Download the free biocyc iphone app to browse biocyc on the go. Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical syndromes, most commonly skin infections in immunocompromised individuals. This repeat does not occur in the genomes of mycobacterium tuberculosis or mycobacterium smegmatis mc 2 155. Insights from the genome sequence of mycobacterium. Ensembl bacteria is a genomecentric portal for bacterial species of scientific interest. Complete genome sequence of mycobacterium tuberculosis k. Pdf complete genome sequence of cluster o mycobacterium. Mmpl3 alter membrane potential, hydrophobicity and antibiotic susceptibility in. Complete genome sequence of cluster o mycobacterium. Mycobacterium smegmatis society for applied microbiology. Determination of the dna genome sequence of this strain has been or is being determined either in whole or in part.
Rapid antibioticresistance predictions from genome. Dec 21, 2015 rapid antibioticresistance predictions from genome sequence data for. The complete genome sequence of mycobacterium aviumsubspecies. Determination of the recognition sequence of mycobacterium. Examples of peaks obtained for genes known to be glnrregulated. Draft genome sequences of 12 mycolicibacterium smegmatis. The cell envelope structure and properties of mycobacterium. The database centralizes information about sequences, gene function, bibliography, protein. It was plaque purified on mycobacterium smegmatis and dna was isolated using the promega wizard dna purification kit. Binding sites were visualised by aligning the 160 million sequence reads to the m. In general, mutants survived stationary phase significantly less well in rich medium than under carbonstarvation conditions. Comparison of the recently sequenced genome of the leprosycausing pathogen mycobacterium leprae with other mycobacterial genomes reveals a drastic gene reduction and decay in m. Here we report the transcriptome, expression profiles and transcriptional structures through growthphasedependent rna sequencing rnaseq as well as other related experiments.
Complete genome sequences of mycobacterium smegmatis. Mycobacterium stephanolepidis is a rapidgrowing nonpigmented species isolated from marine teleost fish stephanolepis cirrhifer and is closely related to mycobacterium chelonae here, we report the complete sequence of its genome, comprising a 4. Cell wall proteome analysis of mycobacterium smegmatis strain. Lilhazelnut is a temperate siphoviridae virus, as is typical of cluster q family members. The effect of mycobacterium tuberculosis crisprassociated. The complete genome sequence of mycobacterium tuberculosis mtb was described in 1998. Lecompte wanted to submit the sequence as a third part annotation, but genbank considered it was a new sequence since some bases are different from the initial tigr sequence. We conducted wholegenome sequencing of the mutant strains and of wildtype m. Dec 18, 2017 the nonpathogenic bacterium mycobacterium smegmatis mc2155 has been widely used as a model organism in mycobacterial research, yet a detailed study about its transcription landscape remains to be established. Genome wide analysis of the complete glnr nitrogenresponse. Of 74 mutants picked by the initial screen, 21 had stationaryphase survival defects and 7 of these were studied in more detail.
Gilles etienne 1, francoise laval 1, christelle villeneuve 1, premkumar dinadayala 1, ahmed abouwarda 1, didier zerbib 1, alexandra galamba 2, mamadou daffe 1. Proteincoding and noncoding genes, splice variants, cdna and protein sequences, noncoding rnas. Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 18981899. A mutant strain of mycobacterium smegmatis mc2155 provided the first plasmid. Starting in 2017, england is the first country in the world to pioneer its use on a national scale for the diagnosis of tuberculosis, detection. The putative role of type vii secretion systems for an intracellular lifestyle within freeliving environmental predators. Complete genome sequences of a mycobacterium smegmatis. Genome sequence of mycobacterium phage lilhazelnut.
We report the whole genome sequences of a mycobacterium smegmatis laboratory wildtype strain mc 2 155 and mutants 4xr1, 4xr2 resistant to isoniazid. Citeseerx document details isaac councill, lee giles, pradeep teregowda. Glnr binding sites identified by chipseq during nitrogen limitation. Escherichia coli and mycobacterium smegmatis mc 2 155 were provided by the institute of modern biopharmaceuticals. Mycolicibacterium smegmatis strain atcc 700084 mc2155. In contrast to the enzyme from vaccinia virus, mycobacterial topoisomerase i is a large, single subunit topoisomerase of 110 kda and belongs to the type ia topoisomerases 19. Noncanonical smc protein in mycobacterium smegmatis. The phages were isolated and annotated by undergraduate students enrolled in the phage discovery course offered by the school of life sciences at the university of nevada las vegas. Reference genome and comparative genome analysis for the who.
