scholarly journals Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350

2008 ◽  
Vol 190 (11) ◽  
pp. 4050-4060 ◽  
Author(s):  
Yasuo Ohnishi ◽  
Jun Ishikawa ◽  
Hirofumi Hara ◽  
Hirokazu Suzuki ◽  
Miwa Ikenoya ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Streptomyces Coelicolor ◽  
Streptomyces Griseus ◽  
Aminoglycoside Antibiotic ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Streptomyces Avermitilis ◽  
Trna Genes ◽  
Biosynthesis Gene Cluster ◽  
Regulatory Cascade

ABSTRACT We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium producing an antituberculosis agent, streptomycin, which is the first aminoglycoside antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929 base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames, six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary structure, consisting of several palindromes with a loop sequence of 5′-GGA-3′, are different from those of typical telomeres conserved among other Streptomyces species. In accordance with the difference, the chromosome has pseudogenes for a conserved terminal protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species, Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed that at least four of these clusters, in addition to the streptomycin biosynthesis gene cluster, were activated directly or indirectly by AdpA, which is a central transcriptional activator for secondary metabolism and morphogenesis in the A-factor (a γ-butyrolactone signaling molecule) regulatory cascade in S. griseus.

scholarly journals Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

2003 ◽  
Vol 185 (17) ◽  
pp. 5220-5233 ◽  
Author(s):  
Eric S. Miller ◽  
John F. Heidelberg ◽  
Jonathan A. Eisen ◽  
William C. Nelson ◽  
A. Scott Durkin ◽  
...  
Keyword(s):  
Host Range ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Group I Introns ◽  
Repair Enzymes ◽  
Group I

ABSTRACT The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.

scholarly journals Complete Genome Sequence of Riemerella anatipestifer Serotype 10 Strain HXb2

2017 ◽  
Vol 5 (18) ◽  
Author(s):  
Qinghai Hu ◽  
Jingjing Qi ◽  
Huimin Bo ◽  
Guangqing Liu ◽  
Minjie Tao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Content Type ◽  
Riemerella Anatipestifer ◽  
Single Circular Chromosome ◽  
Reading Frames

ABSTRACT The complete genome sequence of highly virulent Riemerella anatipestifer strain HXb2 was determined. The genome consisted of a single circular chromosome of 2,425,237 bp containing 2,383 putative open reading frames (ORFs), 9 rRNA operons, and 40 tRNA genes.

scholarly journals Organization and Expression of the Polynucleotide Phosphorylase Gene (pnp) of Streptomyces: Processing of pnp Transcripts in Streptomyces antibioticus

2004 ◽  
Vol 186 (10) ◽  
pp. 3160-3172 ◽  
Author(s):  
Patricia Bralley ◽  
George H. Jones
Keyword(s):  
Intergenic Region ◽  
Transcription Initiation ◽  
Streptomyces Coelicolor ◽  
Open Reading Frames ◽  
Streptomyces Avermitilis ◽  
Polynucleotide Phosphorylase ◽  
Rnase Iii ◽  
Stem Loop ◽  
Streptomyces Antibioticus ◽  
E Coli

ABSTRACT We have examined the expression of pnp encoding the 3′-5′-exoribonuclease, polynucleotide phosphorylase, in Streptomyces antibioticus. We show that the rpsO-pnp operon is transcribed from at least two promoters, the first producing a readthrough transcript that includes both pnp and the gene for ribosomal protein S15 (rpsO) and a second, Ppnp, located in the rpsO-pnp intergenic region. Unlike the situation in Escherichia coli, where observation of the readthrough transcript requires mutants lacking RNase III, we detect readthrough transcripts in wild-type S. antibioticus mycelia. The Ppnp transcriptional start point was mapped by primer extension and confirmed by RNA ligase-mediated reverse transcription-PCR, a technique which discriminates between 5′ ends created by transcription initiation and those produced by posttranscriptional processing. Promoter probe analysis demonstrated the presence of a functional promoter in the intergenic region. The Ppnp sequence is similar to a group of promoters recognized by the extracytoplasmic function sigma factors, sigma-R and sigma-E. We note a number of other differences in rspO-pnp structure and function between S. antibioticus and E. coli. In E. coli, pnp autoregulation and cold shock adaptation are dependent upon RNase III cleavage of an rpsO-pnp intergenic hairpin. Computer modeling of the secondary structure of the S. antibioticus readthrough transcript predicts a stem-loop structure analogous to that in E. coli. However, our analysis suggests that while the readthrough transcript observed in S. antibioticus may be processed by an RNase III-like activity, transcripts originating from Ppnp are not. Furthermore, the S. antibioticus rpsO-pnp intergenic region contains two open reading frames. The larger of these, orfA, may be a pseudogene. The smaller open reading frame, orfX, also observed in Streptomyces coelicolor and Streptomyces avermitilis, may be translationally coupled to pnp and the gene downstream from pnp, a putative protease.

