Relevant
Abstract
Without a doubt, in the past 20 or so years, we have achieved the power of biology in different ways. In the present, we have many tools for developing novel technologies and applications for organism modifications that ultimately let us know many aspects of organisms’ biology and, therefore, apply that knowledge for technological purposes. Of all the model organisms and tools for genetic modification available, Escherichia coli stands out as a model organism and what we would like to call “molecular biologist tool box.” In the present chapter, we aim to review our current knowledge regarding genetic modifications and tools for modifying E. coli to generate plasmid vectors, single and multiple gene knockouts, whole genome editing, biosensor generation and applications and synthetic gene circuits and genomes.
Keywords
- molecular biology tools
- synthetic biology
- biosensors
- plasmids
- bioengineerging
1. Introduction
Who in biology has not heard of
The main reasons why
Typical
In terms of ecology,
Phylogenetically,
The building blocks of
This organism lacks many interesting features for biotechnology, such as growing at extreme temperatures or pH, the capacity to degrade toxic compounds, pollutants, or difficult to degrade polymers [23]. But as we will see later, this bacterium is capable of doing amazing things and its only limit is our imagination.
The advancement of genomic, transcriptomic, and proteomic technologies has led to the development of several online resources for the analysis of molecular and physiological aspects of
Name | URL | Description* |
---|---|---|
EcoCyc: Encyclopedia of | https://ecocyc.org | A comprehensive database joining together genomic information with biochemical features of |
PortEco | http://www.porteco.org | A resource for knowledge and data of the biology of |
EcoliWiki | http://ecoliwiki.net/ | Community-based pages about everything related to the biology of the nonpathogenic |
EcoGen 3.0 | http://ecogene.org/ | A database dedicated to analyzing and comparing genomic and transcriptomic data |
Kegg | http://www.genome.jp/kegg-bin/show_organism?org=eco | A powerful resource for understanding molecular datasets in different contexts, also easy access to gene information |
RegulonDB | http://regulondb.ccg.unam.mx | Database on transcriptional regulation in |
http://cgsc.biology.yale.edu/ | The CGSC Database of |
Recently, using the Genome Conformation Capture technique, it was revealed that the linear organization of the genome is also true for the 3D structure, rendering neighboring genes to form small factories that are coregulated or coexpressed and showed a higher probability of forming protein-protein interactions. This organization represents two important aspects of bacterial genomes, first, the compactness in the 3D space, containing pathways in a nonrandom distribution, and second, genes that are closer to each other tend to be coexpressed and form protein-protein interactions favoring the concept of transcription factor even in microbial cells [27].
In the following sections, we will review what we consider the modern tools for genetic engineering
2. Plasmid and the E. coli revolution
Without a doubt, plasmids are the most important tools not only for the manipulation of
Why plasmids are the basis for genetic engineering? By surveying the literature and commercial sources catalogs, there is a myriad of applications for plasmids: cloning, mutagenesis, protein fusion and overexpression, shuttle vectors from bacteria to a diverse range of hosts, among others. Plasmids must be first presented and then we provide some features that are relevant regarding the importance of plasmids in molecular biology and biotechnology.
Plasmids are extrachromosomal molecules that are self-replicative and sometimes provide interesting features to its host. The term was first coined by Joshua Lederberg in 1952 referring to genetic elements in bacteria that remained as an independent molecule from the chromosome at any stage of their replication cycle [28]. The definition was further refined to all the autonomously replicating DNA molecules to avoid including viruses. These molecules are present not only in eubacteria but also are found in Archea and some lower eukaryotic organisms [29]. In nature, many bacteria contain self-replicating DNA molecules that can be harnessed for molecular biology applications.
In the 1970s, the first generation of cloning plasmids was created, and from that moment on, research in the biological area was enriched with a powerful tool. Plasmids must contain several important features to be used in research: proper size for ease to transform or transfect, selection markers, a replication origin, regulatory elements to control expression, and transcription termination. All features are important when designing a plasmid vector for the desired application, the reader can imagine the goal, and there will always be a way to create the molecular tool for achieving such a goal, and that is possible due to the basic structure of most plasmids used in molecular biology and their modularity [31]. In Table 2, we summarize some of the most important features (modules) that plasmids must have in order to serve for different applications. We point out that sequence composition and structure, copy number, selection marker, and special features such as reporter proteins or regulatory elements are the most important features in a plasmid and can influence the outcome of the desired application.
