Complete Genome Sequence of Caulobacter Crescentus’’ by William C
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Correction MICROBIOLOGY. For the article ‘‘Complete genome sequence of Caulobacter crescentus’’ by William C. Nierman, Tamara V. Feldblyum, Michael T. Laub, Ian T. Paulsen, Karen E. Nelson, Jonathan Eisen, John F. Heidelberg, M. R. K. Alley, Noriko Ohta, Janine R. Maddock, Isabel Potocka, William C. Nelson, Austin Newton, Craig Stephens, Nikhil D. Phadke, Bert Ely, Robert T. DeBoy, Robert J. Dodson, A. Scott Durkin, Michelle L. Gwinn, Daniel H. Haft, James F. Kolonay, John Smit, M. B. Craven, Hoda Khouri, Jyoti Shetty, Kristi Berry, Teresa Utter- back, Kevin Tran, Alex Wolf, Jessica Vamathevan, Maria Er- molaeva, Owen White, Steven L. Salzberg, J. Craig Venter, Lucy Shapiro, and Claire M. Fraser, which appeared in number 7, March 27, 2001, of Proc. Natl. Acad. Sci. USA (98, 4136–4141; First Published March 20, 2001; 10.1073͞pnas.061029298), the authors note the following. Jonathan Eisen should be listed as Jonathan A. Eisen. www.pnas.org͞cgi͞doi͞10.1073͞pnas.131200598 CORRECTION www.pnas.org PNAS ͉ May 22, 2001 ͉ vol. 98 ͉ no. 11 ͉ 6533 Downloaded by guest on October 1, 2021 Complete genome sequence of Caulobacter crescentus William C. Nierman*†, Tamara V. Feldblyum†, Michael T. Laub‡, Ian T. Paulsen†, Karen E. Nelson†, Jonathan Eisen†, John F. Heidelberg†, M. R. K. Alley§, Noriko Ohta¶, Janine R. Maddockʈ, Isabel Potocka§, William C. Nelson†, Austin Newton¶, Craig Stephens**, Nikhil D. Phadkeʈ, Bert Ely††, Robert T. DeBoy†, Robert J. Dodson†, A. Scott Durkin†, Michelle L. Gwinn†, Daniel H. Haft†, James F. Kolonay†, John Smit‡‡, M. B. Craven†, Hoda Khouri†, Jyoti Shetty†, Kristi Berry†, Teresa Utterback†, Kevin Tran†, Alex Wolf†, Jessica Vamathevan†, Maria Ermolaeva†, Owen White†, Steven L. Salzberg†, J. Craig Venter†§§, Lucy Shapiro‡, and Claire M. Fraser† †The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; ‡Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305; §Department of Biochemistry, Imperial College of Science, Technology and Medicine, London SW7 2AY, United Kingdom; ¶Department of Molecular Biology, Princeton University, Princeton, NJ 08544; ʈDepartment of Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048; **Biology Department, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053; ††Department of Biological Sciences, University of South Carolina, Columbia, SC 29208; ‡‡Department of Microbiology and Immunology, no. 300, 6174 University Boulevard, University of British Columbia, Vancouver, BC V6T 1Z3 Canada; and §§Celera Genomics, 45 West Gude Drive, Rockville, MD 20850 Contributed by Lucy Shapiro, January 17, 2001 The complete genome sequence of Caulobacter crescentus was de- minimizes competition during growth in a dilute environment by termined to be 4,016,942 base pairs in a single circular chromosome ensuring that the progeny cell will colonize in a new location (1). encoding 3,767 genes. This organism, which grows in a dilute aquatic The swarmer cell is unable to initiate chromosome replication until environment, coordinates the cell division cycle and multiple cell it differentiates into a stalked cell. The regulation of cell cycle differentiation events. With the annotated genome sequence, a full progression in C. crescentus occurs at several levels (4): temporally description of the genetic network that controls bacterial differenti- controlled transcriptional activation and repression, differential ation, cell growth, and cell cycle progression is within reach. Two- phosphorylation of two-component system regulatory proteins, and component signal transduction proteins are known to play a signif- proteolysis of regulatory and structural proteins. The basic para- icant role in cell cycle progression. Genome analysis revealed that the digm of cell cycle control used by eukaryotic cells, temporally C. crescentus genome encodes a significantly higher number of these controlled transcription, phosphorylation of regulatory factors, and signaling proteins (105) than any bacterial genome sequenced thus targeted proteolysis, has been conserved in C. crescentus, although far. Another regulatory mechanism involved in cell cycle progression the proteins involved in these processes are different. Recent is DNA methylation. The occurrence of the recognition sequence for observations of regulatory proteins dynamically localized to defined an essential DNA methylating enzyme that is required for cell cycle cellular addresses at specific times in the C. crescentus cell cycle regulation is severely limited and shows a bias to intergenic regions. suggest that the three-dimensional organization of