Mmpl3 alter membrane potential, hydrophobicity and antibiotic susceptibility in mycobacterium smegmatis. Genome wide analysis of the complete glnr nitrogen. Interrupted coding sequences in the question of whether bacterial interrupted coding sequences genome sequence is raised after bioinformatic, proteomic and sequdeposited genome sequence of mycobacterium smegmycobacterium smegmatismatis are a result of sequencing errors. Mycobacterium tuberculosis h37rv, laboratory strain. Sequence coverage was calculated as the summed base pairs of the mapped sequence divided by 6,660,144 bp for the m. It is ubiquitous in water and soil habitats, including hospital environments. Nats from many sources acetylate the antitubercular drug isoniazid and so inactivate it. Here we report the transcriptome, expression profiles and transcriptional structures through growthphasedependent rna sequencing rnaseq as well as other related. Here, we describe lilhazelnut, a novel mycobacteriophage that infects mycobacterium smegmatis mc2155. Biochemical analysis of the cell envelope components revealed a lack of polar glycolipids, namely the lipooligosaccharides and the polar subfamilies of glycopeptidolipids, in. Identifying sigma factors in mycobacterium smegmatis by. Apr 22, 2020 when the technology to sequence a complete genome had been realized, among the organisms at the top of the wish list were homo sapiens and mycobacterium smegmatis. The k10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted orfs, 45 trnas, and one rrna operon.
The rcsb pdb also provides a variety of tools and resources. Unlike other strains of this species, mc2 can be 10 to 100 thousand times more efficiently transformed with plasmid vectors using electroporation than the parental strain and thus is invaluable in analysis of mycobacterial gene function, expression and replication. The nonpathogenic bacterium mycobacterium smegmatis mc2155 has been widely used as a model organism in mycobacterial research, yet a detailed study about its transcription landscape remains to be established. Non mycobacterial virulence genes in the genome of the. It has a 67% guanine cytosine content and a 33% adenosine thymine content, and is therefore classified as a high gc content grampositive bacteria discussed below. We report the whole genome sequences of a mycobacterium smegmatis laboratory wildtype strain mc2 155 and mutants 4xr1, 4xr2 resistant to isoniazid. Aug 30, 2005 we describe here the complete genome sequence of a common clone of mycobacterium avium subspecies paratuberculosis map strain k10, the causative agent of johnes disease in cattle and other ruminants. First, we searched for twocomponent genetic systems, which are expected to play a regulatory role in m. Determination of the recognition sequence of mycobacterium smegmatis topoisomerase i on. Complete genome sequences of a mycobacterium smegmatis laboratory strain mc2 155 and isoniazidresistant 4xr1r2 mutant strains. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.
Mutants of mycobacterium smegmatis impaired in stationary. Wholegenome sequencing wgs studies of mycobacterium tuberculosis, the causative agent of tb, have greatly increased our understanding of this pathogen. Genome sequences of two f1 subcluster bacteriophages. Transcriptome landscape of mycobacterium smegmatis frontiers. Mycobacterium tuberculosis and wholegenome sequencing. The upper track indicates chipseq data for glnr immunoprecipitated dna in nitrogen excess conditions, middle track shows the chipseq data. Dec 01, 2019 mycobacterium smegmatis is a fastgrowing, usually nonpathogenic mycobacterium widely used as a model system. Browse the list download sequence and annotation from refseq or genbank try ncbi datasets a new way to download genome sequence and annotation were testing in ncbi labs. A bank of 600 insertional mutants of mycobacterium smegmatis was screened for mutants defective in stationaryphase survival. The thp1 human macrophage cell line was purchased from shanghai institutes for cell resource center, chinese academy of sciences. Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria ntm. Complete genome sequence of mycobacterium tuberculosis k from a korean high school outbreak.
Complete genome sequence of mycobacterium tuberculosis k from. Mycobacterium smegmatis is a fastgrowing, usually nonpathogenic mycobacterium widely used as a model system. Mycobacterium tuberculosis on your iphone and ipad have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster. Rapid antibioticresistance predictions from genome sequence data for. Novel insertion and deletion mutants of rpob that render mycobacterium smegmatis rna polymerase resistant to. Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic infections. The genome of mycobacterium smegmatis is 6,988,209 nucleotides long. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Mycobacterium smegmatis is often used as a surrogate host for pathogenic mycobacteria, especially since the isolation of the transformable smooth morphotype strain mc2155 from the isogenic rough wildtype strain atcc 607. Insights from the genome sequence of mycobacterium paragordonae, a potential novel live vaccine for preventing mycobacterial infections. Mycobacterium smegmatis is an acidfast bacterial species in the phylum actinobacteria and the genus mycobacterium. Never theless, using the sequence of the annotated ksha and. Complete genome sequence of cluster o mycobacterium smegmatis. A crisprassisted nonhomologous endjoining strategy for. Complete genome sequence of mycobacterium fortuitum subsp.
