The Mínimum Cell

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The minimum cell GENOMIC – ADVANCED GENETICS AUTHOR: I. ODEI BARREÑADA Overview The Concept Small genomes Minimal gene set Approache theories Minimal genome proyect Future insight The concept “MINIMUN CELL“ The smallest size (of genetic The smallest unit of life that can information) replicate autonomously = minimum genome Small genomes Circovirus (1.800 base pairs / 3 gens) Virus Carsonella ruddi (159 kb /182 genes) Symbiont Nanoarchaeum equitans (490 kb/ 553 genes) Parasite Mycoplasma genitalium (582 kb/ 521 genes ) Parasite Pelagibacter ubique (1,3 Mb/ 1,370 genes) Free-living Smallest genomes Circovirus (1.800 base pairs / 3 gens) Virus Carsonella ruddi (159 kb /182 genes) Symbiont Nanoarchaeum equitans (490 kb/ 553 genes) Parasite Mycoplasma genitalium (582 kb/ 521 genes ) Parasite Pelagibacter ubique (1,3 Mb/ 1,370 genes) Free-living (Giovannoni et al., 2005) “MINIMAL GENE SET” By genome comparison Ubiquitous genes: Translation Transcription Replication of DNA Variable genes: Depends of environment (Koonin, 2003) Theories for reach the minimum cell Two approaches Top – Down knock-down known organism Bottom-up --> build from synthetics DNA Minimal genome project J. Craig Venter Institute Search of essential genes Gene disruption by transposons Seq the survivors organisms Detect the disrupted gene Declare this genes as NON-ESENTIAL In M. genitalium only 382 of 521 genes are essential (Gibson et al., 2011) Build de novo M. genitalium genome Future insight - Cell design Create artificial cells for: Generation of hydrogen for fuel Capturing excess carbon dioxide in the atmosphere Drug delivery directly into the body As Enzyme therapy Artificial blood cells … And all you can think References Koonin E V. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol. 2003;1(2):127-136. Glass JI, Assad-Garcia N, Alperovich N, et al. Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A. 2006;103(2):425-430. doi:10.1073/pnas.0510013103. Hutchison CA, Smith HO, Venter JC. Global Transposon Mutagenesis and a Minimal Mycoplasma Genome. 1999;2165(1999):2165-2170. Gibson DG, Glass JI, Lartigue C, et al. CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME. 2011. Tamames J, Gil R, Latorre A, Peretó J, Silva FJ, Moya A. The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol Biol. 2007;7:181. Waters E, Hohn MJ, Ahel I, et al. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A. 2003;100(22):12984-12988. THE END .

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The Genome of Nanoarchaeum Equitans: Insights Into Early Archaeal Evolution and Derived Parasitism
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism Elizabeth Waters†‡, Michael J. Hohn§, Ivan Ahel¶, David E. Graham††, Mark D. Adams‡‡, Mary Barnstead‡‡, Karen Y. Beeson‡‡, Lisa Bibbs†, Randall Bolanos‡‡, Martin Keller†, Keith Kretz†, Xiaoying Lin‡‡, Eric Mathur†, Jingwei Ni‡‡, Mircea Podar†, Toby Richardson†, Granger G. Sutton‡‡, Melvin Simon†, Dieter So¨ ll¶§§¶¶, Karl O. Stetter†§¶¶, Jay M. Short†, and Michiel Noordewier†¶¶ †Diversa Corporation, 4955 Directors Place, San Diego, CA 92121; ‡Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182; §Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universita¨tsstrasse 31, D-93053 Regensburg, Germany; ‡‡Celera Genomics Rockville, 45 West Gude Drive, Rockville, MD 20850; Departments of ¶Molecular Biophysics and Biochemistry and §§Chemistry, Yale University, New Haven, CT 06520-8114; and ʈDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, August 21, 2003 (received for review July 22, 2003) The hyperthermophile Nanoarchaeum equitans is an obligate sym- (6–8). Genomic DNA was either digested with restriction en- biont growing in coculture with the crenarchaeon Ignicoccus. zymes or sheared to provide clonable fragments. Two plasmid Ribosomal protein and rRNA-based phylogenies place its branching libraries were made by subcloning randomly sheared fragments point early in the archaeal lineage, representing the new archaeal of this DNA into a high-copy number vector (Ϸ2.8 kbp library) kingdom Nanoarchaeota. The N. equitans genome (490,885 base or low-copy number vector (Ϸ6.3 kbp library). DNA sequence pairs) encodes the machinery for information processing and was obtained from both ends of plasmid inserts to create repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide ‘‘mate-pairs,’’ pairs of reads from single clones that should be biosyntheses.
