151
|
Lee YJ, Choi JJ, Kwon ST. Cloning, expression, and partial characterization of a family B-type DNA polymerase from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
152
|
Stone EA, Cooper GM, Sidow A. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu Rev Genomics Hum Genet 2005; 6:143-64. [PMID: 16124857 DOI: 10.1146/annurev.genom.6.080604.162146] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As whole-genome sequencing efforts extend beyond more traditional model organisms to include a deep diversity of species, comparative genomic analyses will be further empowered to reveal insights into the human genome and its evolution. The discovery and annotation of functional genomic elements is a necessary step toward a detailed understanding of our biology, and sequence comparisons have proven to be an integral tool for that task. This review is structured to broadly reflect the statistical challenges in discriminating these functional elements from the bulk of the genome that has evolved neutrally. Specifically, we review the comparative genomics literature in terms of specificity, sensitivity, and phylogenetic scope, as well as the trade-offs that relate these factors in standard analyses. We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling.
Collapse
Affiliation(s)
- Eric A Stone
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | | | | |
Collapse
|
153
|
Affiliation(s)
- Edwin Southern
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
154
|
Chavan M, Rafi H, Wertz J, Goldstone C, Riley MA. Phage associated bacteriocins reveal a novel mechanism for bacteriocin diversification in Klebsiella. J Mol Evol 2005; 60:546-56. [PMID: 15883889 DOI: 10.1007/s00239-004-0263-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Accepted: 10/11/2004] [Indexed: 10/25/2022]
Abstract
Ninety-six isolates of Klebsiella pneumoniae and K. oxytoca were recovered from wild mammals in Australia. 14.6% of these bacteria produce killing phenotypes that suggest the production of bacteriocin toxins. Cloning and sequencing of the gene clusters encoding two of these killing phenotypes revealed two instances of a bacteriocin associated with a bacteriophage gene, the first such genetic organization described. The newly identified klebicin C gene cluster was discovered in both K. pneumoniae and K. oxytoca. The newly identified klebicin D gene cluster was detected in K. oxytoca. Protein sequence comparisons and phylogenetic inference suggest that klebicin C is most closely related to the rRNase group of colicins (such as colicin E4), while klebicin D is most closely related to the tRNase group of colicins (such as colicin D). The klebicin C and D gene clusters have similar genetic and regulatory organizations. In both cases, an operon structure is inferred consisting of a phage-associated open reading frame and klebicin activity and associated immunity genes. This novel bacteriophage/bacteriocin organization may provide a novel mechanism for the generation of bacteriocin diversity in Klebsiella.
Collapse
Affiliation(s)
- Milind Chavan
- Department of Biology, University of Massachusetts Amherst, 611 North Pleasant Street, Amherst, MA, 01003, USA
| | | | | | | | | |
Collapse
|
155
|
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005; 3:722-32. [PMID: 16138100 DOI: 10.1038/nrmicro1235] [Citation(s) in RCA: 1034] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.
Collapse
Affiliation(s)
- Laura S Frost
- Department of Biological Sciences, Biological Sciences Centre, University of Alberta Edmonton, Alberta T6G 2E9, Canada
| | | | | | | |
Collapse
|
156
|
Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005; 437:69-87. [PMID: 16136131 DOI: 10.1038/nature04072] [Citation(s) in RCA: 1552] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 07/20/2005] [Indexed: 12/18/2022]
Abstract
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
Collapse
|
157
|
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
158
|
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
159
|
Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
160
|
Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
161
|
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
162
|
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
163
|
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1235 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
164
|
Zhao YY, Wu LY, Zhang JH, Wang RS, Zhang XS. Haplotype assembly from aligned weighted SNP fragments. Comput Biol Chem 2005; 29:281-7. [PMID: 16051522 DOI: 10.1016/j.compbiolchem.2005.05.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 05/20/2005] [Accepted: 05/20/2005] [Indexed: 11/22/2022]
Abstract
Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211-213)). In this paper we show that the general WMLF model is NP-hard even for the gapless case. However the algorithmic solutions for selected variants of WMFL can exist and we propose a heuristic algorithm based on a dynamic clustering technique. We also introduce a new formulation of the haplotype assembly problem that we call COMPLETE WMLF (CWMLF). This model and algorithms for its implementation take into account a simultaneous presence of multiple kinds of data errors. Extensive computational experiments indicate that the algorithmic implementations of the CWMLF model achieve higher accuracy of haplotype reconstruction than the WMLF-based algorithms, which in turn appear to be more accurate than those based on MLF.
Collapse
Affiliation(s)
- Yu-Ying Zhao
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China.
| | | | | | | | | |
Collapse
|
165
|
Chen Y, Golding I, Sawai S, Guo L, Cox EC. Population fitness and the regulation of Escherichia coli genes by bacterial viruses. PLoS Biol 2005; 3:e229. [PMID: 15984911 PMCID: PMC1151598 DOI: 10.1371/journal.pbio.0030229] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Accepted: 04/27/2005] [Indexed: 11/18/2022] Open
Abstract
Temperate bacteriophage parasitize their host by integrating into the host genome where they provide additional genetic information that confers higher fitness on the host bacterium by protecting it against invasion by other bacteriophage, by increasing serum resistance, and by coding for toxins and adhesion factors that help the parasitized bacterium invade or evade its host. Here we ask if a temperate phage can also regulate host genes. We find several different host functions that are down-regulated in lysogens. The pckA gene, required for gluconeogenesis in all living systems, is regulated directly by the principal repressor of many different temperate prophage, the cI protein. cI binds to the regulatory region of pckA, thereby shutting down pckA transcription. The pckA regulatory region has target sequences for many other temperate phage repressors, and thus we suggest that down-regulation of the host pckA pathway increases lysogen fitness by lowering the growth rate of lysogens in energy-poor environments, perhaps as an adaptive response to the host predation system or as an aspect of lysogeny that must be offset by down-regulating pckA. Lysogenic bacteriophage such as lambda integrate into their host genome, but do they regulate specific host genes? This study shows that they do, thereby increasing the fitness of the lysogen.
