The Coding and Noncoding Architecture of the Caulobacter crescentus Genome
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Jared M. Schrader | Gene-Wei Li | H. McAdams | L. Shapiro | J. Weissman | T. Long | K. Lasker | Bo Zhou | S. Crosson | J. Schrader | W. S. Childers | Brandon Williams | Keren Lasker | B. Zhou | Schrader Jm | Li | G-W | Lasker K | Childers Ws | Christopher S Hayes
[1] Yves V. Brun,et al. Getting in the Loop: Regulation of Development in Caulobacter crescentus , 2010, Microbiology and Molecular Biology Reviews.
[2] R. Bock,et al. Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites , 2011, PLoS genetics.
[3] Gene-Wei Li,et al. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria , 2012, Nature.
[4] Marco Y. Hein,et al. Decoding Human Cytomegalovirus , 2012, Science.
[5] A. Ninfa,et al. Identification, characterization, and chromosomal organization of cell division cycle genes in Caulobacter crescentus , 1997, Journal of bacteriology.
[6] Patrick T. McGrath,et al. Small non‐coding RNAs in Caulobacter crescentus , 2008, Molecular microbiology.
[7] Nicholas T. Ingolia,et al. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.
[8] H. D. de Boer,et al. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[9] R. Giegerich,et al. Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti1021 , 2013, BMC Genomics.
[10] Y. Shimizu,et al. Evidence for the Translation Initiation of Leaderless mRNAs by the Intact 70 S Ribosome without Its Dissociation into Subunits in Eubacteria* , 2004, Journal of Biological Chemistry.
[11] J. Weissman,et al. Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo , 2011, Cell.
[12] E. Winzeler,et al. Translation of the leaderless Caulobacter dnaX mRNA , 1997, Journal of bacteriology.
[13] D. Dunn,et al. Reading frame switch caused by base‐pair formation between the 3′ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. , 1988, The EMBO journal.
[14] Pascale Cossart,et al. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species , 2012, Molecular systems biology.
[15] Honglak Lee,et al. High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons , 2007, Nature Biotechnology.
[16] O. Sliusarenko,et al. High‐throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio‐temporal dynamics , 2011, Molecular microbiology.
[17] M. Suyama,et al. Transcriptome Complexity in a Genome-Reduced Bacterium , 2009, Science.
[18] Nicholas T. Ingolia,et al. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.
[19] Kristin Reiche,et al. The primary transcriptome of the major human pathogen Helicobacter pylori , 2010, Nature.
[20] G. Storz,et al. An expanding universe of small proteins. , 2011, Current opinion in microbiology.
[21] L. Shapiro,et al. A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus , 2007, Nucleic acids research.
[22] Najaf A. Shah,et al. Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation , 2012, PLoS genetics.
[23] Enrique Merino,et al. ProOpDB: Prokaryotic Operon DataBase , 2011, Nucleic Acids Res..
[24] W. Szer,et al. Interaction of Escherichia coli 30S ribosomal subunits with MS2 phage RNA in the absence of initiation factors. , 1974, Proceedings of the National Academy of Sciences of the United States of America.
[25] J. Steitz,et al. How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. , 1975, Proceedings of the National Academy of Sciences of the United States of America.
[26] L. Shapiro,et al. CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in Caulobacter crescentus , 2010, Journal of bacteriology.
[27] Pimlapas Leekitcharoenphon,et al. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium , 2012, Proceedings of the National Academy of Sciences.
[28] Alison K. Hottes,et al. Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media , 2004, Journal of bacteriology.
[29] P. Porras,et al. One Single In-frame AUG Codon Is Responsible for a Diversity of Subcellular Localizations of Glutaredoxin 2 in Saccharomyces cerevisiae* , 2006, Journal of Biological Chemistry.
[30] M Bjerknes,et al. Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. , 1994, Nucleic acids research.
[31] Isabella Moll,et al. Selective Translation of Leaderless mRNAs by Specialized Ribosomes Generated by MazF in Escherichia coli , 2011, Cell.
[32] K. Keiler,et al. Correct Timing of dnaA Transcription and Initiation of DNA Replication Requires trans Translation , 2009, Journal of bacteriology.
[33] H. McAdams,et al. The architecture and conservation pattern of whole-cell control circuitry. , 2011, Journal of molecular biology.
[34] Olga T. Schubert,et al. Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis , 2014, Cell Reports.
[35] J. Elf,et al. Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage , 2003, Science.
[36] Zoya Ignatova,et al. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding , 2009, Nature Structural &Molecular Biology.
[37] O. MacDougald,et al. A 30-kDa alternative translation product of the CCAAT/enhancer binding protein alpha message: transcriptional activator lacking antimitotic activity. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[38] S. Karlin,et al. Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures , 2002, Journal of bacteriology.
[39] H. McAdams,et al. Regulatory Response to Carbon Starvation in Caulobacter crescentus , 2011, PloS one.
