Papersammlung

Regulation

Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen, Joshua D Rabinowitz
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.
Mol Syst Biol: 2009, 5;302
[PubMed:19690571] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Katrin Gunka, Jens J Landmann, Jörg Stülke
Glutamate metabolism in Bacillus subtilis: gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system.
J Bacteriol: 2008, 190(10);3557-64
[PubMed:18326565] [WorldCat.org] [DOI] (I p)

Susan H Fisher, Lewis V Wray
Bacillus subtilis glutamine synthetase regulates its own synthesis by acting as a chaperone to stabilize GlnR-DNA complexes.
Proc Natl Acad Sci U S A: 2008, 105(3);1014-9
[PubMed:18195355] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Christina Herzberg, Philipp Tripal, Oliver Valerius, Jörg Stülke
A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC.
Mol Microbiol: 2007, 65(3);642-54
[PubMed:17608797] [WorldCat.org] [DOI] (P p)

Dalai Yan
Protection of the glutamate pool concentration in enteric bacteria.
Proc Natl Acad Sci U S A: 2007, 104(22);9475-80
[PubMed:17517610] [WorldCat.org] [DOI] (P p)

Synthetic Biology

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)

Patrick F Suthers, Madhukar S Dasika, Vinay Satish Kumar, Gennady Denisov, John I Glass, Costas D Maranas
A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.
PLoS Comput Biol: 2009, 5(2);e1000285
[PubMed:19214212] [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)

Philip Ball
Synthetic biology: designs for life.
Nature: 2007, 448(7149);32-3
[PubMed:17611530] [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)

John I Glass, Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R Lewis, Mahir Maruf, Clyde A Hutchison, Hamilton O Smith, J Craig Venter
Essential genes of a minimal bacterium.
Proc Natl Acad Sci U S A: 2006, 103(2);425-30
[PubMed:16407165] [WorldCat.org] [DOI] (P p)

Stoffwechsel

Roelco J Kleijn, Joerg M Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich, Uwe Sauer
Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis.
J Biol Chem: 2010, 285(3);1587-96
[PubMed:19917605] [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)

Adam M Feist, Markus J Herrgård, Ines Thiele, Jennie L Reed, Bernhard Ø Palsson
Reconstruction of biochemical networks in microorganisms.
Nat Rev Microbiol: 2009, 7(2);129-43
[PubMed:19116616] [WorldCat.org] [DOI] (I p)

Harald Huber, Martin Gallenberger, Ulrike Jahn, Eva Eylert, Ivan A Berg, Daniel Kockelkorn, Wolfgang Eisenreich, Georg Fuchs
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis.
Proc Natl Acad Sci U S A: 2008, 105(22);7851-6
[PubMed:18511565] [WorldCat.org] [DOI] (I p)

Yasutaro Fujita, Hiroshi Matsuoka, Kazutake Hirooka
Regulation of fatty acid metabolism in bacteria.
Mol Microbiol: 2007, 66(4);829-39
[PubMed:17919287] [WorldCat.org] [DOI] (P p)

Sven Halbedel, Claudine Hames, Jörg Stülke
Regulation of carbon metabolism in the mollicutes and its relation to virulence.
J Mol Microbiol Biotechnol: 2007, 12(1-2);147-54
[PubMed:17183222] [WorldCat.org] [DOI] (P 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)

Systematik

Norman R Pace
Mapping the tree of life: progress and prospects.
Microbiol Mol Biol Rev: 2009, 73(4);565-76
[PubMed:19946133] [WorldCat.org] [DOI] (I p)

Jeffrey E Barrick, Dong Su Yu, Sung Ho Yoon, Haeyoung Jeong, Tae Kwang Oh, Dominique Schneider, Richard E Lenski, Jihyun F Kim
Genome evolution and adaptation in a long-term experiment with Escherichia coli.
Nature: 2009, 461(7268);1243-7
[PubMed:19838166] [WorldCat.org] [DOI] (I p)