Collapse
Affiliation(s)
- Ying Chen
- 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ido Golding
- 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Satoshi Sawai
- 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ling Guo
- 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Edward C Cox
- 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
166
|
Ahn Y, Jung H, Tatavarty R, Choi H, Yang JW, Kim IS. Monitoring of petroleum hydrocarbon degradative potential of indigenous microorganisms in ozonated soil. Biodegradation 2005; 16:45-56. [PMID: 15727154 DOI: 10.1007/s10531-004-0428-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This study was performed to investigate the petroleum hydrocarbon (PH) degradative potential of indigenous microorganisms in ozonated soil to better develop combined pre-ozonation/bioremediation technology. Diesel-contaminated soils were ozonated for 0-900 min. PH and microbial concentrations in the soils decreased with increased ozonation time. The greatest reduction of total PH (TPH, 47.6%) and aromatics (11.3%) was observed in 900-min ozonated soil. The number of total viable heterotrophic bacteria decreased by three orders of magnitude in the soil. Ozonated soils were incubated for 9 weeks for bioremediation. The number of microorganisms in the soils increased during the incubation period, as monitored by culture- and nonculture-based methods. The soils showed additional PH-removal during incubation, supporting the presence of PH-degraders in the soils. The highest removal (25.4%) of TPH was observed during the incubation of 180-min ozonated soil during the incubation while a negligible removal was shown in 900-min ozonated soil. This negligible removal could be explained by the existence of relatively few or undetected PH-degraders in 900-min ozonated soil. After a 9-week incubation of the ozonated soils, 180-min ozonated soil showed the lowest TPH concentration, suggesting that appropriate ozonation and indigenous microorganisms survived ozonation could enhance remediation of PH-contaminated soil. Microbial community composition in 9-week incubated soils revealed a slight difference between 900-min ozonated and unozonated soils, as analyzed by whole cell hybridization. Taken together, this study provided insight into indigenous microbial potential to degrade PH in ozonated soils.
Collapse
Affiliation(s)
- Yeonghee Ahn
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Korea.
| | | | | | | | | | | |
Collapse
|
167
|
Chan EY. Advances in sequencing technology. Mutat Res 2005; 573:13-40. [PMID: 15829235 DOI: 10.1016/j.mrfmmm.2005.01.004] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Revised: 01/04/2005] [Accepted: 01/05/2005] [Indexed: 11/20/2022]
Abstract
Faster sequencing methods will undoubtedly lead to faster single nucleotide polymorphism (SNP) discovery. The Sanger method has served as the cornerstone for genome sequence production since 1977, close to almost 30 years of tremendous utility [Sanger, F., Nicklen, S., Coulson, A.R, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. U.S.A. 74 (1977) 5463-5467]. With the completion of the human genome sequence [Venter, J.C. et al., The sequence of the human genome, Science 291 (2001) 1304-1351; Lander, E.S. et al., Initial sequencing and analysis of the human genome, Nature 409 (2001) 860-921], there is now a focus on developing new sequencing methodologies that will enable "personal genomics", or the routine study of our individual genomes. Technologies that will lead us to this lofty goal are those that can provide improvements in three areas: read length, throughput, and cost. As progress is made in this field, large sections of genomes and then whole genomes of individuals will become increasingly more facile to sequence. SNP discovery efforts will be enhanced lock-step with these improvements. Here, the breadth of new sequencing approaches will be summarized including their status and prospects for enabling personal genomics.
Collapse
Affiliation(s)
- Eugene Y Chan
- The DNA Medicine Institute, 116 Charles Street, Suite 6, Boston, MA 02114, USA.
| |
Collapse
|
168
|
Yeom MS, Lee J. The mechanism of the self-assembly of associating DNA molecules under shear flow: Brownian dynamics simulation. J Chem Phys 2005; 122:184905. [PMID: 15918763 DOI: 10.1063/1.1896346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A shear flow induces the assembly of DNAs with the sticky spots. In order to strictly interpret the mechanism of shear-induced DNA assembly, Brownian dynamics simulations with the bead-spring model were carried out for these molecules at various ranges of the Weissenberg numbers (We). We calculate a formation time and analyze the radial distribution function of end beads and the probability distribution of fractional extension at the formation time to understand the mechanism of shear-induced assembly. At low Weissenberg number the formation time, which is defined as an elapsed time until a multimer forms for the first time, decreases rapidly, reaching a plateau at We = 1000. A shear flow changes the radial distribution of end beads, which is almost the same regardless of the Weissenberg number. A shear flow deforms and stretches the molecules and generates different distributions between end beads with a stickly spot. The fractional extension progresses rapidly in shear flow from a Gaussian-like distribution to a uniform distribution. The progress of the distribution of fractional extension increases the possibility of meeting of end beads. In shear flow, the inducement of the assembly mainly results from the progress of the probability distribution of fractional extension. We also calculate properties such as the radius of gyration, stretch, and so on. As the Weissenberg number increases, the radius of gyration at the formation time also increases rapidly, reaching a plateau at We = 1000.
Collapse
Affiliation(s)
- Min Sun Yeom
- Supercomputing Research Department, Korea Institute of Science and Technology Information, Daejeon 305-806, Korea.
| | | |
Collapse
|
169
|
Datta P, Mallik P, Ghosh AN, Chakravorthy M. Temperature Sensitive Mutation in the 38 kDa Minor Structural Protein Gene of Phage MB78 Interferes with Phage Morphogenesis. Virus Genes 2005; 30:197-207. [PMID: 15744577 DOI: 10.1007/s11262-004-5628-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Accepted: 09/05/2004] [Indexed: 10/25/2022]
Abstract
Temperature sensitive mutation in the gene for the 38 kDa minor structural protein of the phage MB78, a virulent phage of Salmonella enterica serovar typhimurium, interferes with phage development at restrictive temperature. Electron microscopy of particles produced at non-permissive temperature indicated that the particles formed are tailless. Two types of particles are seen: (i) empty capsids, which are not perfect icosahedral (ii) icosahedral particles filled with DNA. The gene for the 38 kDa protein is located in the SalIG fragment of the phage genome. Nucleotide sequence of the SalIG fragment of MB78 as well as its temperature sensitive mutant has been determined and analysed. Such analysis indicated that in the mutant the codon GCA has been changed to GTA resulting in substitution of alanine at position 75 of the protein by valine (A75V). This makes the protein thermolabile. Our results suggest that normal functioning of this 38 kDa protein is necessary for attachment of tail fibre to the capsid. Or in other words, this 38 kDa protein is involved in phage morphogenesis.