Name | Type of element | Characteristics |
---|---|---|
ColE1 | Replication origin | Generates 15–20 copies of each plasmid molecule. Colicin production. Related to plasmids that confer immunity to phage infections [32]. Found in low copy plasmids such as pBR322 [33]. There are mutations in this replication origin that leads to high copy number plasmids, such as pUC series that can render up to 700 copies per cell [34, 35] |
p15A | Replication origin | Low copy number replication origin, estimated in 18–22 copies per cell [36]. This type of replication origin is often found in pACYC and its derivative vectors |
pMB1 | Replication origin | Versatile replication origin. The original sequence generates 15–20 copies per cell, but a mutant version can lead up to 700 copies per cell [37]. This plasmid contains the |
pSC101 | Replication origin | Five copies per cell [38] |
R6K | Replication origin | 15–20 copies per cell. Requires the π protein from the gene |
Ampr, Kanr, Cmr, Tetr among other | Selection markers | Elements required for the selection and maintenance of plasmids in bacterial hosts. Here are listed the resistance cassettes for Ampicillin, Kanamycin, Chloramphenicol, and Tetracycline, which are the most common selection markers. For additional markers, RAC database contains the information regarding antibiotic resistance traits and their sequence [40] or iGEM website for sequence modules bearing the proper syntax for synthetic constructs |
LacZ, CcdB, Green Fluorescent protein (GFP), etc | Additional elements required for positive clone selection, reporter protein fusions among others | Plasmids have been modified so that they contain multiple cloning sites with diverse unique restriction sites, counter selection for positive clone selection. Additional elements such as filamentous origins for single-stranded DNA generation for sequencing of high G+C templates or site-directed mutagenesis |
Some exceptional features of plasmids are they can be used in systems where replication origins (check compatibility first) and selection markers can coexist in the same cell, which can be extremely useful for the coexpression of four different proteins in the same cell (e.g., the four plasmid system developed by Dykxhoorn et al., which are compatible between them [41]); the broad diversity of selection markers and partitioning control elements [30]; cloning capacity [31], which is an important feature for cloning large fragments required for synthetic biology applications or metabolic engineering; reporter proteins useful for selecting positive clones; recombination or assembly technology for easier cloning methods [42, 43], and the ability to be transferred from one host to another like the case of the OriV from RK2 plasmid [44]. We recommend for further information about replication control of plasmids to refer to del Solar et al. [45].
Linear plasmids are common in bacteria (particularly in actinobacteria), but thus far, only N15 plasmid prophage has been isolated from
One of the biggest impediments for plasmid segregation is the insert size. As discussed in Section 5, we are now facing not only the most exciting age of molecular biology but also the most challenging. In order to develop “bugs to the order,” i.e., microbes are “trained” to perform specific tasks [48], from simple pathways to synthesize a specific metabolite to complex genetic circuits that can be controlled for novel environmental responses. In all these cases, plasmids play an important role, from generating site-specific integration of chromosomal fusions to large plasmids that can hold complex constructs for further modification. Another challenging area is the generation of strains capable of producing metabolic products required for the pharmaceutical industry, where metabolic pathways and cell metabolism can be a strong impediment for proper synthesis and purification of relevant precursors [49].
As part of the information needed for plasmid manipulation, databases and repositories are also relevant for the manipulation and selection of the right plasmid for the applications you want to further exploit. Such examples are given: a powerful plasmid repository is Addgene (https://www.addgene.org/vector-database/) where you can get any plasmid in the repository with minimum fees for shipping and handling. This source is important in many aspects; you can gain knowledge about plasmid sequence, special features, creators, and availability to use since you can acquire them with small fees. Also, Harvard University is currently generating a plasmid repository but still under development (https://plasmid.med.harvard.edu/PLASMID/Home.xhtml). These repositories are an excellent option for accelerating research due to finding already generated constructs useful for ongoing projects. Also,
Novel methods such as Gibson assembly, Golden Gate assembly, and AQUA (advanced quick assembly) methods [43, 51, 52] have skyrocketed the possibility to assemble any plasmid with the desired characteristics. These methods are based on designed modules that can either be Polymerase Chain Reaction (PCR) amplified or generated as a complete synthetic construct and then assembled in the desired combination either by an enzymatic process (Gibson and Golden gate) or even enzyme-free methods such as AQUA.