this cell adds yet The genome contains multiple clusters of genes encoding proteins another layer of control (5). The completion of the full genome essential for survival in a nutrient poor habitat. Included are those sequence of this organism provides access to the complete signal involved in chemotaxis, outer membrane channel function, degrada- transduction network that controls differentiation and cell cycle tion of aromatic ring compounds, and the breakdown of plant- progression within the context of a unicellular organism growing in derived carbon sources, in addition to many extracytoplasmic func- a dilute nutrient environment. tion sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our Methods knowledge, the first free-living ␣-class proteobacterium to be se- ORF Prediction and Gene Identification. ORFs were identified by quenced and will serve as a foundation for exploring the biology of using GLIMMER (6). Annotation of the identified ORFs was ac- this group of bacteria, which includes the obligate endosymbiont and complished by manual curation of the outputs of a variety of human pathogen Rickettsia prowazekii, the plant pathogen Agrobac- similarity searches. Searches of the predicted coding regions were terium tumefaciens, and the bovine and human pathogen Brucella performed with BLASTP, as previously described (7). The protein– abortus. protein matches are aligned with blastextendrepraze, a modified Smith–Waterman (8) algorithm that maximally extends regions of aulobacter crescentus, a Gram-negative bacterium that grows in similarity across frameshifts. Gene identification is facilitated by Cdilute aquatic environments, is a member of the ␣-subdivision searching against a database of nonredundant bacterial proteins of proteobacteria. C. crescentus invariably differentiates and divides (nraa) developed at TIGR and curated from the public archives asymmetrically at each cell cycle. Asymmetric cell division and GenBank, Genpept, PIR, and SwissProt. Searches matching entries differentiation are recurring themes that underline cellular diversity in nraa have the corresponding role, gene common name, percent in multicellular organisms. C. crescentus is a simple and highly identity and similarity of match, pairwise sequence alignment, and manipulable single-celled model system to study cellular differen- taxonomy associated with the match assigned to the predicted tiation, asymmetric division, and their coordination with cell cycle progression (1, 2). Caulobacter does all that with less than 4,000 Abbreviations: HMM, hidden Markov model; HPK, histidine protein kinase; RR, response genes, allowing full genome-wide studies of a single differentiating regulator. cell. Data deposition: The sequence reported in this paper has been deposited in the GenBank This stalked bacterium adheres to solid surfaces via a holdfast at database (accession no. AE005673). the tip of the stalk. It also has a motile swarmer cell stage during *To whom reprint requests should be addressed. E-mail: [email protected]. its life cycle. The stalked cell acts like a stem cell, continually giving The publication costs of this article were defrayed in part by page charge payment. This rise to a new swarmer cell at each division (Fig. 1) (3). The article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. production of a swarmer cell with an obligatory motile period §1734 solely to indicate this fact. 4136–4141 ͉ PNAS ͉ March 27, 2001 ͉ vol. 98 ͉ no. 7 www.pnas.org͞cgi͞doi͞10.1073͞pnas.061029298 Fig. 1. Circular representation of the C. crescentus genome. Coordinate markers around the outside of the circle are in base pairs. First circle, predicted coding regions MICROBIOLOGY on the plus strand color coded by role category: violet, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups, and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; gold, DNA metabolism; light gray, energy metabolism; magenta, fatty acid and phospholipid metabolism; pink, protein synthesis͞fate; orange, purines, pyrimidines, nucleosides, nucleotides; olive, regulatory functions; dark green, transcription; teal, transport and binding proteins; salmon, plasmid, phage, and transposon functions; blue, unknown function, hypothetical and conserved hypothetical proteins. Second circle, predicted coding regions on the minus strand color coded by role category. Third circle, genes involved in chemotaxis and motility color coded by role category: olive, two-component regulatory genes; red, methyl-accepting chemotaxis genes; dark green, extracellular function sigma factors; teal, TonB and the TonB-dependent receptors. Fourth circle, cell cycle-regulated genes (2). Fifth circle, atypical