Collapse
Affiliation(s)
- Pinaki Datta
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, U.P., India
| | | | | | | |
Collapse
|
170
|
|
171
|
Han L, Cai C, Ji Z, Chen Y. Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity. Virology 2005; 331:136-43. [PMID: 15582660 PMCID: PMC7111859 DOI: 10.1016/j.virol.2004.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2004] [Revised: 09/15/2004] [Accepted: 10/09/2004] [Indexed: 11/19/2022]
Abstract
The function of a substantial percentage of the putative protein-coding open reading frames (ORFs) in viral genomes is unknown. As their sequence is not similar to that of proteins of known function, the function of these ORFs cannot be assigned on the basis of sequence similarity. Methods complement or in combination with sequence similarity-based approaches are being explored. The web-based software SVMProt (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi) to some extent assigns protein functional family irrespective of sequence similarity and has been found to be useful for studying distantly related proteins [Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, X., Chen, Y.Z., 2003. SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 31(13): 3692–3697]. Here 25 novel viral proteins are selected to test the capability of SVMProt for functional family assignment of viral proteins whose function cannot be confidently predicted on by sequence similarity methods at present. These proteins are without a sequence homolog in the Swissprot database, with its precise function provided in the literature, and not included in the training sets of SVMProt. The predicted functional classes of 72% of these proteins match the literature-described function, which is compared to the overall accuracy of 87% for SVMProt functional class assignment of 34 582 proteins. This suggests that SVMProt to some extent is capable of functional class assignment irrespective of sequence similarity and it is potentially useful for facilitating functional study of novel viral proteins.
Collapse
Affiliation(s)
- L.Y. Han
- Bioinformatics and Drug Design Group, Department of Computational Science, National University of Singapore, Block SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
| | - C.Z. Cai
- Bioinformatics and Drug Design Group, Department of Computational Science, National University of Singapore, Block SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
- Department of Applied Physics, Chongquing University, Chongquing 400044, PR China
| | - Z.L. Ji
- Department of Biology, School of Life Sciences, Xiamen University, Xiamen 361000, FuJian Province, PR China
| | - Y.Z. Chen
- Bioinformatics and Drug Design Group, Department of Computational Science, National University of Singapore, Block SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
- Corresponding author. Fax: +65 6774 6756.
| |
Collapse
|
172
|
Inokuchi H, Inokuti Y. Effective breakage of phage .LAMBDA. DNA by shearing with ceramic-coated needle of syringe. Genes Genet Syst 2005; 80:79-82. [PMID: 15824459 DOI: 10.1266/ggs.80.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The loss of biological activity of phage lambda DNA was much greater when the DNA was sheared using a ceramic-coated needle attached to a syringe compared with a conventional stainless steel needle. Inactivation of the biological activity was due to breakage at the middle of the molecule. The thickness of the ceramic-coating was a crucial factor for the breakage. Because approximately the same level of inactivation was observed with a non-coated needle as with thin glass and quartz tubes, it was concluded that the unknown characteristic(s) of the silicon nitride (SiNx) coating itself resulted in the effective breakage of lambda DNA molecules by shearing force.
Collapse
Affiliation(s)
- Hachiro Inokuchi
- Department of Biotechnology, National Institute of Technology and Evaluation, Kazusa, Chiba, Japan.
| | | |
Collapse
|
173
|
Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, Gupta J, Ho SL, Karlins EM, Maduro QL, Stantripop S, Tsurgeon C, Vogt JL, Walker MA, Masiello CA, Guan X, Bouffard GG, Green ED. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res 2004; 14:2235-44. [PMID: 15479945 PMCID: PMC525681 DOI: 10.1101/gr.2648404] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 08/16/2004] [Indexed: 11/25/2022]
Abstract
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of "sequence finishing" remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, such a high-quality product cannot be cost-justified for large numbers of additional genomes, at least for the foreseeable future. Here we describe the generation and quality of an intermediate grade of finished genomic sequence (termed comparative-grade finished sequence), which is tailored for use in multispecies sequence comparisons. Our analyses indicate that this sequence is very high quality (with the residual gaps and errors mostly falling within repetitive elements) and reflects 99% of the total sequence. Importantly, comparative-grade sequence finishing requires approximately 40-fold less reagents and approximately 10-fold less personnel effort compared to the generation of near-perfect finished sequence, such as that produced for the human genome. Although applied here to finishing sequence derived from individual bacterial artificial chromosome (BAC) clones, one could envision establishing routines for refining sequences emanating from whole-genome shotgun sequencing projects to a similar quality level. Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses.
Collapse
Affiliation(s)
- Robert W Blakesley
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
174
|
Chin V, Valinluck V, Magaki S, Ryu J. KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system. Nucleic Acids Res 2004; 32:e138. [PMID: 15475385 PMCID: PMC524312 DOI: 10.1093/nar/gnh134] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella pneumoniae. Here, the KpnBI modification genes were cloned into a plasmid using a modification expression screening method. The modification genes that consist of both hsdM (2631 bp) and hsdS (1344 bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These two genes overlap by one base and share the same promoter located upstream of the hsdM gene. Using recently developed plasmid R-M tests and a computer program RM Search, the DNA recognition sequence for the KpnBI enzymes was identified as a new 8 nt sequence containing one degenerate base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII sensitivity tests, the methylation loci were predicted to be the italicized third adenine in the 5' specific region and the adenine opposite the italicized thymine in the 3' specific region. Combined with previous sequence data for hsdR, we concluded that the KpnBI system is a typical type I R-M system. The deduced amino acid sequences of the three subunits of the KpnBI system show only limited homologies (25 to 33% identity) at best, to the four previously categorized type I families (IA, IB, IC, and ID). Furthermore, their identity scores to other uncharacterized putative genome type I sequences were 53% at maximum. Therefore, we propose that KpnBI is the prototype of a new 'type IE' family.
