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Chapter 16 : How Many Genes Does a Cell Need?

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How Many Genes Does a Cell Need?, Page 1 of 2

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Abstract:

This chapter reviews, discusses, and proposes studies aimed at determining how many genes are really necessary when cells are grown under ideal laboratory conditions. A list of the 100 protein-coding genes disrupted in the 2006 study is provided in this chapter. Using The Institute for Genomic Research (TIGR) functional classification scheme, the 100 genes can be broken into 15 groups based on their main roles. Seven DNA repair and recombination genes were disrupted, including recA, which is one of the most ubiquitous proteins found in nature. A minimal set of genes cannot be convincingly determined by either comparative genomics or global transposon mutagenesis. However, these studies do identify more than 200 genes for core functions such as DNA replication, transcription, protein translation, energy metabolism, transport, lipid metabolism, nucleotide metabolism, and protein fate, which one has confidence will be represented in the minimal cell. There are three possible approaches to making a minimal cell: (i) cumulative inactivation of genes using mutagens that produce frameshifts, (ii) sequential genome reduction using recombineering methods, and (iii) chemical synthesis of a minimal genome and installation into receptive cell cytoplasm. A minimal genome may not by itself be useful in a practical sense, but one can envision in the not too distance future the ability to design and synthesize microbes for useful purposes such as production of pharmaceutical products, industrial compounds, and fuels. In the future, stripped down organisms outfitted with useful biosynthetic pathways could provide the basis for new industrial processes.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16

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DNA-Directed RNA Polymerase
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Linear Double-Stranded DNA
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Figures

Image of FIGURE 1
FIGURE 1

Comparison of orthologous genes in and Rd ( ). The total number of protein-coding genes in each bacterium is based on the original 1995 annotations, which have been modified several times in the intervening years.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Image of FIGURE 2
FIGURE 2

Evolutionary tree showing the relatedness of 13 mycoplasmas. is an obligate intracellular organism and is thus distinct from others.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Image of FIGURE 3
FIGURE 3

Diagram illustrating transposon mutagenesis. The transposon carries a transposase enzyme, an antibiotic resistance gene (Tet), and terminal sequences recognized by the transposase during transposition. The transposon is generally carried on a plasmid that does not replicate in the cell to be mutagenized. Antibiotic resistance is acquired by the cells only when the transposon jumps into the cell chromosome. A gene is disrupted when the transposon lands inside a gene.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Image of FIGURE 4
FIGURE 4

genome map showing the location of genes and transposon insertion sites.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Image of FIGURE 5
FIGURE 5

Deletion of a gene by recombineering using the lambda red system. Gene A is flanked by 50 bp of sequence on each side that are the targets for a linear piece of DNA that consists of an expressible gene flanked by the two 50-bp sequences. After introduction of the DNA fragment by electroporation, recombination occurs within the two 50-bp homologous segments, thus deleting gene A and replacing it with . Subsequent steps, as described in the text, counterselect for removal of the gene, leaving a clean (“scarless”) deletion. The process can be repeated many times to remove other genes.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Image of FIGURE 6
FIGURE 6

Assembly of multiple overlapping pieces of DNA by in vitro recombination. If vector DNA is included in the reaction and it overlaps sequences at each end of the assembly, then a circular DNA is formed, which can be cloned in a suitable host cell.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Image of FIGURE 7
FIGURE 7

A diagram illustrating the basic tenet of synthetic biology. In analogy to computers, the genome of a cell is the operating system and the cytoplasm of the cell is the hardware that runs the operating system.

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
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Tables

Generic image for table
TABLE 1

Minimal protein-coding gene set defined by comparing and Rd ( )

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
Generic image for table
TABLE 2

Summary of global transposon mutagenesis insertion site data

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16
Generic image for table
TABLE 3

The essential and nonessential genes of are listed by main role and subroles using the TIGR functional classification system

Citation: Smith H, Glass J, Hutchison III C, Venter J. 2008. How Many Genes Does a Cell Need?, p 279-299. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch16

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