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Genome
About: Genome is a research topic. Over the lifetime, 74231 publications have been published within this topic receiving 3819713 citations.
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TL;DR: A comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis, suggests that gene “inventions” along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
Abstract: Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
1,485 citations
TL;DR: The complete genome sequence of uropathogenic Escherichia coli, strain CFT073 is presented and Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages.
Abstract: We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.
1,483 citations
TL;DR: The extent of size reduction within metazoan mitochondrial-transfer RNA (mt-tRNA) gene sets strongly correlates with the degree to which the more variable secondary structure element-forming regions of mt-rRNA genes are lost.
Abstract: Publisher Summary This chapter describes structural features and evolution of metazoan mitochondrial DNA (mtDNA) molecules. Throughout the evolution of metazoa, gene content of mitochondria-genomes is highly conserved, as has the close packing of genes. Most of the occasional sequence expansions that have occurred, by way of either repeated or noncoding unique sequences, are found in the control or putative control region, rather than being dispersed between genes. Of the 13 open reading frames recognized in the human mtDNA molecules, four (COI, COII, COIII, and Cyt b) are originally identified in regard to the proteins they encode, from similarities of their predicted amino acid sequences to known amino acid sequences of bovine proteins, and predicted amino acid sequences of yeast mt-protein genes. Among mtDNAs of vertebrates and higher invertebrates, there are genes that overlap. Some overlaps are among the 3′ ends of two genes that are encoded in opposite strands of the molecule. The extent of size reduction within metazoan mitochondrial-transfer RNA (mt-tRNA) gene sets strongly correlates with the degree to which the more variable secondary structure element-forming regions of mt-rRNA genes are lost.
1,478 citations
TL;DR: It is found that the HPV 18 DNA is integrated into the cellular genome and is amplified in HeLa and 756 cells, and some of the transcripts are composed of HPV 18 and cellular sequences.
Abstract: DNA of human papillomavirus (HPV) types 16 and 18 has been found closely associated with human genital cancer, supporting the concept that members of this virus group are key factors in the aetiology of genital cancer. HPV 18 DNA sequences were also detected in cell lines derived from cervical cancer. We have now analysed these cell lines, HeLa, C4-1 and 756, for the structural organization and transcription of the HPV 18 genome and we find that the HPV 18 DNA is integrated into the cellular genome and is amplified in HeLa and 756 cells. Almost the complete HPV 18 genome seems to be present in 756 cells, with the early region being disrupted into two portions in each integrated copy. In HeLa and C4-1 cells, a 2-3 kilobase (kb) segment of HPV 18-specific sequences is missing from the E2 to L2 region. HPV 18 sequences are specifically transcribed from the E6-E7-E1 region into poly(A)+ RNAs of 1.5-6.5 kb. Hybridization analysis of cDNA clones indicated that some of the transcripts are composed of HPV 18 and cellular sequences. In addition, poly(A)+ RNA hybridizing with HPV 16 DNA was found in two out of three cervical carcinoma biopsies.
1,458 citations
TL;DR: This study establishes that mass spectrometry provides the required throughput, the certainty of identification, and the general applicability to serve as the method of choice to connect genome and proteome.
Abstract: The function of many of the uncharacterized openreadingframesdiscoveredbygenomicsequencingcanbe determined at the level of expressed gene products, the proteome.However,identifyingthecognategenefromminute amounts of protein has been one of the major problems in molecularbiology.Usingyeastasanexample,wedemonstrate here that mass spectrometric protein identification is a generalsolutiontothisproblemgivenacompletelysequenced genome. As a first screen, our strategy uses automated laser desorption ionization mass spectrometry of the peptide mix- tures produced by in-gel tryptic digestion of a protein. Up to 90% of proteins are identified by searching sequence data bases by lists of peptide masses obtained with high accuracy. The remaining proteins are identified by partially sequencing several peptides of the unseparated mixture by nanoelectro- spray tandem mass spectrometry followed by data base searchingwithmultiplepeptidesequencetags.Inblindtrials, themethodledtounambiguousidentificationinallcases.In the largest individual protein identification project to date, a total of 150 gel spots—many of them at subpicomole amounts—were successfully analyzed, greatly enlarging a yeast two-dimensional gel data base. More than 32 proteins were novel and matched to previously uncharacterized open reading frames in the yeast genome. This study establishes that mass spectrometry provides the required throughput, the certainty of identification, and the general applicability to serve as the method of choice to connect genome and proteome.
1,456 citations