Collapse
Affiliation(s)
- V Chin
- Division of Microbiology and Molecular Genetics, Department of Biochemistry and Microbiology, Loma Linda University, Loma Linda, CA 92350, USA
| | | | | | | |
Collapse
|
175
|
Tegenfeldt JO, Prinz C, Cao H, Chou S, Reisner WW, Riehn R, Wang YM, Cox EC, Sturm JC, Silberzan P, Austin RH. From the Cover: The dynamics of genomic-length DNA molecules in 100-nm channels. Proc Natl Acad Sci U S A 2004; 101:10979-83. [PMID: 15252203 PMCID: PMC503729 DOI: 10.1073/pnas.0403849101] [Citation(s) in RCA: 419] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel that scales linearly with the contour length of the polymer, in agreement with the scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly the contour length of single DNA molecules confined in the channels, and the statistical analysis of the dynamics of the polymer in the nanochannel allows us to compute the SD of the mean of the extension. This statistical analysis allows us to measure the extension of lambda DNA multimers with a 130-nm SD in 1 min.
Collapse
|
176
|
Sippy J, Feiss M. Initial cos cleavage of bacteriophage lambda concatemers requires proheads and gpFI in vivo. Mol Microbiol 2004; 52:501-13. [PMID: 15066036 DOI: 10.1111/j.1365-2958.2004.03990.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The development of bacteriophage lambda and double-stranded DNA viruses in general involves the convergence of two separate pathways: DNA replication and head assembly. Clearly, packaging will proceed only if an empty capsid shell, the prohead, is present to receive the DNA, but genetic evidence suggests that proheads play another role in the packaging process. For example, lambda phages with an amber mutation in any head gene or in FI, the gene encoding the accessory packaging protein gpFI, are able to produce normal amounts of DNA concatemers but they are not cut, or matured, into unit length chromosomes for packaging. Similar observations have been made for herpes simplex 1 virus. In the case of lambda, a negative model proposes that in the amber phages, unassembled capsid components are inhibitory to maturation, and a positive model suggests that assembled proheads are required for cutting. We tested the negative model by using a deletion mutant devoid of all prohead genes and FI in an in vivo cos cleavage assay; in this deleted phage, the cohesive ends were not cut. When lambda proheads and gpFI were provided in vivo via a second prophage, cutting was restored, and gpFI was required, results that support the positive model. Phage 21 is a sister phage of lambda, and although its capsid proteins share approximately 60% residue identity with lambda's, phage 21 proheads did not restore cutting, even when provided with the accessory protein gpFI. Models for the role of proheads and gpFI in cos cutting are discussed.
Collapse
Affiliation(s)
- Jean Sippy
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA.
| | | |
Collapse
|
177
|
Murialdo H, Xing X, Tzamtzis D, Haddad A, Gold M. The product of the bacteriophage lambda W gene: purification and properties. Biochem Cell Biol 2004; 81:307-15. [PMID: 14569303 DOI: 10.1139/o03-059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gene W is one of the 10 genes that control the morphogenesis of the bacteriophage lambda head. The morpho genesis of the phage lambda head proceeds through the synthesis of an intermediate assembly called the prohead. This is an empty shell into which the bacteriophage DNA is introduced--packaged--by the phage enzyme DNA terminase. The product of W (gpW) acts after DNA packaging, but before the addition of another phage product, gene product FII, and before the addition of tails. The role of gpW is unknown. The structure of N- and C-tagged gpW has been previously determined by nuclear magnetic resonance (NMR) spectroscopy. Here we report some of the properties of the native protein. The purification of gpW to homogeneity, overproduced by a plasmid derivative, is described. To obtain large amounts of the protein, the ribosome-binding site had to be modified, showing that inefficient translation of the message is the main mechanism limiting W gene expression. The molecular weight of the protein is in close agreement to the value predicted from the DNA sequence of the gene, which suggests that it is not post-transcriptionally modified. It behaves as a monomer in solution. Radioactively labeled gpW is incorporated into phage particles in in vitro complementation, showing that gpW is a structural protein. The stage at which gpW functions and other circumstantial evidence support the idea that six molecules of gpW polymerize on the connector before the incorporation of six molecules of gpFII and before the tail attaches.
Collapse
Affiliation(s)
- Helios Murialdo
- Fundación Ciencia para la Vida and Millennium Institute for Fundamental and Applied Biology, Avenida Marathon 1943, Santiago, Chile.
| | | | | | | | | |
Collapse
|
178
|
Abstract
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site.
Collapse
Affiliation(s)
- Mihai Pop
- The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA.
| | | | | |
Collapse
|
179
|
Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M. Improving gene annotation of complete viral genomes. Nucleic Acids Res 2003; 31:7041-55. [PMID: 14627837 PMCID: PMC290248 DOI: 10.1093/nar/gkg878] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2003] [Revised: 08/02/2003] [Accepted: 10/03/2003] [Indexed: 11/18/2022] Open
Abstract
Gene annotation in viruses often relies upon similarity search methods. These methods possess high specificity but some genes may be missed, either those unique to a particular genome or those highly divergent from known homologs. To identify potentially missing viral genes we have analyzed all complete viral genomes currently available in GenBank with a specialized and augmented version of the gene finding program GeneMarkS. In particular, by implementing genome-specific self-training protocols we have better adjusted the GeneMarkS statistical models to sequences of viral genomes. Hundreds of new genes were identified, some in well studied viral genomes. For example, a new gene predicted in the genome of the Epstein-Barr virus was shown to encode a protein similar to alpha-herpesvirus minor tegument protein UL14 with heat shock functions. Convincing evidence of this similarity was obtained after only 12 PSI-BLAST iterations. In another example, several iterations of PSI-BLAST were required to demonstrate that a gene predicted in the genome of Alcelaphine herpesvirus 1 encodes a BALF1-like protein which is thought to be involved in apoptosis regulation and, potentially, carcinogenesis. New predictions were used to refine annotations of viral genomes in the RefSeq collection curated by the National Center for Biotechnology Information. Importantly, even in those cases where no sequence similarities were detected, GeneMarkS significantly reduced the number of primary targets for experimental characterization by identifying the most probable candidate genes. The new genome annotations were stored in VIOLIN, an interactive database which provides access to similarity search tools for up-to-date analysis of predicted viral proteins.