scholarly journals Genome Sequence of Serratia marcescens subsp. sakuensis Strain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis)

2018 ◽  
Vol 6 (6) ◽  
pp. e00022-18 ◽  
Author(s):  
Tzi Him Cheng ◽  
Jasnizat Saidin ◽  
Muhd Danish-Daniel ◽  
Han Ming Gan ◽  
Mohd Noor Mat Isa ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Genome Sequence ◽  
Marine Bacterium ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Nonribosomal Peptides ◽  
Reading Frames

ABSTRACTSerratia marcescens subsp. sakuensis strain K27 was isolated from sponge (Haliclona amboinensis). The genome of this strain consists of 5,325,727 bp, with 5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for the production of amylases, lipases, and proteases. Gene clusters for the biosynthesis of nonribosomal peptides and thiopeptide were also identified.

scholarly journals Complete Genome Sequence of a Phapecoctavirus Isolated from a Pigeon Cloacal Swab Sample

2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Anthony Khalifeh ◽  
Simona Kraberger ◽  
Daria Dziewulska ◽  
Tomasz Stenzel ◽  
Arvind Varsani
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Columba Livia ◽  
Cloacal Swab ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Reading Frames

ABSTRACT The complete genome sequence of a bacteriophage in the genus Phapecoctavirus (family Myoviridae) isolated from a cloacal swab specimen from a domestic pigeon (Columba livia f. domestica) was identified using a high-throughput sequencing approach. The genome is 150,892 bp with a GC content of 39.1%, containing 269 open reading frames and 11 tRNA genes.

scholarly journals Transcriptional Control by A-Factor of strR, the Pathway-Specific Transcriptional Activator for Streptomycin Biosynthesis in Streptomyces griseus

2005 ◽  
Vol 187 (16) ◽  
pp. 5595-5604 ◽  
Author(s):  
Ayami Tomono ◽  
Yisan Tsai ◽  
Haruka Yamazaki ◽  
Yasuo Ohnishi ◽  
Sueharu Horinouchi
Keyword(s):  
Gene Cluster ◽  
Transcriptional Activation ◽  
Transcriptional Control ◽  
Streptomyces Griseus ◽  
Transcriptional Activator ◽  
Transcriptional Analysis ◽  
Mobility Shift ◽  
Biosynthesis Gene Cluster ◽  
Regulatory Cascade ◽  
Streptomycin Biosynthesis

ABSTRACT A-factor (2-isocapryloyl-3R-hydroxymethyl-γ-butyrolactone) triggers streptomycin production by inducing the transcription of strR, encoding the pathway-specific transcriptional activator, through signal transduction in the A-factor regulatory cascade in Streptomyces griseus. AdpA, one of the key transcriptional activators in the cascade, bound two upstream activation sites, approximately at nucleotide positions −270 and −50 with respect to the transcriptional start point of strR, as determined by gel mobility shift assays and DNase I footprinting. Transcriptional analysis of the strR promoter with mutated AdpA-binding sites showed that both sites were required for full transcriptional activation of strR by AdpA. Potassium permanganate footprinting showed that AdpA assisted RNA polymerase in forming an open complex at an appropriate position for transcriptional initiation of strR. Nine transcriptional units within the streptomycin biosynthesis gene cluster, including the strR-aphD operon, depended on StrR, indicating that StrR is the pathway-specific transcriptional activator for the whole gene cluster. Consistent with this, expression of strR under the control of a constitutively expressed promoter in an adpA null mutant caused the host to produce streptomycin.

scholarly journals Draft Genome Sequence of Saccharomonospora piscinae KCTC 19743T, an Actinobacterium Containing Secondary Metabolite Biosynthetic Gene Clusters

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Ninfa Ramírez-Durán ◽  
Rafael R. de la Haba ◽  
Blanca Vera-Gargallo ◽  
Cristina Sánchez-Porro ◽  
Scarlett Alonso-Carmona ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Polyketide Synthase ◽  
Draft Genome ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Draft Genome Sequence ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Peptide Synthetase ◽  
Reading Frames

The draft genome sequence of Saccharomonospora piscinae KCTC 19743T, with a size of 4,897,614 bp, was assembled into 11 scaffolds containing 4,561 open reading frames and a G+C content of 71.0 mol%. Polyketide synthase and nonribosomal peptide synthetase gene clusters, which are responsible for the biosynthesis of several biomolecules, were identified and located in different regions in the genome.

