scholarly journals Cloning and Analysis of the Telomere and Terminal Inverted Repeat of the Linear Chromosome of Streptomyces griseus

2002 ◽  
Vol 184 (12) ◽  
pp. 3411-3415 ◽  
Author(s):  
Kohei Goshi ◽  
Tetsuya Uchida ◽  
Alexander Lezhava ◽  
Masayuki Yamasaki ◽  
Keiichiro Hiratsu ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Streptomyces Griseus ◽  
Open Reading Frames ◽  
Terminal Inverted Repeat ◽  
Loop Structure ◽  
Hairpin Loop ◽  
Cloning And Sequencing ◽  
Linear Chromosome ◽  
Palindromic Sequences ◽  
Reading Frames

ABSTRACT Cloning and sequencing of the telomere of Streptomyces griseus revealed five palindromic sequences in the terminal 116 nucleotides, all of which can make a hairpin loop structure. However, the end sequence cannot form the foldback secondary structure that is common in Streptomyces telomeres and is suggested to be necessary for terminal replication. Both inside ends of the terminal inverted repeat (TIR) were also cloned and sequenced. The results confirmed the size of the TIR to be 24 kb and identified two almost identical open reading frames that might have been involved in the formation of the TIR.

Phylogenetic analysis reveals Stowaway-like elements may represent a fourth family of the IS630-Tc1-mariner superfamily

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Phylogenetic Analysis ◽  
Inverted Repeat ◽  
Evolutionary Relationship ◽  
Open Reading Frames ◽  
Published Data ◽  
Terminal Inverted Repeat ◽  
Predominant Type ◽  
Sequence Signature ◽  
Eukaryotic Organisms ◽  
Reading Frames

The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630–Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630–Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.Key words: Stowaway, Emigrant, MITE, mariner, transposon.

scholarly journals Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames.

1990 ◽  
Vol 172 (4) ◽  
pp. 1969-1977 ◽  
Author(s):  
N K Menon ◽  
J Robbins ◽  
H D Peck ◽  
C Y Chatelus ◽  
E S Choi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Open Reading Frames ◽  
Cloning And Sequencing ◽  
Reading Frames

scholarly journals Genetic Localization and Molecular Characterization of the nonS Gene Required for Macrotetrolide Biosynthesis inStreptomyces griseus DSM40695

2000 ◽  
Vol 44 (7) ◽  
pp. 1809-1817 ◽  
Author(s):  
Wyatt C. Smith ◽  
Longkuan Xiang ◽  
Ben Shen
Keyword(s):  
Polyketide Synthase ◽  
Isotope Labeling ◽  
Streptomyces Griseus ◽  
Open Reading Frames ◽  
A Cell ◽  
Cyclic Polyethers ◽  
The Difference ◽  
Reading Frames

ABSTRACT The macrotetrolides are a family of cyclic polyethers derived from tetramerization, in a stereospecific fashion, of the enantiomeric nonactic acid (NA) and its homologs. Isotope labeling experiments established that NA is of polyketide origin, and biochemical investigations demonstrated that 2-methyl-6,8-dihydroxynon-2E-enoic acid can be converted into NA by a cell-free preparation from Streptomyces lividans that expresses nonS. These results lead to the hypothesis that macrotetrolide biosynthesis involves a pair of enantiospecific polyketide pathways. In this work, a 55-kb contiguous DNA region was cloned from Streptomyces griseus DSM40695, a 6.3-kb fragment of which was sequenced to reveal five open reading frames, including the previously reported nonR andnonS genes. Inactivation of nonS in vivo completely abolished macrotetrolide production. Complementation of thenonS mutant by the expression of nonS intrans fully restored its macrotetrolide production ability, with a distribution of individual macrotetrolides similar to that for the wild-type producer. In contrast, fermentation of thenonS mutant in the presence of exogenous (±)-NA resulted in the production of nonactin, monactin, and dinactin but not in the production of trinactin and tetranactin. These results prove the direct involvement of nonS in macrotetrolide biosynthesis. The difference in macrotetrolide production between in vivo complementation of the nonS mutant by the plasmid-borne nonSgene and fermentation of the nonS mutant in the presence of exogenously added (±)-NA suggests that NonS catalyzes the formation of (−)-NA and its homologs, supporting the existence of a pair of enantiospecific polyketide pathways for macrotetrolide biosynthesis inS. griseus. The latter should provide a model that can be used to study the mechanism by which polyketide synthase controls stereochemistry during polyketide biosynthesis.