Collapse
Affiliation(s)
- Ryan Mills
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | | | | | | | | |
Collapse
|
180
|
Roche S. Sequence dependent DNA-mediated conduction. PHYSICAL REVIEW LETTERS 2003; 91:108101. [PMID: 14525509 DOI: 10.1103/physrevlett.91.108101] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2003] [Indexed: 05/24/2023]
Abstract
We report on coherent charge transport studies in periodic Poly(dG)-Poly(dC) and aperiodic lambda-phage DNA sequences. The extent and efficiency of charge transfer is discussed as a function of sequence dependent energetics, of temperature dependent base-base couplings, and in relation with experiments.
Collapse
Affiliation(s)
- Stephan Roche
- CEA/DSM/DRFMC/SPSMS, 17 avenue des Martyrs, 38054 Grenoble, France
| |
Collapse
|
181
|
Amavisit P, Lightfoot D, Browning GF, Markham PF. Variation between pathogenic serovars within Salmonella pathogenicity islands. J Bacteriol 2003; 185:3624-35. [PMID: 12775700 PMCID: PMC156220 DOI: 10.1128/jb.185.12.3624-3635.2003] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although four of the five Salmonella pathogenicity islands (SPIs) have been characterized in detail for Salmonella enterica serovar Typhimurium, and the fifth has been characterized for Salmonella enterica serovar Dublin, there have been limited studies to examine them in detail in a range of pathogenic serovars of S. enterica. The aim of this study was to examine these regions, shown to be crucial in virulence, in pathogenic serovars to identify any major deletions or insertions that may explain variation in virulence and provide further understanding of the elements involved in the evolution of these regions. Multiple strains of each of the 13 serovars were compared by Southern blot hybridization using a series of probes that together encompassed the full length of all five SPIs. With the exception of serovar Typhimurium, all strains of the same serovar were identical in all five SPIs. Those serovars that differed from serovar Typhimurium in SPI-1 to SPI-4 and from serovar Dublin in SPI-5 were examined in more detail in the variant regions by PCR, and restriction endonuclease digestion and/or DNA sequencing. While most variation in hybridization patterns was attributable to loss or gain of single restriction endonuclease cleavage sites, three regions, in SPI-1, SPI-3, and SPI-5, had differences due to major insertions or deletions. In SPI-1 the avrA gene was replaced by a 200-base fragment in three serovars, as reported previously. In SPI-5, two serovars had acquired an insertion with similarity to the pagJ and pagK genes between pipC and pipD. In SPI-3 the genes sugR and rhuM were deleted in most serovars and in some were replaced by sequences that were very similar to either the Escherichia coli fimbrial operon, flanked by two distinct insertion sequence elements, or to the E. coli retron phage PhiR73. The distribution of these differences suggests that there have been a number of relatively recent horizontal transfers of genes into S. enterica and that in some cases the same event has occurred in multiple lineages of S. enterica. Thus, it seems that insertion sequences and retron phages are likely to be involved in continuing evolution of the pathogenicity islands of pathogenic Salmonella serovars.
Collapse
Affiliation(s)
- P Amavisit
- Department of Veterinary Science, The University of Melbourne, Parkville 3010, Victoria, Australia
| | | | | | | |
Collapse
|
182
|
Sato T, Shimizu T, Watarai M, Kobayashi M, Kano S, Hamabata T, Takeda Y, Yamasaki S. Distinctiveness of the genomic sequence of Shiga toxin 2-converting phage isolated from Escherichia coli O157:H7 Okayama strain as compared to other Shiga toxin 2-converting phages. Gene 2003; 309:35-48. [PMID: 12727356 DOI: 10.1016/s0378-1119(03)00487-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Shiga toxin 2-converting phage was isolated from Escherichia coli O157:H7 associated with an outbreak that occurred in Okayama, Japan in 1996 (M. Watarai, T. Sato, M. Kobayashi, T. Shimizu, S. Yamasaki, T. Tobe, C. Sasakawa and Y. Takeda, Infect. Immun. 61 (1998) 3210-3204). In this study, we analyzed the complete nucleotide sequence of Shiga toxin 2-converting phage, designated Stx2phi-I, and compared it with three recently reported Stx2-phage genomes. Stx2phi-I consisted of 61,765 bp, which included 166 open reading frames. When compared to 933W, VT2-Sakai and VT2-Sa phages, six characteristic regions (regions I-VI) were found in the Stx2 phage genomes although overall homology was more than 95% between these phages. Stx2phi-I exhibited remarkable differences in these regions as compared with VT-2 Sakai and VT2-Sa genes but not with 933W phage. Characteristic repeat sequences were found in regions I-IV where the genes responsible for the construction of head and tail are located. Regions V and VI, which are the most distinct portion in the entire phage genome were located in the upstream and downstream regions of the Stx2 operons that are responsible for the immunity and replication, and host lysis. These data indicated that Stx2phi-I is less homologous to VT2-Sakai and VT2-Sa phages, despite these three phages being found in the strains isolated at the almost same time in the same geographic region but closely related to 933W phage which was found in the E. coli O157 strain 933W isolated 14 years ago in a different geographic area.
Collapse
Affiliation(s)
- Toshio Sato
- Research Institute, International Medical Center of Japan, 1-21-1, Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | | | | | | | | | | | | | | |
Collapse
|
183
|
Kasarjian JKA, Iida M, Ryu J. New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method. Nucleic Acids Res 2003; 31:e22. [PMID: 12595571 PMCID: PMC149844 DOI: 10.1093/nar/gng022] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The presence of restriction enzymes in bacterial cells has been predicted by either classical phage restriction-modification (R-M) tests, direct in vitro enzyme assays or more recently from bacterial genome sequence analysis. We have applied phage R-M test principles to the transformation of plasmid DNA and established a plasmid R-M test. To validate this test, six plasmids that contain BamHI fragments of phage lambda DNA were constructed and transformed into Escherichia coli strains containing known R-M systems including: type I (EcoBI, EcoAI, Eco124I), type II (HindIII) and type III (EcoP1I). Plasmid DNA with a single recognition site showed a reduction of relative efficiency of transformation (EOT = 10(-1)-10(-2)). When multiple recognition sites were present, greater reductions in EOT values were observed. Once established in the cell, the plasmids were subjected to modification (EOT = 1.0). We applied this test to screen E.coli clinical strains and detected the presence of restriction enzymes in 93% (14/15) of cells. Using additional subclones and the computer program, RM Search, we identified four new restriction enzymes, Eco377I, Eco585I, Eco646I and Eco777I, along with their recognition sequences, GGA(8N)ATGC, GCC(6N)TGCG, CCA(7N)CTTC, and GGA(6N)TATC, respectively. Eco1158I, an isoschizomer of EcoBI, was also found in this study.