J E Barrick, R E Lenski
Genome-wide mutational diversity in an evolving population of Escherichia coli.
Cold Spring Harb Symp Quant Biol: 2009, 74;119-29
[PubMed:19776167] [WorldCat.org] [DOI] (I p)

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

Dan I Andersson, Diarmaid Hughes
Gene amplification and adaptive evolution in bacteria.
Annu Rev Genet: 2009, 43;167-95
[PubMed:19686082] [WorldCat.org] [DOI] (I p)

Carl Zimmer
Origins. On the origin of eukaryotes.
Science: 2009, 325(5941);666-8
[PubMed:19661396] [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)

Valérie Barbe, Stéphane Cruveiller, Frank Kunst, Patricia Lenoble, Guillaume Meurice, Agnieszka Sekowska, David Vallenet, Tingzhang Wang, Ivan Moszer, Claudine Médigue, Antoine Danchin
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later.
Microbiology (Reading): 2009, 155(Pt 6);1758-1775
[PubMed:19383706] [WorldCat.org] [DOI] (P p)

Howard Ochman
Radical views of the tree of life.
Environ Microbiol: 2009, 11(4);731-2
[PubMed:19236444] [WorldCat.org] [DOI] (I p)

Eugene V Koonin
Darwinian evolution in the light of genomics.
Nucleic Acids Res: 2009, 37(4);1011-34
[PubMed:19213802] [WorldCat.org] [DOI] (I p)

Christophe Fraser, Eric J Alm, Martin F Polz, Brian G Spratt, William P Hanage
The bacterial species challenge: making sense of genetic and ecological diversity.
Science: 2009, 323(5915);741-6
[PubMed:19197054] [WorldCat.org] [DOI] (I p)

Cymon J Cox, Peter G Foster, Robert P Hirt, Simon R Harris, T Martin Embley
The archaebacterial origin of eukaryotes.
Proc Natl Acad Sci U S A: 2008, 105(51);20356-61
[PubMed:19073919] [WorldCat.org] [DOI] (I p)

Eugene V Koonin
The Biological Big Bang model for the major transitions in evolution.
Biol Direct: 2007, 2;21
[PubMed:17708768] [WorldCat.org] [DOI] (I e)

Adrian Reyes-Prieto, Andreas P M Weber, Debashish Bhattacharya
The origin and establishment of the plastid in algae and plants.
Annu Rev Genet: 2007, 41;147-68
[PubMed:17600460] [WorldCat.org] [DOI] (P p)

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)

Francesca D Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J Creevey, Berend Snel, Peer Bork
Toward automatic reconstruction of a highly resolved tree of life.
Science: 2006, 311(5765);1283-7
[PubMed:16513982] [WorldCat.org] [DOI] (I 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)

Anne B Simonson, Jacqueline A Servin, Ryan G Skophammer, Craig W Herbold, Maria C Rivera, James A Lake
Decoding the genomic tree of life.
Proc Natl Acad Sci U S A: 2005, 102 Suppl 1(Suppl 1);6608-13
[PubMed:15851667] [WorldCat.org] [DOI] (P p)

Maria C Rivera, James A Lake
The ring of life provides evidence for a genome fusion origin of eukaryotes.
Nature: 2004, 431(7005);152-5
[PubMed:15356622] [WorldCat.org] [DOI] (I p)

Eugene V Koonin
Comparative genomics, minimal gene-sets and the last universal common ancestor.
Nat Rev Microbiol: 2003, 1(2);127-36
[PubMed:15035042] [WorldCat.org] [DOI] (P p)

Mycoplasma

Oscar Q Pich, Raul Burgos, Enrique Querol, Jaume Piñol
P110 and P140 cytadherence-related proteins are negative effectors of terminal organelle duplication in Mycoplasma genitalium.
PLoS One: 2009, 4(10);e7452
[PubMed:19829712] [WorldCat.org] [DOI] (I e)