scholarly journals The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames

2010 ◽  
Vol 192 (20) ◽  
pp. 5289-5303 ◽  
Author(s):  
C. Peter Wolk ◽  
Sigal Lechno-Yossef ◽  
Karin M. Jäger
Keyword(s):  
Transposable Elements ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Direct Repeats ◽  
Homologous Sequences ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Flanking Regions ◽  
Adaptive Role ◽  
Reading Frames

ABSTRACT Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/ ) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.

scholarly journals A TRAP Transporter for Pyruvate and Other Monocarboxylate 2-Oxoacids in the Cyanobacterium Anabaena sp. Strain PCC 7120

2010 ◽  
Vol 192 (22) ◽  
pp. 6089-6092 ◽  
Author(s):  
Rafael Pernil ◽  
Antonia Herrero ◽  
Enrique Flores
Keyword(s):  
Open Reading Frames ◽  
Wild Type ◽  
Cyanobacterium Anabaena ◽  
Anabaena Sp ◽  
Significant Uptake ◽  
Pcc 7120 ◽  
Reading Frames ◽  
T System

ABSTRACT In the cyanobacterium Anabaena sp. strain PCC 7120, open reading frames (ORFs) alr3026, alr3027, and all3028 encode a tripartite ATP-independent periplasmic transporter (TRAP-T). Wild-type filaments showed significant uptake of [14C]pyruvate, which was impaired in the alr3027 and all3028 mutants and was inhibited by several monocarboxylate 2-oxoacids, identifying this TRAP-T system as a pyruvate/monocarboxylate 2-oxoacid transporter.

scholarly journals Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in Anabaena sp. Strain PCC 7120

2005 ◽  
Vol 187 (3) ◽  
pp. 1114-1123 ◽  
Author(s):  
Guocun Huang ◽  
Qing Fan ◽  
Sigal Lechno-Yossef ◽  
Elizabeth Wojciuch ◽  
C. Peter Wolk ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Polysaccharide Layer ◽  
Reading Frames

ABSTRACT As demonstrated with alr2835 (hepA) and alr2834 (hepC) mutants, heterocysts of Anabaena sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep+ phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox+ phenotype). Transpositions presumptively responsible for a Fox− phenotype were localized in open reading frames (ORFs) near hepA and hepC. A mutation in each of nine of these ORFs was complemented by a clone bearing only that single, intact ORF. Heterocysts of the nine mutants were found to lack an envelope polysaccharide layer. Complementation of mutations in alr2832 and alr2840 may have resulted from recombination. However, alr2825, alr2827, alr2831, alr2833, alr2837, alr2839, and alr2841, like hepA and hepC, are required for a Hep+ Fox+ phenotype.

Expression, nucleotide sequence and mutational analysis of two open reading frames in the nif gene region of Anabaena sp. strain PCC 7120

1990 ◽  
Vol 221 (2) ◽  
pp. 227-234 ◽  
Author(s):  
Dulal Borthakur ◽  
Michele Basche ◽  
William J. Buikema ◽  
Pritty B. Borthakur ◽  
Robert Haselkorn
Keyword(s):  
Nucleotide Sequence ◽  
Mutational Analysis ◽  
Open Reading Frames ◽  
Gene Region ◽  
Anabaena Sp ◽  
Nif Gene ◽  
Pcc 7120 ◽  
Reading Frames

scholarly journals First Staphylococcal Cassette ChromosomemecContaining amecB-Carrying Gene Complex Independent of Transposon Tn6045in a Macrococcus caseolyticus Isolate from a Canine Infection

2015 ◽  
Vol 59 (8) ◽  
pp. 4577-4583 ◽  
Author(s):  
Elena Gómez-Sanz ◽  
Sybille Schwendener ◽  
Andreas Thomann ◽  
Stefanie Gobeli Brawand ◽  
Vincent Perreten
Keyword(s):  
Integration Site ◽  
Direct Repeat ◽  
Open Reading Frames ◽  
Gene Complex ◽  
Direct Repeats ◽  
Content Type ◽  
Canine Infection ◽  
The Right ◽  
Lactamase Gene ◽  
Reading Frames

ABSTRACTA methicillin-resistantmecB-positiveMacrococcus caseolyticus(strain KM45013) was isolated from the nares of a dog with rhinitis. It contained a novel 39-kb transposon-defective completemecB-carrying staphylococcal cassette chromosomemecelement (SCCmecKM45013). SCCmecKM45013contained 49 coding sequences (CDSs), was integrated at the 3′ end of the chromosomalorfXgene, and was delimited at both ends by imperfect direct repeats functioning as integration site sequences (ISSs). SCCmecKM45013presented two discontinuous regions of homology (SCCmeccoverage of 35%) to the chromosomal and transposon Tn6045-associated SCCmec-like element ofM. caseolyticusJCSC7096: (i) themecgene complex (98.8% identity) and (ii) theccr-carrying segment (91.8% identity). Themecgene complex, located at the right junction of the cassette, also carried the β-lactamase geneblaZm(mecRm-mecIm-mecB-blaZm). SCCmecKM45013contained two cassette chromosome recombinase genes,ccrAm2andccrBm2, which shared 94.3% and 96.6% DNA identity with those of the SCCmec-like element of JCSC7096 but shared less than 52% DNA identity with the staphylococcalccrABandccrCgenes. Three distinct extrachromosomal circularized elements (the entire SCCmecKM45013, ΨSCCmecKM45013lacking theccrgenes, and SCCKM45013lackingmecB) flanked by one ISS copy, as well as the chromosomal regions remaining after excision, were detected. An unconventional circularized structure carrying themecBgene complex was associated with two extensive direct repeat regions, which enclosed two open reading frames (ORFs) (ORF46 and ORF51) flanking the chromosomalmecB-carrying gene complex. This study revealedM. caseolyticusas a potential disease-associated bacterium in dogs and also unveiled an SCCmecelement carryingmecBnot associated with Tn6045in the genusMacrococcus.