Completed in 2006, twothirds of its dna, almost 7 million nucleotides long, was discovered to consist of the base pairs guanine and cytosine. Rapid antibioticresistance predictions from genome sequence. Complete genome sequence and alignment of the different mycobacterium phlei genomes. A the original laboratory and the edited strains were subjected to whole genome sequencing. Download dna sequence fasta display your data in ensembl bacteria. Mycobacterium smegmatis is a saprophytic species that has been used for 15 years as a model to perform heterologous regulation and virulence studies of mycobacterium tuberculosis. Citeseerx poster presentation sequence and annotation. Deciphering the biology of mycobacterium tuberculosis from the complete genome sequence. Since then, wholegenome sequencing wgs has been applied to a wide range of clinical scenarios, with the potential to revolutionize tuberculosis tb diagnosis, outbreak investigation, drug and vaccine development, plus assist in understanding mtb evolution and pathogenicity. Complete genome sequence of mycobacterium stephanolepidis. Apr 15, 2000 the only other topoisomerase i having comparable sequence specificity was recently characterised from mycobacterium smegmatis. The genome of a representative isolate strain go 06 recovered from wound samples from patients.
The complete genome sequence of the emerging pathogen. Burwell21 has a 58,098basepair doublestranded dna genome, with 99 proteincoding genes predicted, whereas nivrat has a 58,009basepair genome, with 102 proteincoding genes predicted. The cell envelope structure and properties of mycobacterium smegmatis mc 2 155. Protein sequence files are available for download in the releases section. Reference genome and comparative genome analysis for the. Determining the complete genome sequence of a single bacteriophage requires a. We present the complete genomes of the mycobacterium smegmatis phages carlyle and nihilnomen, isolated from soil in las vegas, nevada. Mycolicibacterium smegmatis mc2 155 mycobacterium smegmatis mc2 155. Arylamine n acetyltransferases nats are found in many eukaryotic organisms, including humans, and have previously been identified in the prokaryote salmonella typhimurium. Nearly two decades after completion of the genome sequence of mycobacterium tuberculosis mtb, and with the advent of next generation sequencing technologies ngs, whole genome sequencing wgs has been applied to a wide range of clinical scenarios.
A circos plot showing the complete genome sequence of m. By combining second illumina and third pacbio generation sequencing in an integrated genome analysis workflow for bcg, we could construct the completely assembled genome sequence of bcg danish 31 07270 and an engineered derivative that is studied as an improved vaccine candidate, a sapm ko, including the resolution of the. Deciphering drug resistance in mycobacterium tuberculosis. Complete genome sequence of cluster o mycobacterium smegmatis bacteriophage ryadel. Nearly two decades after completion of the genome sequence of mycobacterium tuberculosis mtb, and with the advent of next generation sequencing technologies ngs, wholegenome sequencing wgs has been applied to a wide range of clinical scenarios. A the original laboratory and the edited strains were subjected to wholegenome sequencing.
We describe here the complete genome sequence of a common clone of mycobacterium avium subspecies paratuberculosis map strain k10, the causative agent of johnes disease in cattle and other ruminants. Download genome annotation in gff, genbank or tabular format blast against mycobacterium tuberculosis genome, protein all 6554 genomes for species. Mycobacterium abscessus is an emerging rapidly growing mycobacterium rgm causing a pseudotuberculous lung disease to which patients with cystic fibrosis cf are particularly susceptible. This mycobacterium smegmatis gene database is uniprotcentric in that the main data source primary id system for gene ids and annotation is the uniprot complete proteome set for mycobacterium smegmatis, made available as an xml download by the integr8 resource. The dna was sequenced at the virginia commonwealth university by roche 454 dna sequencing. Green histogram track represents the average sequencing read depth for the complete genome. As a member of the wwpdb, the rcsb pdb curates and annotates pdb data according to agreed upon standards. Oct 14, 2015 mycobacterium tuberculosis k, a member of the beijing family, was first identified in 1999 as the most prevalent genotype in south korea among clinical isolates of m. Taxonomy browser mycolicibacterium smegmatis mc2 155. Since then, whole genome sequencing wgs has been applied to a wide range of clinical scenarios, with the potential to revolutionize tuberculosis tb diagnosis, outbreak investigation, drug and vaccine development, plus assist in understanding mtb evolution and pathogenicity. Members of the extracytoplasmic sigma factors family, which are required for adaptive responses to various environmental stresses, are responsible for some of the virulence traits of m.
The sequence represents essential data for future phylogenetic and comparative genome studies of this fish pathogen. Using a combination of illumina, pacbio, and sanger. Tuberculosis tb is a global infectious threat that is intensified by an increasing incidence of highly drugresistant disease. Interrupted coding sequences in mycobacterium smegmatis. The genome quality was confirmed in consed 1 and found to be 51,034 bp in length.
Starting in 2017, england is the first country in the world to pioneer its use on a national scale for the diagnosis of. Proteomes mycolicibacterium smegmatis strain atcc 700084 mc2155. The complete genome sequence of mycobacterium avium. Pdf complete genome sequence of mycobacterium massiliense.
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