scholarly journals Characterization of ssfR andssgA, Two Genes Involved in Sporulation ofStreptomyces griseus

2000 ◽  
Vol 182 (19) ◽  
pp. 5521-5529 ◽  
Author(s):  
Hao Jiang ◽  
Kathleen E. Kendrick
Keyword(s):  
Stop Codon ◽  
Streptomyces Griseus ◽  
Large Family ◽  
Resistant Mutant ◽  
Open Reading Frames ◽  
Dna Fragment ◽  
Morphological Differences ◽  
White Mutant ◽  
Reading Frames

ABSTRACT In the presence of cefoxitin, which inhibits septum formation during sporulation, Streptomyces griseus is unable to sporulate, retaining the sonication sensitivity of nonsporulating hyphae. Cefoxitin- and sonication-resistant mutant SKK2600 was isolated and showed many morphological differences from its parental strain. A 3.6-kb DNA fragment that complemented the mutations of SKK2600 contained two open reading frames (ORFs), either of which could complement SKK2600. One ORF, designated ssfR, encoded a protein containing a potential DNA-binding helix-turn-helix motif close to its N terminus. SsfR is similar to members of a large family of transcriptional regulators, particularly IclR of Escherichia coli. The second ORF was identified as ssgA, a previously described sporulation gene from S. griseus (S. Kawamoto and J. C. Ensign, Actinomycetology 9:136–151, 1995). A point mutation of C to T seven nucleotides upstream of the UGA stop codon of ssfR was responsible for the phenotype of isolated mutant strain SKK2600. Surprisingly, this mutation should not change the primary structure of SsfR. The ssfR andssgA disruption mutants were constructed and showed the “white” mutant phenotype, with some growth medium dependence. In addition, the ssfR null mutant sporulated ectopically in phosphate starvation medium.

scholarly journals Chromosomal Arm Replacement in Streptomyces griseus

2003 ◽  
Vol 185 (3) ◽  
pp. 1120-1124 ◽  
Author(s):  
Tetsuya Uchida ◽  
Mariko Miyawaki ◽  
Haruyasu Kinashi
Keyword(s):  
Dna Repair ◽  
Deletion Mutant ◽  
Streptomyces Griseus ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequencing Analysis ◽  
Chromosomal Deletion ◽  
Terminal Inverted Repeats ◽  
Left And Right ◽  
Reading Frames

ABSTRACT UV irradiation of Streptomyces griseus 2247 yielded a new chromosomal deletion mutant, MM9. Restriction and sequencing analysis revealed that homologous recombination between two similar lipoprotein-like open reading frames, which are located 450 and 250 kb from the left and right ends, respectively, caused chromosomal arm replacement. As a result, new 450-kb terminal inverted repeats (TIRs) were formed in place of the original 24-kb TIRs. Frequent homologous recombinations in Streptomyces strains suggest that telomere deletions can usually be repaired by recombinational DNA repair functioning between the intact and deleted TIR sequences on the same chromosome.

scholarly journals Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Alicja Macko-Podgórni ◽  
Katarzyna Stelmach ◽  
Kornelia Kwolek ◽  
Dariusz Grzebelus
Keyword(s):  
Transposable Elements ◽  
Daucus Carota ◽  
Inverted Repeat ◽  
Insertion Site ◽  
Open Reading Frames ◽  
Genomic Diversity ◽  
Untranslated Regions ◽  
Substantial Contribution ◽  
Insertion Sites ◽  
Reading Frames

Abstract Background Miniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives. Stowaway MITEs are derived from and mobilised by elements from the mariner superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by Daucus carota Stowaway MITEs (DcStos), their association with genes and their putative impact on genome evolution has not been comprehensively analysed. Results Fourteen families of Stowaway elements DcStos occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated Daucus carota, yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism. DcSto element demography differed based on the origin of the host populations, and corresponded with the four major groups of D. carota, wild European, wild Asian, eastern cultivated and western cultivated. The DcStos elements were associated with genes, and most frequently occurred in 5′ and 3′ untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly, DcSto copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all DcSto insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The DcSto7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified Dcmar1 as an active carrot mariner element and a possible source of the transposition machinery for DcSto7b. Conclusion Stowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.