[40] B. Palsson,et al. Structural and operational complexity of the Geobacter sulfurreducens genome. , 2010, Genome research.
[41] Ignacio Tinoco,et al. Following translation by single ribosomes one codon at a time , 2008, Nature.
[42] Jeffrey M. Skerker,et al. Identification and cell cycle control of a novel pilus system in Caulobacter crescentus , 2000, The EMBO journal.
[43] E. O’Shea,et al. A serine sensor for multicellularity in a bacterium , 2013, eLife.
[44] Y. Brun,et al. Cell cycle‐dependent abundance, stability and localization of FtsA and FtsQ in Caulobacter crescentus , 2004, Molecular microbiology.
[45] Luis R Comolli,et al. Oligomerization and higher‐order assembly contribute to sub‐cellular localization of a bacterial scaffold , 2013, Molecular microbiology.
[46] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[47] B. Ely,et al. Principal sigma subunit of the Caulobacter crescentus RNA polymerase , 1995, Journal of bacteriology.
[48] Joshua W. Modell,et al. A DNA damage checkpoint in Caulobacter crescentus inhibits cell division through a direct interaction with FtsW. , 2011, Genes & development.
[49] Mladen A. Vouk,et al. Predicting Shine–Dalgarno Sequence Locations Exposes Genome Annotation Errors , 2006, PLoS Comput. Biol..
[50] Pohl Milón,et al. Kinetic control of translation initiation in bacteria , 2012, Critical reviews in biochemistry and molecular biology.
[51] M. Østerås,et al. Identification of the Protease and the Turnover Signal Responsible for Cell Cycle-Dependent Degradation of the Caulobacter FliF Motor Protein , 2004, Journal of bacteriology.
[52] B. Ely,et al. Regulation of Caulobacter crescentus ilvBN gene expression , 1994, Journal of bacteriology.
[53] Eduardo Abeliuk,et al. Assembly of the Caulobacter cell division machine , 2011, Molecular microbiology.
[54] Eduardo Abeliuk,et al. The essential genome of a bacterium , 2011, Molecular systems biology.
[55] S Kobayashi,et al. Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis , 2010, Science.
[56] C. Gualerzi,et al. Selective stimulation of translation of leaderless mRNA by initiation factor 2: evolutionary implications for translation , 2000, The EMBO journal.
[57] J. Vogel,et al. An atlas of Hfq‐bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs , 2012, The EMBO journal.
[58] J. Vogel,et al. Hfq and its constellation of RNA , 2011, Nature Reviews Microbiology.
[59] G. Janssen,et al. Leaderless mRNAs Bind 70S Ribosomes More Strongly than 30S Ribosomal Subunits in Escherichia coli , 2002, Journal of bacteriology.
[60] P. Farabaugh. Programmed translational frameshifting. , 1996, Annual review of genetics.
[61] W. Szer,et al. Purification and properties of initiation factor IF-3 from Caulobacter crescentus. , 1974, The Journal of biological chemistry.
[62] Robert D. Finn,et al. Rfam: Wikipedia, clans and the “decimal” release , 2010, Nucleic Acids Res..
[63] Ian T. Paulsen,et al. Complete genome sequence of Caulobacter crescentus , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[64] C. Yanofsky. Attenuation in the control of expression of bacterial operons , 1981, Nature.
[65] Najaf A. Shah,et al. Evidence for context-dependent complementarity of non-Shine-Dalgarno ribosome binding sites to Escherichia coli rRNA. , 2013, ACS chemical biology.
[66] Peter F. Stadler,et al. ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.
[67] Michael T. Laub,et al. Regulation of the bacterial cell cycle by an integrated genetic circuit , 2006, Nature.
[68] Saman Halgamuge,et al. Analysis of SD sequences in completed microbial genomes: non-SD-led genes are as common as SD-led genes. , 2006, Gene.
[69] L. Shapiro,et al. ClpXP and ClpAP proteolytic activity on divisome substrates is differentially regulated following the Caulobacter asymmetric cell division , 2014, Molecular microbiology.
[70] B. Shen,et al. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution , 2012, Proceedings of the National Academy of Sciences.
[71] Temple F. Smith,et al. Operons in Escherichia coli: genomic analyses and predictions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[72] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[73] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[74] T. Gojobori,et al. Dynamic evolution of translation initiation mechanisms in prokaryotes , 2010, Proceedings of the National Academy of Sciences.
[75] G. Storz,et al. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. , 2011, Cold Spring Harbor perspectives in biology.
[76] Z. She,et al. Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes , 2011, BMC Genomics.
[77] Mikael Bodén,et al. MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..
[78] Jeffrey W. Roberts,et al. High-resolution view of bacteriophage lambda gene expression by ribosome profiling , 2013, Proceedings of the National Academy of Sciences.
[79] Greg L. Hersch,et al. Sculpting the Proteome with AAA+ Proteases and Disassembly Machines , 2004, Cell.