Abstract:
:Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional characterization. Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned the genomes of Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) and M. mycoides subspecies capri (1.1 Mb) as yeast circular centromeric plasmids. These genomes appear to be stably maintained in a host that has efficient, well-established methods for DNA manipulation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Benders GA,Noskov VN,Denisova EA,Lartigue C,Gibson DG,Assad-Garcia N,Chuang RY,Carrera W,Moodie M,Algire MA,Phan Q,Alperovich N,Vashee S,Merryman C,Venter JC,Smith HO,Glass JI,Hutchison CA 3rddoi
10.1093/nar/gkq119subject
Has Abstractpub_date
2010-05-01 00:00:00pages
2558-69issue
8eissn
0305-1048issn
1362-4962pii
gkq119journal_volume
38pub_type
杂志文章abstract::Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky033
更新日期:2018-03-16 00:00:00
abstract::The nucleotide sequences of the LTRs and their adjacent regions from 19 type C and one type B retrovirus were compared. Salient features are: (a) The R regions in the genomes of most of the type C retroviruses begin with GC and end with CA. (b) The mammalian type C retroviruses have a polyadenylation signal "AATAAA" i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.4.1767
更新日期:1984-02-24 00:00:00
abstract::The spliceosomal protein Prp1 (Prp6/U5-102 K) is necessary for the integrity of pre-catalytic spliceosomal complexes. We have identified a novel regulatory function for Prp1. Expression of mutations in the N-terminus of Prp1 leads to the accumulation of pre-catalytic spliceosomal complexes containing the five snRNAs U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1155
更新日期:2010-03-01 00:00:00
abstract::The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins contains a divergent N-terminus,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt166
更新日期:2013-05-01 00:00:00
abstract::Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1230
更新日期:2010-05-01 00:00:00
abstract::We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku556
更新日期:2014-09-01 00:00:00
abstract::PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set com...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.61
更新日期:2001-01-01 00:00:00
abstract::Members of the pentatricopeptide repeat domain (PPR) protein family bind RNA and are important for post-transcriptional control of organelle gene expression in unicellular eukaryotes, metazoans and plants. They also have a role in human pathology, as mutations in the leucine-rich PPR-containing (LRPPRC) gene cause sev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1132
更新日期:2014-12-16 00:00:00
abstract::The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks994
更新日期:2013-01-01 00:00:00
abstract::Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf508
更新日期:2002-09-01 00:00:00
abstract::A segment of 1160 nucleotides of the FMDV genome has been sequenced using three overlapping fragments of cloned cDNA from FMDV strain O1K. This sequence contains the coding sequence for the viral capsid protein VP1 as shown by its homology to known and newly determined amino acid sequences from this man antigenic poly...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.8.1919
更新日期:1981-04-24 00:00:00
abstract::The CRT10 gene was identified through screening of the Saccharomyces cerevisiae deletion library for hydroxyurea (HU) resistance. CRT10 encodes a putative 957 amino acid, 110 kDa protein with a leucine repeat and a WD40 repeat near the N-terminus. Deletion of CRT10 resulted in an enhanced resistance to HU reminiscent ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl100
更新日期:2006-04-05 00:00:00
abstract::Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl539
更新日期:2006-01-01 00:00:00
abstract::We have isolated and sequenced a cDNA clone coding for human Retinol Binding Protein. The sequence indicates that Retinol Binding Protein is synthesized as a single polypeptide chain precursor which is then matured to the secreted protein by removal of a leader peptide. Southern and Northern blot analysis suggest that...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.22.7769
更新日期:1983-11-25 00:00:00
abstract::The 2'-5' oligoadenylate synthetases form a well conserved family of interferon induced proteins, presumably present throughout the mammalian class. Using the Expressed Sequence Tag databases, we have identified a novel member of this family. This protein, which we named p59 2'-5' oligoadenylate synthetase-like protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.18.4121
更新日期:1998-09-15 00:00:00
abstract::Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily fo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.19.3899
更新日期:1999-10-01 00:00:00
abstract::The putative role of double-strand breaks (DSBs) created in vitro by restriction enzyme cleavage in or near CGG*CCG or CTG*CAG repeat tracts on their genetic instabilities, both within the repeats and in their flanking sequences, was investigated in an Escherichia coli plasmid system. DSBs at TRS junctions with the ve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl612
更新日期:2006-01-01 00:00:00
abstract::Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl578
更新日期:2006-01-01 00:00:00
abstract::Segments of SV40 DNA having homologous overlapping termini recombine to produce viable genomes in monkey cells. Frequencies of recombination on either side of a deletion marker are non-random; replication and palindromes do not appear to be essential. Since recombination involves host enzymes, a suitable system has be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.12.2725
更新日期:1980-06-25 00:00:00
abstract::Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, repr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa106
更新日期:2020-05-07 00:00:00
abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2723
更新日期:1998-06-01 00:00:00
abstract::T1DBase (http://www.t1dbase.org) is web platform, which supports the type 1 diabetes (T1D) community. It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. This update describes the incorporation of new dat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq912
更新日期:2011-01-01 00:00:00
abstract::The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw157
更新日期:2016-06-02 00:00:00
abstract::Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt915
更新日期:2014-01-01 00:00:00
abstract::Stringent starvation protein A (SspA) is an RNA polymerase (RNAP)-associated protein involved in nucleotide metabolism, acid tolerance and virulence of bacteria. Despite extensive biochemical and genetic analyses, the precise regulatory role of SspA in transcription is still unknown, in part, because of a lack of stru...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa672
更新日期:2020-09-25 00:00:00
abstract::We report the synthesis of new phosphoramidite building blocks and their use for the modification of oligonucleotides with hydrazides. The reaction of these hydrazide oligonucleotides with active esters and aldehydes is demonstrated for solution conjugation and immobilization. Compared with the established amino modif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf594
更新日期:2002-11-01 00:00:00
abstract::Lytic infection with polyoma virus leads in Go-arrested primary mouse kidney cell cultures to a mitotic host response. In the present work we focused our attention on cellular RNA synthesis shortly after onset of polyoma T-antigen synthesis. Onset of polyoma-induced stimulation of 45S pre-rRNA synthesis was determined...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.19.6611
更新日期:1983-10-11 00:00:00
abstract::Pairing of a given E3 ubiquitin ligase with different E2s allows synthesis of ubiquitin conjugates of different topologies. While this phenomenon contributes to functional diversity, it remains largely unknown how a single E3 ubiquitin ligase recognizes multiple E2s, and whether identical structural requirements deter...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr655
更新日期:2012-01-01 00:00:00
abstract::Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx376
更新日期:2017-07-03 00:00:00
abstract::We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.9.2193
更新日期:1976-09-01 00:00:00