The whole-genome sequencing and synthetic biology for improving organisms and creating new life

Bioinformatics Group

Abstract


Since the development of DNA sequencing technologies in 1960s, Sanger’s chain-termination sequencing and Maxam-Gilbert’s chemical sequencing methods were widely used and were regarded as the first generation of DNA sequencing technologies. At the end of 1980s, the next-generation of DNA sequencing technology was developed, which was originally based on enzymatic method for monitoring pyrophosphate synthesis. The multiple next-generation sequencing technologies have been developed and might be sub-divided into the second and third generations of sequencing including the recently developed nanopore sequencing technology. With the rapid development of these technologies, huge numbers of genomes from various organisms have been sequenced including microorganisms, plants and animals. In this review, we have briefly summarized the recent progress on genome sequencing technologies. Based on our analysis using publicly available datasets, 68176 genomes have been completed in their sequencing, which include 49074 bacteria, 6187 viruses, 12029 eukaryotes, 857 archaea and 29 others. These genomes come from 27310 species of bacteria, 5891 species of viruses, 1514 species of eukaryotes, 701 species of archaea and 59 species for Others. After genome sequencing, many of these genomes have been annotated by assigning their candidate protein coding genes. By the investigation of the genome size and the annotated genes from 56 completely sequenced genomes, our data showed different genomes have different sizes with different protein coding genes and there might not have co-relationship between genome size and annotated genes. Our data also showed that mobile elements significantly contributed to the genome expansion, thereby, contributing to genome size. In addition, we have also briefly reviewed the contribution of genome sequencing to synthetic biology. With the rapid progresses on the whole genome sequencing and functional genomics as well as synthetic biology, it is becoming possible to design and construct novel biological systems to manufacture new drugs / antibodies or new compounds to benefit human beings. Furthermore, cell-free synthetic biology or in vitro metabolic engineering have been progressed well and show the perspectives for biomanufacturing high-value products or for environmental sensing.


Full Text:

PDF html

| Article View Counter:  Abstract - 51 times | PDF - 2 times | html - 17 times |

References


Anthony JF Griffiths, Jeffrey H Miller, David T Suzuki, Richard C Lewontin, and William M Gelbart. 2000. An Introduction to Genetic Analysis, 7th edition. WH Freeman and Company. New York. Pp. 1-860.

Auslander, S. & Fussenegger, M. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol. 31, 155–168 (2013).

Bennett S (2004) Solexa Ltd. Pharmacogenomics 5: 433-438.

Cameron DE, Bashor CJ, Collins JJ. 2014. A brief history of synthetic biology. Nat Rev Microbiol. 2014 May;12(5):381-90. doi: 10.1038/nrmicro3239.

Chénais B, Caruso A, Hiard S, Casse N. 2012. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene. 509: 7-15.

Davies J. 2017. Using synthetic biology to explore principles of development. Development. 144: 1146-1158.

Dodsworth S, Leitch AR, Leitch IJ. 2015. Genome size diversity in angiosperms and its influence on gene space. Curr Opin Genet Dev. 35: 73-78.

El Baidouri M, Panaud O. 2013. Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biol Evol. 5: 954-965.

Erb TJ, Jones PR, Bar-Even A. 2017. Synthetic metabolism: metabolic engineering meets enzyme design. Curr Opin Chem Biol. 37: 56-62.

Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M. 1976. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260: 500-507.

Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269: 496-512.

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. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 329: 52-56.

Guo W, Sheng J, Feng X. 2017. Mini-review: In vitro Metabolic Engineering for Biomanufacturing of High-value Products. Comput Struct Biotechnol J. 15: 161-167. doi: 10.1016/j.csbj.2017.01.006.

Gut IG (2013) New sequencing technologies. Clin Transl Oncol 15: 879-881.

Guzmán-Trampe S, Ceapa CD, Manzo-Ruiz M3, Sánchez S4. 2017. Synthetic biology era: Improving antibiotic's world. Biochem Pharmacol. pii: S0006-2952(17)30045-X. doi: 10.1016/j.bcp.2017.01.015. In press.

Heather JM, Chain B (2016) The sequence of sequencers: The history of sequencing DNA. Genomics 107: 1-8.

