Genes and Regulatory Sites of the ``Host-Takeover Module'' in the Terminal Redundancy of Bacillus subtilis Bacteriophage SPO1
Charles R. Stewart,Irphan Gaslightwala,Kaede Hinata,Katherine A. Krolikowski,David S. Needleman,Angela Shu-Yuen Peng,Mark A. Peterman,Angela Tobias,Ping Wei +8 more
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TLDR
The nucleotide sequence of this 11.5-kb "host-takeover module" appears to be designed for particularly efficient expression, and has additional conserved features which are not characteristic of their host counterparts and which may be important for competition with host genes for the cellular biosynthetic machinery.About:
This article is published in Virology.The article was published on 1998-07-05 and is currently open access. It has received 45 citations till now. The article focuses on the topics: Codon usage bias & Operon.read more
Citations
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Journal ArticleDOI
The Terminally Redundant, Nonpermuted Genome of Listeria Bacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria
Jochen Klumpp,Julia Dorscht,Rudi Lurz,Regula Bielmann,Matthias Wieland,Matthias Wieland,Markus Zimmer,Richard Calendar,Martin J. Loessner +8 more
TL;DR: It is proposed that SPO1-like myoviruses are characterized by their infection of gram-positive, low-G+C-content bacteria; a wide host range within the host bacterial genus and a strictly virulent lifestyle; similar morphology, sequence relatedness, and collinearity of the phage genome organization.
Journal ArticleDOI
Pairwise sequence alignment below the twilight zone
Jonathan D. Blake,Fred E. Cohen +1 more
TL;DR: Improved pairwise alignment is demonstrated by using superpositions of homologous domains extracted from a structural database as a gold standard and a new cyclic permutation strategy to identify distant homologues that experienced gene duplication and subsequent deletions is described.
Journal ArticleDOI
Identification and Characterization of Novel Surface Proteins in Lactobacillus johnsonii and Lactobacillus gasseri
TL;DR: The results suggest that APF is a novel surface protein of the Lactobacillus acidophilus B-homology group which might belong to an S-layer-like family.
Journal ArticleDOI
The Genome of Bacillus Subtilis Bacteriophage SPO1.
Charles R. Stewart,Sherwood R. Casjens,Steven G. Cresawn,Jennifer M. Houtz,Alexis L. Smith,Michael E. Ford,Craig L. Peebles,Graham F. Hatfull,Roger W. Hendrix,Wai Mun Huang,Marisa L. Pedulla +10 more
TL;DR: A pattern similar to what has been noted in phage T4 and its relatives is noted, in which there is minimal successful horizontal exchange of genes among a "core" set of genes that includes most of the virion structural genes and some genes of DNA metabolism, but there is extensive horizontal transfer of genes over the remainder of the genome.
Book ChapterDOI
Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era.
Małgorzata Łobocka,Monika S. Hejnowicz,Kamil Dąbrowski,Kamil Dąbrowski,Agnieszka Gozdek,Jarosław Kosakowski,Magdalena Witkowska,Magdalena Ulatowska,Beata Weber-Dąbrowska,Magdalena Kwiatek,Sylwia Parasion,Jan Gawor,Helena Kosowska,Aleksandra Głowacka,Aleksandra Głowacka +14 more
TL;DR: Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications and can be predicted based on their homology to prototypical genes of model spounavirus SPO1.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature.
J. Marmur,Paul Doty +1 more
TL;DR: The previously discovered linear relation between the base composition of DNA, expressed in percentage of guanine plus cytosine bases, and the denaturation temperature, T m, has been further investigated and it appears that the measurement of the T m is a satisfactory means of determining base composition in DNA.
Journal ArticleDOI
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Paul M. Sharp,Wen-Hsiung Li +1 more
TL;DR: A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed, useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons ofCodon usage in different organisms.
Journal ArticleDOI
Improved Estimation of Secondary Structure in Ribonucleic Acids
Ignacio Tinoco,Philip N. Borer,Barbara Dengler,Mark D. Levin,Olke C. Uhlenbeck,Donald M. Crothers,J. Bralla +6 more
TL;DR: This method can be used for predicting and assessing possible secondary structures for recently determined RNA sequences and new experimental and theoretical results allow us to improve the method, without making it more complicated.
Journal ArticleDOI
Origin of concatemeric T7 DNA.
TL;DR: The observed concatemers of T7 DNA are consistent with replication schemes resulting in double-helical molecules with 3´ ended tails as discussed by the authors, and they can then join to form dimers which on further replication similarly form larger concatures.
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