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Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- Ulrich Omasits,
- Maxime Quebatte,
- Daniel J. Stekhoven,
- Claudia Fortes,
- Bernd Roschitzki,
- Mark D. Robinson,
- Christoph Dehio,
- and Christian H. Ahrens
Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
..., orthology, and other information to enable further analyses. Genome Research 1917 www..org Covering complete expressed prokaryotic proteomes protein-coding genes actively transcribed in a given state (Ahrens et al. 2010). A recent proteogenomics study of 46 prokaryotes indicated that, on average, only 0...
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Method: Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling
- Yo Suzuki,
- Nacyra Assad-Garcia,
- Maxim Kostylev,
- Vladimir N. Noskov,
- Kim S. Wise,
- Bogumil J. Karas,
- Jason Stam,
- Michael G. Montague,
- Timothy J. Hanly,
- Nico J. Enriquez,
- Adi Ramon,
- Gregory M. Goldgof,
- R. Alexander Richter,
- Sanjay Vashee,
- Ray-Yuan Chuang,
- Elizabeth A. Winzeler,
- Clyde A. Hutchison III,
- Daniel G. Gibson,
- Hamilton O. Smith,
- John I. Glass,
- and J. Craig Venter
Genome Res. March 2015 25: 435-444; Published in Advance February 5, 2015, doi:10.1101/gr.182477.114
..., La Jolla, California 92093, USA Corresponding author: ysuzuki@jcvi.org Abstract The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest...
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LETTER: Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea
- Odile Lecompte,
- Raymond Ripp,
- Valérie Puzos-Barbe,
- Simone Duprat,
- Roland Heilig,
- Jacques Dietrich,
- Jean-Claude Thierry,
- and Olivier Poch
Genome Res. June 1, 2001 11: 981-993; Published in Advance May 8, 2001, doi:10.1101/gr.165301
..., Mycoplasma pneumoniae and Mycoplama genitalium ( Himmelreich et al. 1997 ; Herrmann and Reiner 1998 ). Regarding dot plots of gene similarities, the level of DNA reorganization observed between Chamydia trachomatis and C. pneumoniae ( Kalman et al. 1999 ; Read et al. 2000 ) is of the same range...
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ARTICLE: Structural Characterization of the Human Proteome
- Arne Müller,
- Robert M. MacCallum,
- and Michael J.E. Sternberg
Genome Res. November 1, 2002 12: 1625-1641; doi:10.1101/gr.221202
...% observed in Mycoplasma genitalium as the smallest . There is a very rapid increase in the extent of domain duplication in the bacteria and archaea until the size of smallest eukaryote included in our analysis (yeast) is reached. However, one does not observe a marked difference in the extent of duplication...
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Methods: Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
- Nitin Gupta,
- Stephen Tanner,
- Navdeep Jaitly,
- Joshua N. Adkins,
- Mary Lipton,
- Robert Edwards,
- Margaret Romine,
- Andrei Osterman,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. September 2007 17: 1362-1377; Published in Advance August 9, 2007, doi:10.1101/gr.6427907
.... The identified peptides validate the predicted genes, correct erroneous gene annotations, and reveal some completely missed genes. Church and colleagues used proteomic data for analysis of relatively small bacterium, Mycoplasma pneumoniae ( Jaffe et al. 2004a ), and later on the newly sequenced Mycoplasma mobile...
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LETTER: Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias
- Rong Wang,
- John T. Prince,
- and Edward M. Marcotte
Genome Res. August 2005 15: 1118-1126; doi:10.1101/gr.3994105
...this method, ∼1500 Saccharomyces cerevisiae proteins were detected ( Washburn et al. 2001 ; Peng et al. 2003 ). Similarly, in mycoplasma, Jaffe et al. ( 2004 ) detected the expression of 557 open reading frames (ORFs) in Mycoplasma pneumoniae strain M129 by using proteogenomic mapping, the mapping of peptides...
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PERSPECTIVE: Insights on biology and evolution from microbial genome sequencing
- Claire M. Fraser-Liggett
Genome Res. December 2005 15: 1603-1610; doi:10.1101/gr.3724205
...; Sassetti et al. 2003 ; Krause and Balish 2004 ) and theoretical ( Koonin 2003 ; Klasson and Andersson 2004 ) approaches. One of the first studies employed transposon mutagenesis in the minimal organisms Mycoplasma genitalium and Mycoplasma pneumoniae , based on the assumption that there would be a limited...
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LETTER: Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
- Claire Amadou,
- Géraldine Pascal,
- Sophie Mangenot,
- Michelle Glew,
- Cyril Bontemps,
- Delphine Capela,
- Sébastien Carrère,
- Stéphane Cruveiller,
- Carole Dossat,
- Aurélie Lajus,
- Marta Marchetti,
- Véréna Poinsot,
- Zoé Rouy,
- Bertrand Servin,
- Maged Saad,
- Chantal Schenowitz,
- Valérie Barbe,
- Jacques Batut,
- Claudine Médigue,
- and Catherine Masson-Boivin
Genome Res. September 2008 18: 1472-1483; Published in Advance May 19, 2008, doi:10.1101/gr.076448.108
...in obligatory parasites/symbionts such as Mycoplasma , Rickettsia , Wolbachia , and Buchnera . These three clusters include metabolic and housekeeping genes (e.g., ilvC , pdhAa , pdhAb , mdh , pckA , ppiB , hemA , ccmAC , cycLJK , relA , tig , greA , purl , ntrC , glnB , glgA1 , pgm , queA , acpxL , lps...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...Material) were obtained from authenticated sources and tested negative for mycoplasma. Cell lines were cultured in medium conditions optimized per cell type, with fetal bovine serum and penicillin/streptomycin supplementation.Construction of LTR7-PLAAT4 overexpressing cell linesThe predicted sequences...
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LETTER: Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence
- Sean P. Kennedy,
- Wailap Victor Ng,
- Steven L. Salzberg,
- Leroy Hood,
- and Shiladitya DasSarma
Genome Res. October 1, 2001 11: 1641-1650; doi:10.1101/gr.190201
...in the region spanning positions 672,176–676,486 bp near the first inflection point. These two genes occur in the same order ( gyr B followed by gyr A) in close proximity to the origin in the s of Borrelia burgdorferi, Mycoplasma genitalium, Mycoplasma pneumoniae, Bacillus subtilis , and Mycobacterium...

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