Finally, plasmid biology is still under scrutiny, for their involvement in the mobility of traits that are important for human health such as antibiotic resistance, the distribution of pathogenicity islands, and genome evolution. Recently, novel tools for plasmid mining have been developed and uncover from Next Generation Sequencing data that plasmids can be uncovered and analyzed for further characterization [53, 54].
We are still in the process of truly knowing the potential of
3. Genome modifications to understand E. coli
One of the basic questions in biology is: what is life? Defining life imposes a challenging burden both intellectual and experimental. Many attempts have been done to answer this.
In
Larger genomic editions are needed to understand how far we can delete redundant or nonessential sequences. By using Cre/lox recombination, substantial genomic fragments can be deleted or sequentially removed, rendering the nonessential regions (regardless the genes present) from the genome [59–61].
Studies regarding genome size analyzed through deletions of specific genes or complete genomic regions have led on thinking about the minimal genome. In the case of
All these methods rely on basic bacterial genetics founded with
The most relevant study revealed that genome size has an impact on
After 6 years, in 2016, the first bacteria operating under a “minimal chemically synthesized genome” was created after the first fully functioning synthetic genome [64, 65].
This research we believe has an impact in the following areas. First, both studies settled the basis for whole genome synthetic biology, which will lead to important findings in many research areas. Second, the extensive transposon-based mutagenesis studies on the genome of
4. E. coli -based biosensors: tools for many applications
In biotechnology, biosensors are broadly defined as any device based on biological part, cell, tissue, or protein complex that are linked to a mechanical sensor or analytical receptor that provides a measurable signal proportional to the analyte in the reaction [66, 67].
In Figure 1, we depict the basic design for whole-cell biosensors and some applications. Plasmid vectors with all the possible modifications can lead to almost endless combinations. For practical applications, there are commercial vectors that can be used for such purposes or as mentioned in the previous sections, plasmid methods are powerful enough for fast and robust biosensor design.
The basic design considers the following: copy number, reporter proteins, detection methods, and control elements. The latter is basically the most important feature. As shown in Table 1, the available databases provide enough information for promoter selection and design. Bioinformatic tools can make this process easier [71]. Also, generation and detection of this kind of biosensors are cost-effective and easy to generate and reasonably sensitive [71]. In terms of speed, sample analysis with whole-cell biosensors is fast and cheap in comparison with analytical methods. The sensitivity of analytical methods is higher and more accurate, but biosensors are a good alternative for fast detection of hazards. Also, they can be coupled with the controlled production of metabolites of commercial importance.
In the literature, there are several reports where
With the improvement of DNA synthesis, recoding protein-coding genes for the desired function is expanding the capabilities of transcription factors, and reporter proteins have created novel sensor modules. For example, XilR recoding has led to a sensor that can detect millimolar concentrations of trinitrotoluene and its derivative compounds [83]. By using shuttle vectors, we can generate biosensors that we can transfer from one host to another, which can provide information about differences in physiological responses during the exposure to a given environmental trait.
In the following section, we provide our final overview of the impact of
5. Genetic engineering and synthetic biology of E. coli
With the avenue of
Synthetic biology is a relatively new branch of molecular genetics that incorporate engineering principles for modifying several aspects of cell physiology, rewiring genetic circuits, creating novel circuits, and synthesizing custom-made DNA sequences and even genomes [87]. This particular branch of biology needs to be supported by an extensive knowledge of the organism that modifications or even whole genome synthesis is attempted, several novel tools for analyzing big datasets and molecular tools for that particular organism, for the generation of sequences and the computational design of DNA molecules, and a goal that can be achieved with the desired organism.
Multiplexing is the novel approach for redesigning organisms to do desired tasks [90]. By cycling through design-build–test framework we can achieve novel features in existing proteins and can further the advancement of genetic engineering. Thus far the most complicated and time-consuming part of this framework is the testing of the novel designs. High-throughput approaches have led to the development of fast and reliable screening methods and advances in this area, such as designed biosensors for the screening of metabolite producing strains or high-throughput methods for product screening, where the use of fluorescent proteins, colorimetric assays, and mass spectrometry are cornerstones for the development of screening methods for assessing success in strain engineering [90, 91]. DNA sequencing and synthesis coupled with good screening methods is the platform for future tools for the development of designed microorganism that can do desired tasks.