Collapse
Affiliation(s)
- Julie K A Kasarjian
- Division of Microbiology and Molecular Genetics, Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | | | | |
Collapse
|
184
|
Humphry DR, Black GW, Cummings SP. Reclassification of 'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. Int J Syst Evol Microbiol 2003; 53:393-400. [PMID: 12710603 DOI: 10.1099/ijs.0.02271-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 has been demonstrated by a polyphasic taxonomic approach to be a member of the genus Cellvibrio. 16S rDNA sequence analysis suggests that this is the only genus that could accept this specimen. The sequence is 95.5% similar to that of Cellvibrio mixtus subsp. mixtus ACM 2601T (the type strain of the type species of the genus), which is its closest relation. The genomic DNA G + C content was determined to be 53.3 mol%, which is similar to the values obtained for the validly described Cellvibrio species. DNA-DNA hybridization experiments have shown that strain NCIMB 10462T (= NCDO 2697T) represents a novel species; therefore, it is proposed that it be designated as the type strain of the novel species Cellvibrio japonicus sp. nov. This study also used 16S rDNA analysis, DNA-DNA hybridization experiments and phenotypic testing to revive the species Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. C. vulgaris NCIMB 8633T (=LMG 2848T) and C. fulvus NCIMB 8634T (=LMG 2847T) are the proposed type strains.
Collapse
Affiliation(s)
- David R Humphry
- The School of Health, Natural and Social Sciences, University of Sunderland, Sunderland SR1 3SD, UK
| | - Gary W Black
- School of Applied Sciences, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST, UK
| | - Stephen P Cummings
- The School of Health, Natural and Social Sciences, University of Sunderland, Sunderland SR1 3SD, UK
| |
Collapse
|
185
|
Abstract
The Phusion assembler has assembled the mouse genome from the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at ~7.5x sequence coverage, producing a high-quality draft assembly 2.6 gigabases in size, of which 90% of these bases are in 479 scaffolds. For the mouse genome, which is a large and repeat-rich genome, the input dataset was designed to include a high proportion of paired end sequences of various size selected inserts, from 2-200 kbp lengths, into various host vector templates. Phusion uses sequence data, called reads, and information about reads that share common templates, called read pairs, to drive the assembly of this large genome to highly accurate results. The preassembly stage, which clusters the reads into sensible groups, is a key element of the entire assembler, because it permits a simple approach to parallelization of the assembly stage, as each cluster can be treated independent of the others. In addition to the application of Phusion to the mouse genome, we will also present results from the WGS assembly of Caenorhabditis briggsae sequenced to about 11x coverage. The C. briggsae assembly was accessioned through EMBL, http://www.ebi.ac.uk/services/index.html, using the series CAAC01000001-CAAC01000578, however, the Phusion mouse assembly described here was not accessioned. The mouse data was generated by the Mouse Genome Sequencing Consortium. The C. briggsae sequence was generated at The Wellcome Trust Sanger Institute and the Genome Sequencing Center, Washington University School of Medicine.
Collapse
Affiliation(s)
- James C Mullikin
- Informatics Department, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | | |
Collapse
|
186
|
Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 2003; 13:91-6. [PMID: 12529310 PMCID: PMC430950 DOI: 10.1101/gr.828403] [Citation(s) in RCA: 244] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Accepted: 10/30/2002] [Indexed: 10/27/2022]
Abstract
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).
Collapse
Affiliation(s)
- David B Jaffe
- Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA.
| | | | | | | | | | | | | | | |
Collapse
|
187
|
Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol 2002; 184:6403-5; discusion 6405. [PMID: 12426324 PMCID: PMC135419 DOI: 10.1128/jb.184.23.6403-6405.2002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Claire M Fraser
- The Institute for Genomic Research, Rockville, Maryland 20850, USA.
| | | | | | | | | |
Collapse
|
188
|
Pardanani A, Wieben ED, Spelsberg TC, Tefferi A. Primer on medical genomics. Part IV: Expression proteomics. Mayo Clin Proc 2002; 77:1185-96. [PMID: 12440555 DOI: 10.4065/77.11.1185] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteomics, simply defined, is the study of proteomes. More completely, proteomics is defined as the study of all proteins, including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Proteins carry out the biological functions encoded by genes; hence, once the initial stage of genome sequencing and gene discovery is completed, a study of the proteome must be undertaken to address fundamental biological questions. The 3 broad areas are expression proteomics, which catalogues the relative abundance of proteins; cell-mapping or cellular proteomics, which delineates functional protein-protein interactions and organelle-specific protein distribution; and structural proteomics, which characterizes the 3-dimensional structure of proteins. With these approaches, proteins are studied on a global scale using a synergistic combination of powerful, high-throughput technologies, including 2-dimensional polyacrylamide gel electrophoresis, mass spectrometry, multidimensional liquid chromatography, and bioinformatics. Mass spectrometry, which provides highly accurate molecular mass measurements, has emerged as the analytical technology of choice for protein identification, characterization, and sequencing. This task has been made considerably easier with the availability of complete, nonredundant, and annotated genome sequence databases for many organisms. This article reviews the area of expression proteomics.
Collapse
Affiliation(s)
- Animesh Pardanani
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minn 55905, USA
| | | | | | | |
Collapse
|
189
|
Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 2002; 184:4891-905. [PMID: 12169615 PMCID: PMC135278 DOI: 10.1128/jb.184.17.4891-4905.2002] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2002] [Accepted: 04/23/2002] [Indexed: 11/20/2022] Open
Abstract
The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.