Hershey AD, Chase M (1952). Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 36: 39-56.

Holley RW, Apgar J, Everett GA, Madison JT, Marquisee M, Merrill SH, Penswick JR, Zamir A (1965) Structure Of a ribonucleic acid. Science 147: 1462-1465.

Hutchison CA, 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. 2016. Design and synthesis of a minimal bacterial genome. Science 351: aad6253.

Hyman ED (1988) A new method for sequencing DNA. Anal Biochem 174: 423-436.

Jain M, Olsen HE, Paten B, Akeson M (2016) The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17: 239.

Karig DK (2017) Cell-free synthetic biology for environmental sensing and remediation. Curr Opin Biotechnol.45: 69-75. doi: 10.1016/j.copbio.2017.01.010

Karlsson, M. & Weber, W. Therapeutic synthetic gene networks. Curr. Opin. Biotechnol. 23, 703–711 (2012).

Khorana HG, Agarwal KL, Büchi H, Caruthers MH, Gupta NK, Kleppe K, Kumar A, Otsuka E, RajBhandary UL, Van de Sande JH, Sgaramella V, Terao T, Weber H, Yamada T. 1972. Studies on polynucleotides. 103. Total synthesis of the structural gene for an alanine transfer ribonucleic acid from yeast. J Mol Biol. 72: 209-217.

Kosuri, S. & Church, G.M. (2014). "Large-scale de novo DNA synthesis: technologies and applications". Nature Methods. 11: 499-507.

Lee SI, Kim NS. 2014. Transposable elements and genome size variations in plants. Genomics Inform. 12: 87-97.

Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD. 2013. The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics. 14: 476. doi: 10.1186/1471-2164-14-476.

Maxam AM, W. Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci USA 74: 560-564.

McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19: 1527-1541.

Michael TP. 2014. Plant genome size variation: bloating and purging DNA. Brief Funct Genomics. 13: 308-317.

Min-Jou W, Haegeman G, Ysebaert M, Fiers W (1972) Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature 237: 82-88.

Mol M, Raj Bejugam P, Singh S. 2015. Synthetic biology at the interface of functional genomics. Brief Funct Genomics. 14: 180-188.

Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TB (2017) Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res 45(D1): D446-D456.

Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M. 2006. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science. 314: 267.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH. 2014. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol. 15: R59. doi: 10.1186/gb-2014-15-3-r59.

Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (2011) Landscape of next-generation sequencing technologies. Anal Chem 83: 4327-4341.

Nyrén P, Lundin A (1985) Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal Biochem 151: 504-509.

Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52: 413-435.

Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all? Bot J Linn Soc, 164: 10-15.

Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C. 2013. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science. 341: 281-286. doi: 10.1126/science.1239181.

Roberts MA, Cranenburgh RM, Stevens MP, Oyston PC. 2013. Synthetic biology: biology by design. Microbiology. 159(Pt 7): 1219-1220.

Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-452.

Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M. 1977. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265: 687-695.

Sanger F, Brownlee G, Barrell B (1965) A two-dimensional fractionation procedure for radioactive nucleotides. J Mol Biol 13: 373-398.

Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Hum Mol Genet 19: R227-R240.

Schubert I, Vu GT. 2016. Genome Stability and Evolution: Attempting a Holistic View. Trends Plant Sci. 21: 749-757.

The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. 10.1038/35048692.

Tombácz D, Balázs Z, Csabai Z, Moldován N, Szűcs A, Sharon D, Snyder M, Boldogkői Z (2017) Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing. Sci Rep 7: 43751.

Watson JD, Crick FHC (1953) A structure for deoxyribose nucleic acid. Nature 171: 737-738.

Wendel JF, Jackson SA, Meyers BC, Wing RA. 2016. Evolution of plant genome architecture. Genome Biol. 17: 37.

Zou X, Wang L, Li Z, Luo J, Wang Y, Deng Z, Du S, Chen S. 2017. Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics. Med Res Rev. In press. doi: 10.1002/med.21439.




************************************************************************************************

Recently Published Papers by Research Consultants and Publisher:

 
 
 
Matthew Bernard
 
Ethan Gardner