mentions puts it well very:
One group, the Mycoplasma, comprises mostly parasites, many of which live inside other cells. Mycoplasma cells are tiny, with very small genomes. M. genitalium, discovered in 1981, has the smallest known genome of any bacterial cell, encoding fewer than genes. Despite its simplicity, it ranks among the most common of sexually transmitted diseases, producing symptoms similar to Chlamydia infection. It is so small (less than a third of a micron in diameter, or an order of magnitude smaller than most bacteria) that it must normally be viewed under the electron microscope; and difficulties culturing it meant its significance was not appreciated until the important advances in gene sequencing in the early 1990s. Like Rickettsia, Mycoplasma have lost virtually all the genes required for making nucleotides, amino acids, and so forth. Unlike Rickettsia, however, Mycoplasma have also lost all the genes for oxygen respiration, or indeed any other form of membrane respiration: they have no cytochromes, and so must rely on fermentation for energy.
Downsides mentioned at youtu.be/PSDd3oHj548?t=293:
- too small to see on light microscope
- difficult to genetically manipulate. TODO why?
- less literature than E. Coli.
Data:
- www.ncbi.nlm.nih.gov/bioproject/97 contains genome, genes, proteins.
- www.genome.jp/kegg-bin/show_pathway?mge01100 all known pathways. TODO: numerical reaction coefficients? Which enzyimes mediate what? Appears to factor pathways across organisms, which is awesome.
GPU accelerated, simulates the Craig's minimized M. genitalium, JCVI-syn3A at a particle basis of some kind.
Lab head is the cutest-looking lady ever: chemistry.illinois.edu/zan, Zaida (Zan) Luthey-Schulten.
- 2022 paper: www.cell.com/cell/fulltext/S0092-8674(21)01488-4 Fundamental behaviors emerge from simulations of a living minimal cell by Thornburg et al. (2022) published on Cell
- faculty.scs.illinois.edu/schulten/lm/ actual source code. No Version control and non-code drop release, openess and best practices haven't reached such far obscure reaches of academia yet. One day.
- blogs.nvidia.com/blog/2022/01/20/living-cell-simulation/ Nvidia announcement. That's how they do business, it is quite interesting how they highlight this kind of research.
- catalog.ngc.nvidia.com/orgs/hpc/containers/lattice-microbes has a container
www.wholecellviz.org/viz.php awesome visualization of simtk, paper: www.ncbi.nlm.nih.gov/pmc/articles/PMC3413483/ A Whole-Cell Computational Model Predicts Phenotype from Genotype - 2013 - Jonathan R. Karr.
Followed up by the E. Coli Whole Cell Model by Covert Lab.
www.newyorker.com/magazine/2022/03/07/a-journey-to-the-center-of-our-cells A Journey to the Center of Our Cells (2022) by James Somers comments on M. genitalium in general, and in particular on the JCVI strains.
essential metabolism for a minimal cell (2019) mentions:
JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the basics of life.
Based on JCVI-syn3.0, they've added a few genes back to give better phenotypes, including slightly faster duplication time. Because the development cycle time is your God is also true in biology.
As of essential metabolism for a minimal cell (2019) it had only 91 genes of unknown function! So funny.
Bibliograpy:
essential metabolism for a minimal cell (2019) mentions:
- NCBI: www.ncbi.nlm.nih.gov/nuccore/CP014940.1
- 473 genes
phenomena.nationalgeographic.com/2016/04/21/we-built-the-worlds-simplest-cell-but-dunno-how-it-works/ likely talks about it.
Stuff built on top:
www.biorxiv.org/content/10.1101/2022.09.19.508583v1.fullIt is also interesting to see how they are interested in co-culture with HeLa cells, presumably to enable infectious bacterial disease studies.
CVI-syn3B strains differ from JCVI-syn3.0 by the presence of 19 additional non-essential genes that result in a more easily manipulated cell. JCVI-syn3B additionally includes a dual loxP landing pad that enables easy Cre recombinase mediated insertion of genes
At biology.indiana.edu/news-events/news/2023/lennon-minimal-cells.html (2023) they let it re-evove to it it would regain some fitness, and it did.
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