Collapse
Affiliation(s)
- Jeffrey G Lawrence
- Department of Biological Sciences, Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | | | | |
Collapse
|
190
|
Klein R, Baranyi U, Rössler N, Greineder B, Scholz H, Witte A. Natrialba magadii virus phiCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol Microbiol 2002; 45:851-63. [PMID: 12139629 DOI: 10.1046/j.1365-2958.2002.03064.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The double-stranded (ds)DNA virus phiCh1 infects the haloalkaliphilic archaeon Natrialba magadii. The complete DNA sequence of 58 498 bp of the temperate virus was established, and the probable functions of 21 of 98 phiCh1-encoded open reading frames (ORFs) have been assigned. This knowledge has been used to propose functional modules each required for specific functions during virus development. The phiCh1 DNA is terminally redundant and circularly permuted and therefore appears to be packaged by the so-called headful mechanism. The presence of ORFs encoding homologues of proteins involved in plasmid replication as well as experimental evidence indicate a plasmid-mediated replication strategy of the virus. Results from nanosequencing of virion components suggest covalent cross-linking of monomers of at least one of the structural proteins during virus maturation. A comparison of the phiCh1 genome with the partly sequenced genome of Halobacterium salinarum virus phiH revealed a close relationship between the two viruses, although their host organisms live in distinct environments with respect to the different pH values required for growth.
Collapse
Affiliation(s)
- R Klein
- Institute of Microbiology and Genetics, University of Vienna, Austria
| | | | | | | | | | | |
Collapse
|
191
|
Abstract
The purpose of this study was to determine the presence of stx genes in avian pathogenic Escherichia coli (APEC). We examined 97 APEC isolates: 34 from lesions of avian cellulitis, 31 from avian septicemia, 13 from swollen head syndrome (SHS) in chickens, and 19 from diseased turkeys. We also examined five isolates from the feces of healthy chickens. All 102 E. coli isolates were tested for the presence of stx genes by PCR amplification and by colony blots using probes specific for stx1 and stx2. Fifty-three percent (52) of the 97 APEC carried stx gene sequences: one isolate carried stx2 sequences, two carried both stx1 and stx2 sequences, and the remaining 49 isolates carried only stx1 sequences. Twenty-six isolates were positive by both hybridization and PCR amplification, 10 were positive by PCR only, and 16 were positive by hybridization only. All the stx-positive isolates were negative by PCR for the eae and E-hlyA genes. The five isolates from healthy chickens were all negative for stx. All 13 SHS isolates were positive for the stx1 gene and had low titres for cytotoxicity in the Vero cell assay (VCA). Other stx-positive isolates were negative in the VCA. The stx1 gene from one SHS E. coli isolate was cloned and sequenced and shown to be identical to that of the stx gene of Shigella dysenteriae. The observations indicate that stx1 gene sequences are widespread among APEC but that cytotoxicity on Vero cells is uncommon.
Collapse
Affiliation(s)
- V R Parreira
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ont., Canada
| | | |
Collapse
|
192
|
Swan KA, Curtis DE, McKusick KB, Voinov AV, Mapa FA, Cancilla MR. High-throughput gene mapping in Caenorhabditis elegans. Genome Res 2002; 12:1100-5. [PMID: 12097347 PMCID: PMC186621 DOI: 10.1101/gr.208902] [Citation(s) in RCA: 425] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Positional cloning of mutations in model genetic systems is a powerful method for the identification of targets of medical and agricultural importance. To facilitate the high-throughput mapping of mutations in Caenorhabditis elegans, we have identified a further 9602 putative new single nucleotide polymorphisms (SNPs) between two C. elegans strains, Bristol N2 and the Hawaiian mapping strain CB4856, by sequencing inserts from a CB4856 genomic DNA library and using an informatics pipeline to compare sequences with the canonical N2 genomic sequence. When combined with data from other laboratories, our marker set of 17,189 SNPs provides even coverage of the complete worm genome. To date, we have confirmed >1099 evenly spaced SNPs (one every 91 +/- 56 kb) across the six chromosomes and validated the utility of our SNP marker set and new fluorescence polarization-based genotyping methods for systematic and high-throughput identification of genes in C. elegans by cloning several proprietary genes. We illustrate our approach by recombination mapping and confirmation of the mutation in the cloned gene, dpy-18.
Collapse
Affiliation(s)
- Kathryn A Swan
- Exelixis, Inc., South San Francisco, California 94083-0511, USA
| | | | | | | | | | | |
Collapse
|
193
|
Brizuela L, Richardson A, Marsischky G, Labaer J. The FLEXGene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era. Arch Med Res 2002; 33:318-24. [PMID: 12234520 DOI: 10.1016/s0188-4409(02)00372-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thanks to the results of the multiple completed and ongoing genome sequencing projects and to the newly available recombination-based cloning techniques, it is now possible to build gene repositories with no precedent in their composition, formatting, and potential. This new type of gene repository is necessary to address the challenges imposed by the post-genomic era, i.e., experimentation on a genome-wide scale. We are building the FLEXGene (Full Length EXpression-ready) repository. This unique resource will contain clones representing the complete ORFeome of different organisms, including Homo sapiens as well as several pathogens and model organisms. It will consist of a comprehensive, characterized (sequence-verified), and arrayed gene repository. This resource will allow full exploitation of the genomic information by enabling genome-wide scale experimentation at the level of functional/phenotypic assays as well as at the level of protein expression, purification, and analysis. Here we describe the rationale and construction of this resource and focus on the data obtained from the Saccharomyces cerevisiae project.
Collapse
Affiliation(s)
- Leonardo Brizuela
- Department of Biological Chemistry and Molecular Pharmacology, Institute of Proteomics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
194
|
Wieczorek DJ, Didion L, Feiss M. Alterations of the portal protein, gpB, of bacteriophage lambda suppress mutations in cosQ, the site required for termination of DNA packaging. Genetics 2002; 161:21-31. [PMID: 12019220 PMCID: PMC1462103 DOI: 10.1093/genetics/161.1.21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The cosQ site of bacteriophage lambda is required for DNA packaging termination. Previous studies have shown that cosQ mutations can be suppressed in three ways: by a local suppressor within cosQ, an increase in the length of the lambda chromosome, and missense mutations affecting the prohead's portal protein, gpB. In the present work, revertants of a set of lethal cosQ mutants were screened for suppressors. Seven new cosQ suppressors affected gene B, which encodes the portal protein of the prohead. All seven were allele-nonspecific suppressors of cosQ mutations. Experiments with several phages having two cosQ suppressors showed that the suppression effects were additive. Furthermore, these double suppressors had minimal effects on the growth of cosQ(+) phages. These trans-acting suppressors affecting the portal protein are proposed to allow the mutant cosQ site to be more efficiently recognized, due to the slowing of the rate of translocation.