With all the technologies available, the advancement of using
Synthesis of important metabolites can be difficult, and researchers must face the stubbornness of microorganisms to redirect carbon flux to their own processes, rendering the production of relevant molecules costly and inefficient. But
Several aromatic compounds have been successfully synthesized in
Another relevant area was
Another important field where
Due to the modularity of polyketide synthases, they are excellent candidates for engineering, for either the production of novel compounds from existing gene clusters (through module shuffling, mutagenesis or deletions), or by the introduction of novel environmentally sequenced gene clusters and heterologous production [102, 103]
Therefore, the production of diverse metabolites or biological or industrially relevant molecules can be successfully achieved in
6. Future
With all the research that is currently conducted in
With all the data available, we are on the verge of really important findings and novel biotechnological procedures using
In the rest of the biotechnology fields, we have enough information that suggests
Acknowledgments
The authors acknowledge the generous support from CONACyT-CIBIOGEM grant CB-4O-040116, CONACyT grant CB-2012-01 182671, and Guanajuato University grant 1081/2016 (DAIP). NVM acknowledge the support from CONACyT for a scholarship grant. We also acknowledge the support from Dr. Felipe Padilla Vaca.
References
- 1.
Schönheit P, Buckel W, Martin WF. On the origin of heterotrophy. Trends Microbiol. 2016; 24 :12-25. - 2.
Crick FH, Barnett L, Brenner S, Watts-Tobin RJ. General nature of the genetic code for proteins. Nature. 1961; 192 :1227-32. - 3.
Lehman IR, Bessman MJ, Simms ES, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli . J Biol Chem. 1958;233 :163-70. - 4.
Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961; 3 :318-56. doi: 10.1016/S0022-2836 (61)80072-7. - 5.
Jacob F, Perrin D, Sanchez C, Monod J. L’ opéron: groupe de génes à expression coordonnée par un opérateur (The operon: a group of genes whose expression is coordinated by an operator). Comptes Rendus Hebdomadaires Des Séances De l’Acade´mie Des Sciences. 1960; 250 :1727-9. doi: 10.1016/j.crvi.2005. 04.005. - 6.
Lederberg J, Lederberg E. Replica plating and indirect selection of bacterial mutants. J Bacteriol. 1952; 63 :399-406 - 7.
Luria SE, Delbrück M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics. 1943; 28 :491-511. - 8.
Cohen S, Chang A, Boyer H, Helling R. Construction of biologically functional bacterial plasmids in vitro . Proc Natl Acad Sci U S A. 1973;70 :3240-4. doi: 10.1073/pnas. 70.11.3240. - 9.
Chen X, Zhou L, Tian K, Kumar A, Singh S, Prior BA, Wang Z. Metabolic engineering of Escherichia coli : a sustainable industrial platform for bio-based chemical production. Biotechnol Adv. 2013;31 :1200-23. doi: 10.1016/j.biotechadv.2013.02.009. - 10.
El-Hajj ZW, Newman EB. An Escherichia coli mutant that makes exceptionally long cells. J Bacteriol. 2015;197 :1507-14. doi: 10.1128/JB.00046-15. - 11.
Malpica R, Sandoval GR, Rodríguez C, Franco B, Georgellis D. Signaling by the arc two-component system provides a link between the redox state of the quinone pool and gene expression. Antioxid Redox Signal. 2006; 8 :781-95. - 12.
Malpica R, Franco B, Rodriguez C, Kwon O, Georgellis D. Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. Proc Natl Acad Sci U S A. 2004; 101 :13318-23. - 13.
Georgellis D, Kwon O, Lin EC. Quinones as the redox signal for the arc two-component system of bacteria. Science. 2001; 292 :2314-6. - 14.
Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007; 5 :e177. - 15.
Garrity G, Brenner DJ, Krieg NR, Staley JR. Bergey’s Manual of Systematic Bacteriology, Volume 2. The Proteobacteria, Part B: The Gammaproteobacteria. New York: Springer. pp. 587-850. - 16.
Stouthamer AH. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie van Leeuwenhoek. 1973; 39 :545-65. - 17.
Lengeler JW, et al ., eds Biology of the Prokaryotes, Thieme, 1999. Blackwell Science, Stuttgart. - 18.
Neidhardt FC, et al ., eds Physiology of the Bacterial Cell, Sinauer Associates, Chicago, 1990. - 19.
Romeo T, Vakulskas CA, Babitzke P. Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems. Environ Microbiol. 2013; 15 :313-24. doi: 10.1111/j.1462-2920.2012.02794.x. - 20.
