CH391L/S13/CleanGenomes

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Introduction)
Line 1: Line 1:
[[Category:CH391L_S13]]
[[Category:CH391L_S13]]
-
===Introduction===
+
=Introduction=
A clean or minimal genome refers to the minimum set of genes that an organism needs to survive and reproduce.  This implies that there are genes that are “nonessential” to the organism’s survival and can be removed without destroying the cell or disrupting its growth cycle.  Proposed minimal genomes would eliminate extraneous DNA.  Examples of nonessential DNA would include duplicate genes, transposable elements and catabolic pathways used for the intake and breakdown of complex biomolecules and would be removed from a minimal genome.<cite>ForsterChurch2006</cite><cite>Hutchison1999</cite>
A clean or minimal genome refers to the minimum set of genes that an organism needs to survive and reproduce.  This implies that there are genes that are “nonessential” to the organism’s survival and can be removed without destroying the cell or disrupting its growth cycle.  Proposed minimal genomes would eliminate extraneous DNA.  Examples of nonessential DNA would include duplicate genes, transposable elements and catabolic pathways used for the intake and breakdown of complex biomolecules and would be removed from a minimal genome.<cite>ForsterChurch2006</cite><cite>Hutchison1999</cite>
 +
 +
A reduced genome is..............................
===Advantages of a Minimal Genome===
===Advantages of a Minimal Genome===
Line 15: Line 17:
Future advances in genome replication, unnatural amino acids, drug development, fuel production and biomaterial synthesis could be accelerated by simplifying and streamlining the genome used to code for a cell.<cite>ForsterChurch2006</cite><cite>JewettForster2010</cite>
Future advances in genome replication, unnatural amino acids, drug development, fuel production and biomaterial synthesis could be accelerated by simplifying and streamlining the genome used to code for a cell.<cite>ForsterChurch2006</cite><cite>JewettForster2010</cite>
-
===Genome Reduction===
+
===Minimal/Clean Genomes vs. Wild Type Genomes vs. Reduced Genomes===
 +
 
 +
===Estimating the Number of Essential Genes===
 +
 
 +
 
 +
==Genome Reduction==
One approach to creating more reliable, efficient host organisms for synthetic constructs is the reduction of the genome to eliminate extraneous genes, mutagenic mobile elements, and other unnecessary or destabilizing factors. This can be viewed as a form of reverse engineering of extant strains.   
One approach to creating more reliable, efficient host organisms for synthetic constructs is the reduction of the genome to eliminate extraneous genes, mutagenic mobile elements, and other unnecessary or destabilizing factors. This can be viewed as a form of reverse engineering of extant strains.   
Line 31: Line 38:
-
===Minimal Genome Synthesis===
+
==Minimal Genome Synthesis==
Another approach is the synthesis of a minimal, designed genome from scratch using DNA synthesis technology and the transformation of this genome into cells to create a viable, novel, synthetic organism. This approach can be viewed as forward engineering of a novel organism, but would likely be informed by studies which determine the minimal set of genes necessary for a living organism.
Another approach is the synthesis of a minimal, designed genome from scratch using DNA synthesis technology and the transformation of this genome into cells to create a viable, novel, synthetic organism. This approach can be viewed as forward engineering of a novel organism, but would likely be informed by studies which determine the minimal set of genes necessary for a living organism.

Revision as of 04:34, 3 February 2013

Contents

Introduction

A clean or minimal genome refers to the minimum set of genes that an organism needs to survive and reproduce. This implies that there are genes that are “nonessential” to the organism’s survival and can be removed without destroying the cell or disrupting its growth cycle. Proposed minimal genomes would eliminate extraneous DNA. Examples of nonessential DNA would include duplicate genes, transposable elements and catabolic pathways used for the intake and breakdown of complex biomolecules and would be removed from a minimal genome.[1][2]

A reduced genome is..............................

Advantages of a Minimal Genome

As the complexity of synthetic biology projects increases, so too will the problems it will run into due to the somewhat inherent randomness inside each cell. A minimal genome would give synthetic biologists a reliable and predictable “chassis” that could provide an ideal platform for perusing new research.

