Sandbox

Identification of a minimal gene set

Yusuke Azuma, Motonori Ota
An evaluation of minimal cellular functions to sustain a bacterial cell.
BMC Syst Biol: 2009, 3;111
[PubMed:19943949] [WorldCat.org] [DOI] (I e)

Steps on the way to an artificial organism

Daniel G Gibson, John I Glass, Carole Lartigue, Vladimir N Noskov, Ray-Yuan Chuang, Mikkel A Algire, Gwynedd A Benders, Michael G Montague, Li Ma, Monzia M Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A Denisova, Lei Young, Zhi-Qing Qi, Thomas H Segall-Shapiro, Christopher H Calvey, Prashanth P Parmar, Clyde A Hutchison, Hamilton O Smith, J Craig Venter
Creation of a bacterial cell controlled by a chemically synthesized genome.
Science: 2010, 329(5987);52-6
[PubMed:20488990] [WorldCat.org] [DOI] (I p)

Carole Lartigue, Sanjay Vashee, Mikkel A Algire, Ray-Yuan Chuang, Gwynedd A Benders, Li Ma, Vladimir N Noskov, Evgeniya A Denisova, Daniel G Gibson, Nacyra Assad-Garcia, Nina Alperovich, David W Thomas, Chuck Merryman, Clyde A Hutchison, Hamilton O Smith, J Craig Venter, John I Glass
Creating bacterial strains from genomes that have been cloned and engineered in yeast.
Science: 2009, 325(5948);1693-6
[PubMed:19696314] [WorldCat.org] [DOI] (I p)

Daniel G Gibson, Gwynedd A Benders, Cynthia Andrews-Pfannkoch, Evgeniya A Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B Stockwell, Anushka Brownley, David W Thomas, Mikkel A Algire, Chuck Merryman, Lei Young, Vladimir N Noskov, John I Glass, J Craig Venter, Clyde A Hutchison, Hamilton O Smith
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.
Science: 2008, 319(5867);1215-20
[PubMed:18218864] [WorldCat.org] [DOI] (I p)

Carole Lartigue, John I Glass, Nina Alperovich, Rembert Pieper, Prashanth P Parmar, Clyde A Hutchison, Hamilton O Smith, J Craig Venter
Genome transplantation in bacteria: changing one species to another.
Science: 2007, 317(5838);632-8
[PubMed:17600181] [WorldCat.org] [DOI] (I p)

Metabolism

Frederik M Meyer, Jan Gerwig, Elke Hammer, Christina Herzberg, Fabian M Commichau, Uwe Völker, Jörg Stülke
Physical interactions between tricarboxylic acid cycle enzymes in Bacillus subtilis: evidence for a metabolon.
Metab Eng: 2011, 13(1);18-27
[PubMed:20933603] [WorldCat.org] [DOI] (I p)

Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley M Deacon, John Wooley, Scott A Lesley, Ian A Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.
Science: 2009, 325(5947);1544-9
[PubMed:19762644] [WorldCat.org] [DOI] (I p)

Bryson D Bennett, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien, Joshua D Rabinowitz
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.
Nat Chem Biol: 2009, 5(8);593-9
[PubMed:19561621] [WorldCat.org] [DOI] (I p)

Wataru Iwasaki, Toshihisa Takagi
Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages.
PLoS Genet: 2009, 5(3);e1000402
[PubMed:19266023] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Fabian M Rothe, Christina Herzberg, Eva Wagner, Daniel Hellwig, Martin Lehnik-Habrink, Elke Hammer, Uwe Völker, Jörg Stülke
Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing.
Mol Cell Proteomics: 2009, 8(6);1350-60
[PubMed:19193632] [WorldCat.org] [DOI] (I p)

Armen Y Mulkidjanian, Eugene V Koonin, Kira S Makarova, Sergey L Mekhedov, Alexander Sorokin, Yuri I Wolf, Alexis Dufresne, Frédéric Partensky, Henry Burd, Denis Kaznadzey, Robert Haselkorn, Michael Y Galperin
The cyanobacterial genome core and the origin of photosynthesis.
Proc Natl Acad Sci U S A: 2006, 103(35);13126-31
[PubMed:16924101] [WorldCat.org] [DOI] (P p)

M Ribbe, D Gadkari, O Meyer
N2 fixation by Streptomyces thermoautotrophicus involves a molybdenum-dinitrogenase and a manganese-superoxide oxidoreductase that couple N2 reduction to the oxidation of superoxide produced from O2 by a molybdenum-CO dehydrogenase.
J Biol Chem: 1997, 272(42);26627-33
[PubMed:9334244] [WorldCat.org] [DOI] (P p)

Systematics

James A Lake
Evidence for an early prokaryotic endosymbiosis.
Nature: 2009, 460(7258);967-71
[PubMed:19693078] [WorldCat.org] [DOI] (I p)

Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.
BMC Genomics: 2009, 10;358
[PubMed:19656368] [WorldCat.org] [DOI] (I e)

Antoine Danchin, Gang Fang, Stanislas Noria
The extant core bacterial proteome is an archive of the origin of life.
Proteomics: 2007, 7(6);875-89
[PubMed:17370266] [WorldCat.org] [DOI] (P p)

J Peter Gogarten, Jeffrey P Townsend
Horizontal gene transfer, genome innovation and evolution.
Nat Rev Microbiol: 2005, 3(9);679-87
[PubMed:16138096] [WorldCat.org] [DOI] (P p)

Marcus Richter

Yunrong Chai, Thomas Norman, Roberto Kolter, Richard Losick
An epigenetic switch governing daughter cell separation in Bacillus subtilis.
Genes Dev: 2010, 24(8);754-65
[PubMed:20351052] [WorldCat.org] [DOI] (I p)

Daniel Lopez, Hera Vlamakis, Roberto Kolter
Generation of multiple cell types in Bacillus subtilis.
FEMS Microbiol Rev: 2009, 33(1);152-63
[PubMed:19054118] [WorldCat.org] [DOI] (P p)