Machado D, Herrgård MJ, Rocha I. Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli . Front Bioeng Biotechnol. 2015;3 :154. doi: 10.3389/fbioe.2015.00154. - 21.
Romeo T. Post-transcriptional regulation of bacterial carbohydrate metabolism: evidence that the gene product CsrA is a global mRNA decay factor. Res Microbiol. 1996; 147 :505-12. - 22.
Conway T, Krogfelt KA, Cohen PS. The life of commensal Escherichia coli in the mammalian intestine. EcoSal Plus. 2004;1 (1). doi: 10.1128/ecosalplus.8.3.1.2. - 23.
Blount ZD. The unexhausted potential of E. coli . Elife. 2015;4 . doi: 10.7554/eLife.05826. - 24.
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 1997;277 :1453-62. - 25.
Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 2009;7 :e96. doi: 10.1371/journal.pbio.1000096. - 26.
Kurokawa M, Seno S, Matsuda H, Ying BW. Correlation between genome reduction and bacterial growth. DNA Res. 2016. pii: dsw035. - 27.
Xie T, Fu LY, Yang QY, Xiong H, Xu H, Ma BG, Zhang HY. Spatial features for Escherichia coli genome organization. BMC Genomics. 2015;16 :37. doi: 10.1186/s12864-015-1258-1. - 28.
Lederberg J. Cell genetics and hereditary symbiosis. Physiol Rev. 1952; 32 :403-30. - 29.
Summers DK. The Biology of Plasmids, Oxford: Blackwell Science. 1996. - 30.
Hayes F. The function and organization of plasmids. Methods Mol Biol. 2003; 235 :1-17. - 31.
Preston A. Choosing a cloning vector. Methods Mol Biol. 2003; 235 :19-26. - 32.
Chan PT, Ohmori H, Tomizawa J, et al . Nucleotide sequence and gene organization of ColE1 DNA. J Biol Chem. 1985;260 :8925-35. - 33.
Bolivar F, Rodriguez RL, Greene PJ, et al . Construction and characterization of new cloning vehicles, II: a multipurpose cloning system. Gene. 1977;2 :95-113. - 34.
Lin-Chao S, Chen WT, Wong TT. High copy number of the pUC plasmid results from a Rom/Rop-suppressible point mutation in RNA II. Mol Microbiol. 1992; 6 :3385-93. - 35.
Vieira J, Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982; 19 :259-68. - 36.
Chang AC, Cohen SN. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the p15A cryptic miniplasmid. J Bacteriol. 1978; 134 :1141-56. - 37.
Betlach M, Hershfield V, Chow L, et al . A restriction endonuclease analysis of the bacterial plasmid controlling theEco RI restriction and modification of DNA. Fed Proc. 1976;35 :2037-43. - 38.
Stoker NG, Fairweather NF, Spratt BG. Versatile low-copy-number plasmid vectors for cloning in Escherichia coli . Gene. 1982;18 :335-41. - 39.
Kolter R, Inuzuka M, Helinski DR. Trans-complementation-dependent replication of a low molecular weight origin fragment from plasmid R6K. Cell. 1978; 15 :1199-208. - 40.
Tsafnat G, Copty J, Partridge SR. RAC: Repository of Antibiotic resistance Cassettes. Database (Oxford). 2011; 2011 :bar054. - 41.
Dykxhoorn DM, St Pierre R, Linn T. A set of compatible tac promoter expression vectors. Gene. 1996; 177 :133-6. - 42.
Sasaki Y, Sone T, Yoshida S, Yahata K, Hotta J, Chesnut JD, Honda T, Imamoto F. Evidence for high specificity and efficiency of multiple recombination signals in mixed DNA cloning by the Multisite Gateway system. J Biotechnol. 2004; 107 :233-43. - 43.
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009; 6 :343-5. - 44.
Doran KS, Konieczny I, Helinski DR. Replication origin of the broad host range plasmid RK2. Positioning of various motifs is critical for initiation of replication. J Biol Chem. 1998; 273 :8447-53. - 45.
del Solar G, Giraldo R, Ruiz-Echevarría MJ, Espinosa M, Díaz-Orejas R. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev. 1998; 62 :434-64. - 46.
Ravin NV. Replication and maintenance of linear phage-plasmid N15. Microbiol Spectr. 2015; 3 :PLAS-0032-2014. doi: 10.1128/microbiolspec.PLAS-0032-2014. - 47.