Oxidation and amidation of salicylate by Streptomyces species

1996 ◽  
Vol 42 (8) ◽  
pp. 867-869 ◽  
Author(s):  
Stanislav Pospíšil ◽  
Věra Přikrylová ◽  
Jan Němeček ◽  
Jaroslav Spížek
Keyword(s):  
Time Course ◽  
Streptomyces Coelicolor ◽  
Streptomyces Griseus ◽  
Culture Broth ◽  
Streptomyces Avermitilis ◽  
Resonance Spectroscopy ◽  
Streptomyces Species ◽  
Streptomyces Spp ◽  
Streptomyces Cinnamonensis ◽  
Layer Chromatography

Seven streptomycete strains were tested for biotransformation of salicylate. The products were identified by nuclear magnetic resonance spectroscopy and three types of conversion were found. Streptomyces cinnamonensis and Streptomyces spectabilis formed gentisate and salicylamide concurrently. Streptomyces rimosus transformed salicylate to salicylamide. Streptomyces lividans, Streptomyces coelicolor, Streptomyces griseus and Streptomyces avermitilis produced only gentisate. Time course studies of salicylate conversion by thin-layer chromatography and high pressure liquid chromatography showed that salicylamide was accumulated in the culture broth, whereas gentisate was further metabolized.Key words: salicylate, gentisate, salicylamide, biotransformation, Streptomyces spp.

scholarly journals Genome Sequence of Bacillus sp. Strain UMTAT18 Isolated from the Dinoflagellate Alexandrium tamiyavanichii Found in the Straits of Malacca

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Muhd Danish-Daniel ◽  
Gan Han Ming ◽  
Mohd Ezhar Mohd Noor ◽  
Yeong Yik Sung ◽  
Gires Usup
Keyword(s):  
Stress Tolerance ◽  
Genome Sequence ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Nonribosomal Peptides ◽  
Bacillus Sp ◽  
Straits Of Malacca ◽  
Reading Frames ◽  
Harmful Dinoflagellate

Bacillus sp. strain UMTAT18 was isolated from the harmful dinoflagellate Alexandrium tamiyavanichii . Its genome consists of 5,479,367 bp with 5,546 open reading frames, 102 tRNAs, and 29 rRNAs. Gene clusters for biosynthesis of nonribosomal peptides, bacteriocin, and lantipeptide were identified. It also contains siderophore and genes related to stress tolerance.

scholarly journals Synthesis and Uptake of the Compatible Solutes Ectoine and 5-Hydroxyectoine by Streptomyces coelicolor A3(2) in Response to Salt and Heat Stresses

2008 ◽  
Vol 74 (23) ◽  
pp. 7286-7296 ◽  
Author(s):  
Jan Bursy ◽  
Anne U. Kuhlmann ◽  
Marco Pittelkow ◽  
Holger Hartmann ◽  
Mohamed Jebbar ◽  
...  
Keyword(s):  
Heat Stress ◽  
Streptomyces Coelicolor ◽  
Compatible Solutes ◽  
Streptomyces Griseus ◽  
Streptomyces Avermitilis ◽  
Cell Physiology ◽  
Environmental Cues ◽  
Stress Protection ◽  
Low Concentrations ◽  
As Stress

ABSTRACT Streptomyces coelicolor A3(2) synthesizes ectoine and 5-hydroxyectoine upon the imposition of either salt (0.5 M NaCl) or heat stress (39°C). The cells produced the highest cellular levels of these compatible solutes when both stress conditions were simultaneously imposed. Protection against either severe salt (1.2 M NaCl) or heat stress (39°C) or a combination of both environmental cues could be accomplished by adding low concentrations (1 mM) of either ectoine or 5-hydroxyectoine to S. coelicolor A3(2) cultures. The best salt and heat stress protection was observed when a mixture of ectoine and 5-hydroxyectoine (0.5 mM each) was provided to the growth medium. Transport assays with radiolabeled ectoine demonstrated that uptake was triggered by either salt or heat stress. The most effective transport and accumulation of [14C]ectoine by S. coelicolor A3(2) were achieved when both environmental cues were simultaneously applied. Our results demonstrate that the accumulation of the compatible solutes ectoine and 5-hydroxyectoine allows S. coelicolor A3(2) to fend off the detrimental effects of both high salinity and high temperature on cell physiology. We also characterized the enzyme (EctD) required for the synthesis of 5-hydroxyectoine from ectoine, a hydroxylase of the superfamily of the non-heme-containing iron(II)- and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). The gene cluster (ectABCD) encoding the enzymes for ectoine and 5-hydroxyectoine biosynthesis can be found in the genome of S. coelicolor A3(2), Streptomyces avermitilis, Streptomyces griseus, Streptomyces scabiei, and Streptomyces chrysomallus, suggesting that these compatible solutes play an important role as stress protectants in the genus Streptomyces.

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