Current model organisms used in modern research contain deleterious DNA and gene products (like insertion sequences and unforeseen molecular interactions) which could disable or prohibit future endeavors by interacting unfavorably with whatever the “subject of interest” is.[1][3] Smaller amounts of extraneous gene products would simplify and reduce the cost of extraction and purification of cell parts, biomolecules and pharmaceuticals, many of which would be more expensive and time consuming to separate from a population of cells by conventional means.[4]

Gene stability in reduced genomes has been improved by removing transposable elements (TEs), error prone DNA polymerases and the enzymes responsible for the SOS response. Spontaneous, random genetic changes would be extremely harmful toward a minimal cell lacking a number of redundant systems. A stable genome would be a very desirable trait for research and experiment replication.[4][5]

Future advances in genome replication, unnatural amino acids, drug development, fuel production and biomaterial synthesis could be accelerated by simplifying and streamlining the genome used to code for a cell.[1][3]

Minimal/Clean Genomes vs. Wild Type Genomes vs. Reduced Genomes

Estimating the Number of Essential Genes

Genome Reduction

One approach to creating more reliable, efficient host organisms for synthetic constructs is the reduction of the genome to eliminate extraneous genes, mutagenic mobile elements, and other unnecessary or destabilizing factors. This can be viewed as a form of reverse engineering of extant strains.

Systematic Genome Reduction

One natural approach to engineering strains with a reduced genome is to systematically identify and delete regions of the genome not necessary for host cell survival. Posfai et al. created the MDS strains (multiple deletion strains) by aligning the genomes of multiple genomes of E. coli, identifying regions which were absent in multiple strains, and deleting them via Lambda Red recombination. All IS elements were removed as well, lowering the mutation rate and increasing the stability of genetic constructs introduced into the cell. The strain had comparable growth rate compared to wild type.[4][6]

Ara et al. constructed a minimal version of the B. subtilis genome in 2007. [7] This strain had slightly decreased growth rate compared to wild-type, but displayed normal morphology and similar protein production capabilities.

Selection for Reduced Genome

Long-term evolution of strains under the correct conditions could select for a genome of minimal size. Such conditions may include growth in rich media lacking sugars to favor the loss of biosynthetic pathways or sugar metabolism operons, growth in structured environments which favor a smaller cell, or growth under other conditions which favor the loss of unnecessary genes.

Mycoplasma mycoides genome synthesis strategy
Mycoplasma mycoides genome synthesis strategy


Minimal Genome Synthesis

Another approach is the synthesis of a minimal, designed genome from scratch using DNA synthesis technology and the transformation of this genome into cells to create a viable, novel, synthetic organism. This approach can be viewed as forward engineering of a novel organism, but would likely be informed by studies which determine the minimal set of genes necessary for a living organism.

Mycoplasma mycoides Synthesis

Gibson et al synthesized the first artificial cell by generating the Mycoplasma mycoides genome from digitized genome information and transforming it into Mycoplasma capricolum cells devoid of genomic information. These cells were capable of continuous self-replication and were identified by "watermarks" inserted in the genome. This technology could be utilized in the future to create cells with novel and useful properties from scratch.[8][9]

References

  1. Forster AC and Church GM. . pmid:16924266. PubMed HubMed [ForsterChurch2006]
  2. Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, and Venter JC. . pmid:10591650. PubMed HubMed [Hutchison1999]
  3. Jewett MC and Forster AC. . pmid:20638265. PubMed HubMed [JewettForster2010]
  4. Kolisnychenko V, Plunkett G 3rd, Herring CD, Fehér T, Pósfai J, Blattner FR, and Pósfai G. . pmid:11932248. PubMed HubMed [Kolisnychenko2002]
  5. Kolisnychenko V, Plunkett G 3rd, Herring CD, Fehér T, Pósfai J, Blattner FR, and Pósfai G. . pmid:11932248. PubMed HubMed [Kolisnychenko2002]
  6. Iwadate Y, Honda H, Sato H, Hashimoto M, and Kato J. . pmid:21658106. PubMed HubMed [Iwadate2011]
  7. Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, and Blattner FR. . pmid:16645050. PubMed HubMed [Posfai2006]
  8. Ara K, Ozaki K, Nakamura K, Yamane K, Sekiguchi J, and Ogasawara N. . pmid:17115975. PubMed HubMed [Ara2007]
  9. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:18218864. PubMed HubMed [Gibson2008]
  10. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. . pmid:20488990. PubMed HubMed [Gibson2010]
All Medline abstracts: PubMed HubMed
Personal tools