Godiska R, Mead D, Dhodda V, Wu C, Hochstein R, Karsi A, Usdin K, Entezam A, Ravin N. Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli . Nucleic Acids Res. 2010;38 (6):e88. doi: 10.1093/nar/gkp1181. - 48.
Ferber D. Synthetic biology. Microbes made to order. Science. 2004; 9 :158-61. - 49.
Baeshen MN, Al-Hejin A, Bora RS, Ahmed MM, Ramadan HA, Saini KS, Baeshen NA, Redwan EM. Production of biopharmaceuticals in E. coli : current scenario and future perspectives. J Microbiol Biotechnol. 2015;28 :953-62. - 50.
Casali N. Escherichia coli host strains. Methods Mol Biol. 2003;235 :27-48. - 51.
Engler C, Gruetzner R, Kandzia R, Marillonnet S. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One. 2013; 4 :e5553. - 52.
Beyer HM, Gonschorek P, Samodelov SL, Meier M, Weber W, Zurbriggen MD. AQUA cloning: a versatile and simple enzyme-free cloning approach. PLoS One. 2015; 10 (9):e0137652. - 53.
de Toro M, Garcilláon-Barcia MP, De La Cruz F. Plasmid diversity and adaptation analyzed by massive sequencing of Escherichia coli plasmids. Microbiol Spectr. 2014;2 (6). doi: 10.1128/microbiolspec.PLAS-0031-2014. - 54.
Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences. PLoS Genet. 2014;10 (12):e1004766. doi: 10.1371/journal.pgen.1004766. - 55.
Padilla-Vaca F, Anaya-Velázquez F, Franco B. Synthetic biology: novel approaches for microbiology. Int Microbiol. 2015; 18 :71-84. - 56.
Baba T, Ara T, Hasegawa M, et al . Construction ofEscherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006;2 :2006 0008. - 57.
Yamamoto N, Nakahigashi K, Nakamichi T, et al . Update on the Keio collection ofEscherichia coli single-gene deletion mutants. Mol Syst Biol. 2009;5 :335. - 58.
Yong HT, Yamamoto N, Takeuchi R, Hsieh YJ, Conrad TM, Datsenko KA, Nakayashiki T, Wanner BL, Mori H. Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12. Genes Genet Syst. 2013;88 :233-40. - 59.
Posfai G, Plunkett G 3rd, Feher T, et al . Emergent properties of reduced-genomeEscherichia coli . Science. 2006;312 :1044-6. - 60.
Kato J, Hashimoto M. Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol. 2007;3 :132. - 61.
Mizoguchi H, Sawano Y, Kato J, Mori H. Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome. DNA Res. 2008;15 :277-84. - 62.
Choe D, Cho S, Kim SC, Cho BK. Minimal genome: worthwhile or worthless efforts toward being smaller? Biotechnol J. 2016; 11 (2):199-211. - 63.
Park MK, Lee SH, Yang KS, Jung SC, Lee JH, Kim SC. Enhancing recombinant protein production with an Escherichia coli host strain lacking insertion sequences. Appl Microbiol Biotechnol. 2014;98 (15):6701-13. doi: 10.1007/s00253-014-5739-y. - 64.
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, Venter JC. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 2010; 329 (5987):52-6. - 65.
Hutchison CA 3rd, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC. Design and synthesis of a minimal bacterial genome. Science. 2016; 351 (6280):aad6253. - 66.
Bhalla N, Jolly P, Formisano N, Estrela P. Introduction to biosensors. Essays Biochem. 2016; 60 (1):1-8. - 67.
Daunert S, Barrett G, Feliciano JS, Shetty RS, Shrestha S, Smith-Spencer W. Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem Rev. 2000; 100 (7):2705-38. - 68.
Raut N, O’Connor G, Pasini P, Daunert S. Engineered cells as biosensing systems in biomedical analysis. Anal Bioanal Chem. 2012; 402 :3147-59. - 69.
Robbens J, Dardenne F, Devriese L, De Coen W, Blust R. Escherichia coli as a bioreporter in ecotoxicology. Appl Microbiol Biotechnol. 2010;88 (5):1007-25. - 70.
Padilla-Martínez F, Carrizosa-Villegas LA, Rangel-Serrano Á, Paramo-Pérez I, Mondragón-Jaimes V, Anaya-Velázquez F, Padilla-Vaca F, Franco B. Cell damage detection using Escherichia coli reporter plasmids: fluorescent and colorimetric assays. Arch Microbiol. 2015;197 (6):815-21. - 71.