scholarly journals Chromosome and Linear Plasmid Sequences of a 2015 Human Isolate of the Tick-Borne Relapsing Fever Spirochete, Borrelia turicatae

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Luke C. Kingry ◽  
Dhwani Batra ◽  
Adam Replogle ◽  
Christopher Sexton ◽  
Lori Rowe ◽  
...  
Keyword(s):  
Human Isolate ◽  
Open Reading Frames ◽  
Linear Plasmid ◽  
Linear Plasmids ◽  
Relapsing Fever ◽  
Linear Chromosome ◽  
Plasmid Sequence ◽  
Reading Frames

The sequences of the complete linear chromosome and 7 linear plasmids of the relapsing fever spirochete Borrelia turicatae are presented in this report. The 925,547 bp of chromosome and 380,211 bp of plasmid sequence were predicted to contain a total of 1,131 open reading frames, with an average G+C content of 29.7%.

scholarly journals Evolution of the Xenopus piggyBac Transposon Family TxpB: Domesticated and Untamed Strategies of Transposon Subfamilies

2007 ◽  
Vol 24 (12) ◽  
pp. 2648-2656 ◽  
Author(s):  
Akira Hikosaka ◽  
Toshihiro Kobayashi ◽  
Yumiko Saito ◽  
Akira Kawahara
Keyword(s):  
Phylogenetic Analyses ◽  
Single Species ◽  
Single Copy ◽  
Open Reading Frames ◽  
Terminal Inverted Repeat ◽  
Repeat Sequences ◽  
New Family ◽  
Molecular Phylogenetic ◽  
Multiple Copies ◽  
Reading Frames

Abstract A new family, termed TxpB, of DNA transposons belonging to the piggyBac superfamily was found in 3 Xenopus species (Xenopus tropicalis, Xenopus laevis, and Xenopus borealis). Two TxpB subfamilies of Kobuta and Uribo1 were found in all the 3 species, and another subfamily termed Uribo2 was found in X. tropicalis. Molecular phylogenetic analyses of their open reading frames (ORFs) revealed that TxpB transposons have been maintained for over 100 Myr. Both the Uribo1 and the Uribo2 ORFs were present as multiple copies in each genome, and some of them were framed by terminal inverted repeat sequences. In contrast, all the Kobuta ORFs were present as a single copy in each genome and exhibited high evolutionary conservation, suggesting domestication of Kobuta genes by the host. Genomic insertion polymorphisms of the Uribo1 and Uribo2 transposons (nonautonomous type) were observed in a single species of X. tropicalis, indicating recent transposition events. Transfection experiments in cell culture revealed that an expression vector construct for the intact Uribo2 ORF caused precise excision of a nonautonomous Uribo2 element from the target vector construct but that for the Kobuta ORF did not. The present results support our viewpoint that some Uribo2 members are naturally active autonomous transposons, whereas Kobuta members may be domesticated by hosts.

An Origin of Transfer (oriT) on the Conjugative Element pRS01 from Lactococcus lactis subsp.lactis ML3

1998 ◽  
Vol 64 (4) ◽  
pp. 1541-1544 ◽  
Author(s):  
David A. Mills ◽  
Trevor G. Phister ◽  
Gary M. Dunny ◽  
Larry L. McKay
Keyword(s):  
Sequence Analysis ◽  
Lactococcus Lactis ◽  
Intergenic Region ◽  
Inverted Repeat ◽  
Previous Analysis ◽  
Open Reading Frames ◽  
Wild Type ◽  
Derivatives Of ◽  
Reading Frames ◽  
Origin Of Transfer

ABSTRACT Previous analysis of the Tra1 region of the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3 suggested that an origin of transfer (oriT) was present. Deletion derivatives of this cloned Tra1 region were assayed for mobilization in the presence of the wild-type pRS01 element intrans. The pRS01 oriT was localized to a 446-nucleotide segment in the intergenic region between open reading frames ltrD and ltrE. Sequence analysis of this region revealed a cluster of direct and inverted repeat structures characteristic of oriT regions associated with other conjugative systems.

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