Biology Reference
In-Depth Information
From genes to genome
Selected ORF:
Based on elucidated function
Genome A
Designed genes
Genome B
Accessory sequences for
functional Genes:
Promoters, Terminators, etc.
Assembly of Genes for DNA:
Order and orientation of genes
Intra gene sequences, etc.
Functional genome:
Circular form with
replication origin sequence,
etc.
FIGURE 12.5
Flows from genes to genome. Design of a new genome needs a number of factors in addition to the list of genes. Genes are
selected from various existing genome resources or de novo designed ones on top. Variety of accessory sequence
information is needed for these genes to function appropriately in the second step. Relevant genes assembled in one DNA
molecule separately in the third step. Finally, combining all the DNA molecules into one circular form with nucleotide
sequences in need. Our model is shown in
Figure 12.6
.
236
general
should be far more valuable and BGM cell might be likely a plausible
one (Itaya, unpublished).
'
chassis
'
Complete Nucleotide Sequence for Designed Genome
There are numerous approaches to reorganize genomes starting with a small number of
genes.
47,48
These approaches unveil how to modify certain genes in primary metabolic
pathways of interest, and are not expanded to large-scale alteration of host genomes as
illustrated in
Figure 12.5
. Considering that genes with unknown functions still amount to
up to 40% of all genes even for most well-studied
E. coli
K-12, genes pertinent to a de novo
genome blueprint ought to be limited to genes with known functions. Function unknown
genes are conversely in favor of reducing the number of genes and promoters towards a
minimal genome construction. For example, approximately 270
350 essential genes for
single bacterial life have been estimated.
47,48
The list of essential genes possesses ORF
information only. Their promoters, terminators, differences in codon usages, etc. are all
neglected, and remain options to draw complete nucleotide sequences of newly designed
genomes as illustrated in
Figure 12.5
. Complete nucleotide sequences in addition to
promoters and termination should be properly provided. Additional factors, gene orders,
gene orientations, sequences between genes, origin of chromosome replication (
oriC
),
termination sequence (
terC
), and location of genes in the genome should be taken into
account to draw the complete sequence, as summarized in
Figure 12.5
. Less attention at
present is paid to additional factors such as ribosome RNA genes, GC content, copy number
per genome, and multiplicity of genomes per cell.
Smallest Genome versus Minimal Set of Genes
The increasing number and variety of complete genome sequences raised a fundamental
question of how many genes are essential for cellular life, and if a genome carrying those