Ford TJ, Silver PA. Synthetic biology expands chemical control of microorganisms. Curr Opin Chem Biol. 2015; 28 :20-8. - 72.
Belkin S, Smulski DR, Vollmer AC, Van Dyk TK, LaRossa RA. Oxidative stress detection with Escherichia coli harboring a katG’: lux fusion. Appl Environ Microbiol. 1996;62 :2252-6. - 73.
Lu C, Albano CR, Bentley WE, Rao G. Quantitative and kinetic study of oxidative stress regulons using green fluorescent protein. Biotechnol Bioeng. 2005; 89 (5):574-87. - 74.
Vollmer AC, Belkin S, Smulski DR, Van Dyk TK, LaRossa RA. Detection of DNA damage by use of Escherichia coli carryingrec A’:lux ,uvr A’:lux , or alkA’: lux reporter plasmids. Appl Environ Microbiol. 1997;63 :2566-71. - 75.
Bechor O, Smulski DR, Van Dyk TK, LaRossa RA, Belkin S. Recombinant microorganisms as environmental biosensors: pollutants detection by Escherichia coli bearingfab A’:lux fusions. J Biotechnol. 2002;94 :125-32. - 76.
Van Dyk TK, Majarian WR, Konstantinov KB, Young RM, Dhurjati PS, LaRossa RA. Rapid and sensitive pollutant detection by induction of heat shock gene-bioluminescence gene fusions. Appl Environ Microbiol. 1994; 60 (5):1414-20. - 77.
Berno E, Pereira Marcondes DF, Ricci Gamalero S, Eandi M. Recombinant Escherichia coli for the biomonitoring of benzene and its derivatives in the air. Ecotoxicol Environ Saf. 2004;57 (2):118-22. - 78.
Vangnai AS, Kataoka N, Soonglerdsongpha S, Kalambaheti C, Tajima T, Kato J. Construction and application of an Escherichia coli bioreporter for aniline and chloroaniline detection. J Ind Microbiol Biotechnol. 2012;39 :1801-10. - 79.
Anu Prathap MU, Chaurasia AK, Sawant SN, Apte SK. Polyaniline-based highly sensitive microbial biosensor for selective detection of lindane. Anal Chem. 2012; 84 (15):6672-8. - 80.
Truffer F, Buffi N, Merulla D, Beggah S, van Lintel H, Renaud P, van der Meer JR, Geiser M. Compact portable biosensor for arsenic detection in aqueous samples with Escherichia coli bioreporter cells. Rev Sci Instrum. 2014;85 :015120. - 81.
Melamed S, Lalush C, Elad T, Yagur-Kroll S, Belkin S, Pedahzur R. A bacterial reporter panel for the detection and classification of antibiotic substances. Microb Biotechnol. 2012; 5 (4):536-48. doi: 10.1111/j.1751-7915.2012.00333.x. - 82.
Kohlmeier S, Mancuso M, Tecon R, Harms H, van der Meer JR, Wells M. Bioreporters: gfp versus lux revisited and single-cell response. Biosens Bioelectron. 2007; 22 :1578-85. - 83.
Galvão TC, de Lorenzo V. Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol. 2006; 17 (1):34-42. - 84.
Røkke G, Korvald E, Pahr J, Oyås O, Lale R. BioBrick assembly standards and techniques and associated software tools. Methods Mol Biol. 2014; 1116 :1-24. doi: 10.1007/978-1-62703-764-8_1. - 85.
Sleight SC, Sauro HM. BioBrick™ assembly using the In-Fusion PCR Cloning Kit. Methods Mol Biol. 2013; 1073 :19-30. - 86.
Webb AJ, Kelwick R, Doenhoff MJ, Kylilis N, MacDonald JT, Wen KY, McKeown C, Baldwin G, Ellis T, Jensen K, Freemont PS. A protease-based biosensor for the detection of Schistosome cercariae . Sci Rep. 2016;6 :24725. doi: 10.1038/srep24725. - 87.
Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng. 2013; 4 :69-102. doi: 10.1146/annurev-chembioeng-061312-103351. - 88.
Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Cells as Experimental Models. Available from: http://www.ncbi.nlm.nih.gov/books/NBK9917/ - 89.