Collapse
Affiliation(s)
- Douglas J Wieczorek
- Genetics Ph.D. Program and Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA.
| | | | | |
Collapse
|
195
|
Tarkowski TA, Mooney D, Thomason LC, Stahl FW. Gene products encoded in the ninR region of phage lambda participate in Red-mediated recombination. Genes Cells 2002; 7:351-63. [PMID: 11952832 DOI: 10.1046/j.1365-2443.2002.00531.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that were previously shown to have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda. RESULTS When lambda DNA replication is blocked, recombination is focused at the termini of the virion chromosome. Deletion of the ninR region of lambda decreases the sharpness of the focusing without diminishing the overall rate of recombination. The phenotype is accounted for in large part by the deletion of rap and of orf. Mutation of the recJ gene of the host partially suppresses the Rap- phenotype. CONCLUSION ninR functions Orf and Rap participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells. The ability of recJ mutation to suppress the Rap- phenotype indicates that RecJ exonuclease can participate in Red-mediated recombination, at least in the absence of Rap function. A model is presented for Red-mediated RecA-dependent recombination that includes these newly identified participants.
Collapse
Affiliation(s)
- Trudee A Tarkowski
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
| | | | | | | |
Collapse
|
196
|
Morgan GJ, Hatfull GF, Casjens S, Hendrix RW. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J Mol Biol 2002; 317:337-59. [PMID: 11922669 DOI: 10.1006/jmbi.2002.5437] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the complete 36,717 bp genome sequence of bacteriophage Mu and provide an analysis of the sequence, both with regard to the new genes and other genetic features revealed by the sequence itself and by a comparison to eight complete or nearly complete Mu-like prophage genomes found in the genomes of a diverse group of bacteria. The comparative studies confirm that members of the Mu-related family of phage genomes are genetically mosaic with respect to each other, as seen in other groups of phages such as the phage lambda-related group of phages of enteric hosts and the phage L5-related group of mycobacteriophages. Mu also possesses segments of similarity, typically gene-sized, to genomes of otherwise non-Mu-like phages. The comparisons show that some well-known features of the Mu genome, including the invertible segment encoding tail fiber sequences, are not present in most members of the Mu genome sequence family examined here, suggesting that their presence may be relatively volatile over evolutionary time. The head and tail-encoding structural genes of Mu have only very weak similarity to the corresponding genes of other well-studied phage types. However, these weak similarities, and in some cases biochemical data, can be used to establish tentative functional assignments for 12 of the head and tail genes. These assignments are strongly supported by the fact that the order of gene functions assigned in this way conforms to the strongly conserved order of head and tail genes established in a wide variety of other phages. We show that the Mu head assembly scaffolding protein is encoded by a gene nested in-frame within the C-terminal half of another gene that encodes the putative head maturation protease. This is reminiscent of the arrangement established for phage lambda.
Collapse
Affiliation(s)
- Gregory J Morgan
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | | | | |
Collapse
|
197
|
Waterston RH, Lander ES, Sulston JE. On the sequencing of the human genome. Proc Natl Acad Sci U S A 2002; 99:3712-6. [PMID: 11880605 PMCID: PMC122589 DOI: 10.1073/pnas.042692499] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2001] [Accepted: 12/21/2001] [Indexed: 01/13/2023] Open
Abstract
Two recent papers using different approaches reported draft sequences of the human genome. The international Human Genome Project (HGP) used the hierarchical shotgun approach, whereas Celera Genomics adopted the whole-genome shotgun (WGS) approach. Here, we analyze whether the latter paper provides a meaningful test of the WGS approach on a mammalian genome. In the Celera paper, the authors did not analyze their own WGS data. Instead, they decomposed the HGP's assembled sequence into a "perfect tiling path", combined it with their WGS data, and assembled the merged data set. To study the implications of this approach, we perform computational analysis and find that a perfect tiling path with 2-fold coverage is sufficient to recover virtually the entirety of a genome assembly. We also examine the manner in which the assembly was anchored to the human genome and conclude that the process primarily depended on the HGP's sequence-tagged site maps, BAC maps, and clone-based sequences. Our analysis indicates that the Celera paper provides neither a meaningful test of the WGS approach nor an independent sequence of the human genome. Our analysis does not imply that a WGS approach could not be successfully applied to assemble a draft sequence of a large mammalian genome, but merely that the Celera paper does not provide such evidence.
Collapse
Affiliation(s)
- Robert H Waterston
- Genome Sequencing Center, Washington University, Saint Louis, MO 63108, USA.
| | | | | |
Collapse
|
198
|
Duffy C, Feiss M. The large subunit of bacteriophage lambda's terminase plays a role in DNA translocation and packaging termination. J Mol Biol 2002; 316:547-61. [PMID: 11866517 DOI: 10.1006/jmbi.2001.5368] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. The role of terminase in the initial stages of packaging involving the site-specific binding and cutting of the DNA has been well characterized. While it is believed that terminase plays an active role in later post-cleavage stages of packaging, such as the translocation of DNA into the head shell, this has not been demonstrated. Accordingly, we undertook a generalized mutagenesis of lambda's A gene and found ten lethal mutations, nine of which cause post-cleavage packaging defects. All were located in the amino-terminal two-thirds of gpA, separate from the carboxy-terminal region where mutations affecting the protein's endonuclease activity have been found. The mutants fall into five groups according to their packaging phenotypes: (1) two mutants package part of the lambda chromosome, (2) one mutant packages the entire chromosome, but very slowly compared to wild-type, (3) two mutants do not package any DNA, (4) four mutants, though inviable, package the entire lambda chromosome, and (5) one mutant may be defective in both early and late stages of DNA packaging. These results indicate that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
Collapse
Affiliation(s)
- Carol Duffy
- Department of Microbiology College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | | |
Collapse
|
199
|
|
200
|
Asp718 from a non-pathogenic species of the genusAchromobacter: aKpnI isoschizomer generating DNA-fragments with 5'-protruding ends. FEBS Lett 2001. [DOI: 10.1016/0014-5793(85)81169-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|