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Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
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Analysis of the genome architecture of the hyperthermopholic Title archaeon Thermococcus kodakarensis( Dissertation_全文 ) Author(s) Maruyama, Hugo Citation 京都大学 Issue Date 2011-03-23 URL https://doi.org/10.14989/doctor.k16233 Right Type Thesis or Dissertation Textversion author Kyoto University Analysis of the genome architecture of the hyperthermophilic archaeon Thermococcus kodakarensis Hugo Maruyama 要旨ゲノム DNA は細胞内で高度に折りたたまれ、この染色体高次構造は転写・複製・染色体分配といった機構と密接に結びついている。染色体の主要な構成タンパク質は真核生物ではヒストン、バクテリアでは HU と全く異なるが、一様な基本構造を基にゲノム DNA が階層的に折りたたまれている点で両者の染色体構造は共通している。アーキアは真核生物・バクテリアと並ぶ生命の第三のドメインであり、遺伝情報の発現（複製・転写・翻訳）の機構は真核生物に、代謝経路はバクテリアに近い。アーキアには染色体を構成するタンパク質として真核生物のヒストンに相同なもの、バクテリアの HU に相同なもの、アーキア特有の Alba と呼ばれるタンパク質などが存在し、種によってゲノムがコードするタンパク質の組合せが異なる。様々なアーキアのゲノムがどのような高次構造を形成しているかを明らかにすることで、三つのドメインにわたるゲノム構造の共通性あるいは多様性を明らかにできる。本研究ではその第一歩としてヒストンを持つ超好熱性アーキア Thermococcus kodakarensis の染色体構造を解析した。 T. kodakarensis の染色体に含まれるタンパク質を質量分析により同定した結果、ヒストン、Alba、TK0471（TrmBL2）、 RNA ポリメラーゼ等の DNA 結合タンパク質が含まれることが分かった。TK0471 は転写因子 TrmB と相同な機能未知の DNA 結合タンパク質であった。次に、染色体をミクロコッカルヌクレアーゼで部分消化した後、5%-20%のショ糖密度勾配遠心により構成タンパク質の異なる染色体断片が分離された。原子間力顕微鏡による解析から、ヒストンは DNA 上に beads-on-a-string 構造を、TK0471 は線維状の構造を形成することが示された。また大腸菌で発現させた組換えタンパク質（ヒストンおよび TK0471）を用いて同様の構造が DNA 上に再構成された。ショ糖密度勾配で分離されたそれぞれの染色体断片に含まれる DNA 配列を超並列シークエンサーで同定した結果、ヒストンおよび TK0471 はゲノム上のプロモーター領域にもコーディング領域にも偏りなく存在するが、両者の存在する領域は重複しない傾向があった。以上の結果から、T. kodakarensis の染色体上には、構成タンパク質および構造の異なる領域が存在することが明らかとなった。相同組換えにより TK0471 遺伝子を破壊すると染色体の DNA 消化酵素に対する感受性が高まった。また、約 100 個の遺伝子の転写産物量が増加した。TK0471 破壊株における各
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Analysis of the genome architecture of the hyperthermopholic Title archaeon Thermococcus kodakarensis( Dissertation_全文 ) Author(s) Maruyama, Hugo Citation Kyoto University (京都大学) Issue Date 2011-03-23 URL http://dx.doi.org/10.14989/doctor.k16233 Right Type Thesis or Dissertation Textversion author Kyoto University Analysis of the genome architecture of the hyperthermophilic archaeon Thermococcus kodakarensis Hugo Maruyama 要旨ゲノム DNA は細胞内で高度に折りたたまれ、この染色体高次構造は転写・複製・染色体分配といった機構と密接に結びついている。染色体の主要な構成タンパク質は真核生物ではヒストン、バクテリアでは HU と全く異なるが、一様な基本構造を基にゲノム DNA が階層的に折りたたまれている点で両者の染色体構造は共通している。アーキアは真核生物・バクテリアと並ぶ生命の第三のドメインであり、遺伝情報の発現（複製・転写・翻訳）の機構は真核生物に、代謝経路はバクテリアに近い。アーキアには染色体を構成するタンパク質として真核生物のヒストンに相同なもの、バクテリアの HU に相同なもの、アーキア特有の Alba と呼ばれるタンパク質などが存在し、種によってゲノムがコードするタンパク質の組合せが異なる。様々なアーキアのゲノムがどのような高次構造を形成しているかを明らかにすることで、三つのドメインにわたるゲノム構造の共通性あるいは多様性を明らかにできる。本研究ではその第一歩としてヒストンを持つ超好熱性アーキア Thermococcus kodakarensis の染色体構造を解析した。 T. kodakarensis の染色体に含まれるタンパク質を質量分析により同定した結果、ヒストン、Alba、TK0471（TrmBL2）、 RNA ポリメラーゼ等の DNA 結合タンパク質が含まれることが分かった。TK0471 は転写因子 TrmB と相同な機能未知の DNA 結合タンパク質であった。次に、染色体をミクロコッカルヌクレアーゼで部分消化した後、5%-20%のショ糖密度勾配遠心により構成タンパク質の異なる染色体断片が分離された。原子間力顕微鏡による解析から、ヒストンは DNA 上に beads-on-a-string 構造を、TK0471 は線維状の構造を形成することが示された。また大腸菌で発現させた組換えタンパク質（ヒストンおよび TK0471）を用いて同様の構造が DNA 上に再構成された。ショ糖密度勾配で分離されたそれぞれの染色体断片に含まれる DNA 配列を超並列シークエンサーで同定した結果、ヒストンおよび TK0471 はゲノム上のプロモーター領域にもコーディング領域にも偏りなく存在するが、両者の存在する領域は重複しない傾向があった。以上の結果から、T. kodakarensis の染色体上には、構成タンパク質および構造の異なる領域が存在することが明らかとなった。相同組換えにより TK0471 遺伝子を破壊すると染色体の DNA 消化酵素に対する感受性が高まった。また、約 100 個の遺伝子の転写産物量が増加した。TK0471
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