Davis RH. The age of model organisms. Nat Rev Genet. 2004; 5 (1):69-76. - 90.
Rogers JK, Church GM. Multiplexed engineering in biology. Trends Biotechnol. 2016; 34 (3):198-206. - 91.
Raman S, Rogers JK, Taylor ND, Church GM. Evolution-guided optimization of biosynthetic pathways. Proc Natl Acad Sci U S A. 2014; 111 (50):17803-8. doi: 10.1073/pnas.1409523111. - 92.
Becker J, Wittmann C. Systems metabolic engineering of Escherichia coli for the heterologous production of high value molecules-a veteran at new shores. Curr Opin Biotechnol. 2016;42 :178-88. - 93.
Tuli HS, Chaudhary P, Beniwal V, Sharma AK. Microbial pigments as natural color sources: current trends and future perspectives. J Food Sci Technol. 2015; 52 :4669-78. - 94.
Liu W, Zhang R, Tian N, Xu X, Cao Y, Xian M, Liu H. Utilization of alkaline phosphatase PhoA in the bioproduction of geraniol by metabolically engineered Escherichia coli . Bioengineered. 2015;6 (5):288-93. doi: 10.1080/21655979.2015.1062188. - 95.
Schalk M, Pastore L, Mirata MA, Khim S, Schouwey M, Deguerry F, Pineda V, Rocci L, Daviet L. Toward a biosynthetic route to sclareol and amber odorants. J Am Chem Soc. 2012; 134 (46):18900-3. doi: 10.1021/ja307404u. - 96.
Koppolu V, Vasigala VK. Role of Escherichia coli in biofuel production. Microbiol Insights. 2016;9 :29-35. - 97.
Bentley GJ, Jiang W, Guamán LP, Xiao Y, Zhang F. Engineering Escherichia coli to produce branched-chain fatty acids in high percentages. Metab Eng. 2016;38 :148-58. - 98.
Jawed K, Mattam AJ, Fatma Z, Wajid S, Abdin MZ, Yazdani SS. Engineered production of short chain fatty acid in Escherichia coli using fatty acid synthesis pathway. PLoS One. 2016;11 (7):e0160035. - 99.
Howard TP, Middelhaufe S, Moore K, Edner C, Kolak DM, Taylor GN, Parker DA, Lee R, Smirnoff N, Aves SJ, Love J. Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli . Proc Natl Acad Sci U S A. 2013;110 (19):7636-41. - 100.
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng. 2014;25 :140-58. - 101.
Yang J, Xiong ZQ, Song SJ, Wang JF, Lv HJ, Wang Y. Improving heterologous polyketide production in Escherichia coli by transporter engineering. Appl Microbiol Biotechnol. 2015;99 (20):8691-700. - 102.
Zhang G, Li Y, Fang L, Pfeifer BA. Tailoring pathway modularity in the biosynthesis of erythromycin analogs heterologously engineered in E. coli . Sci Adv. 2015;1 (4):e1500077. - 103.
Meng HL, Xiong ZQ, Song SJ, Wang J, Wang Y. Construction of polyketide overproducing Escherichia coli strains via synthetic antisense RNAs based onin silico fluxome analysis and comparative transcriptome analysis. Biotechnol J. 2016;11 (4):530-41. - 104.
Yaung SJ, Church GM, Wang HH. Recent progress in engineering human-associated microbiomes. Methods Mol Biol. 2014; 1151 :3-25. - 105.
Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang HH, Gerber GK. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. Mol Syst Biol. 2015;11 (1):788. - 106.
Lee HH, Ostrov N, Wong BG, Gold MA, Khalil A, Church GM. Vibrio natriegens , a new genomic powerhouse. BioRxiv. 2016; 058487. doi: http://dx.doi.org/10.1101/058487. - 107.
Simons KL, Thomas SM, Anderson PA. Identification of Vibrio natriegens uvr A anduvr B genes and analysis of gene regulation using transcriptional reporter plasmids. J Microbiol. 2010;48 (5):644-56. - 108.
Garnier M, Labreuche Y, Garcia C, Robert M, Nicolas JL. Evidence for the involvement of pathogenic bacteria in summer mortalities of the Pacific oyster Crassostrea gigas . Microb Ecol. 2007;53 (2):187-96. - 109.
Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM. Biocontainment of genetically modified organisms by synthetic protein design. Nature. 2015; 518 (7537):55-60.