Biology Reference
In-Depth Information
Category of function
Number
Clustered DNA with single promoter
DNA metabolism
27
14
95
44
8
8
22
10
15
15
11
271
RNA metabolism
Protein synthesis
Cell envelope
Cell shape and division
Glycolysis
Respiratory pathways
Nucleotides
Cofactors
Other
Unknown
Total
De novo
Minimal genome
Composite 13 operons
oriC
terC
FIGURE 12.6
A scenario to produce a novel genome with a few promoters. A minimum set of genes elucidated on B. subtilis
52
is listed on
the left by function category. Relevant genes in each category if assembled under a promoter shown in the center might
function as an operon (Tsuge and Itaya, unpublished). Assembly of these operons in a circular form should result in a
genome with fewer promoters and accordingly less complicated regulation.
practical use becomes more complex when an increased number of genes have to be
handled.
47,48
Here is a good opportunity to address my motivation to advance the entire genome cloning.
As soon as I noticed plausible rough borders on genome size between eukaryotes and
prokaryotes, as well as prokaryotes and noncellular DNA as indicated in
Figure 12.1
,an
experiment was designed to prove how big the
B. subtilis
genome, at present 4.2 Mbp,
20
can
become. About 10 years later, the genome size increased to 7.7 Mbp, still in a circular
form.
3
I
240
ve learned many fundamental rules underlying the circular genome structure
described in this chapter through DNA assembly in the BGM system. In order for the size of
the
B. subtilis
genome to approach and exceed the yeast genome size, certain large DNA,
neutral in terms of gene expression influencing host
B. subtilis
, should be megacloned. Use
of the yeast genome might be a plausible neutral DNA option.
25
'
Aside from the personal ideas for innovation, the multipurpose BGM system will play
significant roles in versatile gene/genome production and delivery steps. The huge and solid
promising framework is able to aim at not only microbial breeding, but also cell
engineering and genome engineering in all disciplines of life sciences.
References
1. Itaya M. In: Pengcheng F, Latterich M, Panke. S, eds.
Systems Biology and Synthetic Biology
. John Wiley & Sons,
Inc.; 2009:155.
2. Cambray G, Mutalik VK, Arkin AP. Toward rational design of bacterial genomes.
Curr Opin Microbiol
.
2011;14:624
630.
3.
Itaya M, Tsuge K, Koizumi M, Fujita K. Combining two genomes in one cell: stable cloning of the Synechocystis
PCC6803 genome in the
Bacillus subtilis
168 genome
. Proc Natl Acad Sci USA
. 2005;102:15971
15976.
4. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H. Complete chemical synthesis,
assembly, and cloning of a
Mycoplasma genitalium
genome
Science
. 2008;319:1215
1220.
5. Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY. Sequence analysis of a complete 1.66 Mb
Prochlorococcus
marinus
MED4 genome cloned in yeast.
Nucleic Acids Res
. 2012;40(20):10375
10383.
6. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA. Creation of a bacterial cell controlled by a
chemically synthesized genome
. Science
. 2010;329:52
56.
7. Nandagopal N, Elowitz MB. Synthetic biology: integrated gene circuits.
Science
. 2011;333:1244
1248.
8. Kaneko S, Itaya M. Production of multi-purpose BAC clones in the novel
Bacillus subtilis
based host systems.
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Bacterial Artificial Chromosomes
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