scholarly journals Precise Excision of the Large Pathogenicity Island, SPI7, in Salmonella enterica Serovar Typhi

2004 ◽  
Vol 186 (10) ◽  
pp. 3202-3213 ◽  
Author(s):  
Susan M. Bueno ◽  
Carlos A. Santiviago ◽  
Alejandro A. Murillo ◽  
Juan A. Fuentes ◽  
A. Nicole Trombert ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Pathogenicity Island ◽  
Open Reading Frames ◽  
Epithelial Cell Line ◽  
Direct Repeats ◽  
Salmonella Enterica Serovar Typhi ◽  
Precise Excision ◽  
Join Point ◽  
Reading Frames ◽  
Vi Antigen

ABSTRACT The large pathogenicity island (SPI7) of Salmonella enterica serovar Typhi is a 133,477-bp segment of DNA flanked by two 52-bp direct repeats overlapping the pheU (phenylalanyl-tRNA) gene, contains 151 potential open reading frames, and includes the viaB operon involved in the synthesis of Vi antigen. Some clinical isolates of S. enterica serovar Typhi are missing the entire SPI7, due to its precise excision; these strains have lost the ability to produce Vi antigen, are resistant to phage Vi-II, and invade a human epithelial cell line more rapidly. Excision of SPI7 occurs spontaneously in a clinical isolate of S. enterica serovar Typhi when it is grown in the laboratory, leaves an intact copy of the pheU gene at its novel join point, and results in the same three phenotypic consequences. SPI7 is an unstable genetic element, probably an intermediate in the pathway of lateral transfer of such pathogenicity islands among enteric gram-negative bacteria.

scholarly journals Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

2002 ◽  
Vol 68 (3) ◽  
pp. 1220-1227 ◽  
Author(s):  
Masayuki Hashimoto ◽  
Mitsuru Fukui ◽  
Kouichi Hayano ◽  
Masahito Hayatsu
Keyword(s):  
Nucleotide Sequence ◽  
Insertion Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Homology Search ◽  
Sequencing Analysis ◽  
Terminal Sequence ◽  
Homologous Sequences ◽  
Naphthyl Acetate ◽  
Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

scholarly journals Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 484
Author(s):  
Michael Sadler ◽  
Melanie R. Mormile ◽  
Ronald L. Frank
Keyword(s):  
Insertion Sequence ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Genome Plasticity ◽  
Mobile Dna ◽  
Dna Elements ◽  
Left And Right ◽  
Evolutionary Role ◽  
Reading Frames

Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction.

scholarly journals Purification and Molecular Characterization of a Tripeptidase (PepT) from Lactobacillus helveticus

2000 ◽  
Vol 66 (2) ◽  
pp. 794-800 ◽  
Author(s):  
Kirsi Savijoki ◽  
Airi Palva
Keyword(s):  
Maximum Activity ◽  
Lactobacillus Helveticus ◽  
Open Reading Frames ◽  
Transcription Start ◽  
Sequence Analyses ◽  
Repeat Structure ◽  
Flanking Regions ◽  
Dairy Starter ◽  
Reading Frames

ABSTRACT A tripeptidase (PepT) from a thermophilic dairy starter strain ofLactobacillus helveticus was purified by four chromatographic steps. PepT appeared to be a trimeric metallopeptidase with a molecular mass of 150 kDa. PepT exhibited maximum activity against hydrophobic tripeptides, with the highest activity for Met-Gly-Gly (Km , 2.6 mM;V max, 80.2 μmol · min−1 · μg−1). Some of the hydrophobic dipeptides were slowly hydrolyzed, distinguishing theLactobacillus PepT from its counterpart in mesophilicLactococcus lactis. No activity against tetrapeptides or amino acid p-nitroanilide derivatives was observed. ThepepT gene and its flanking regions were isolated by PCR and sequenced by cyclic sequencing. The sequence analyses revealed open reading frames (ORFs) 816 bp (ORF1) and 1,239 bp (ORF2) long. ORF2 encoded a 47-kDa PepT protein which exhibited 53% identity with the PepT from L. lactis. The mRNA analyses indicated thatpepT conforms a novel operon structure with an ORF1 located upstream. Several putative −35/−10 regions preceded the operon, but only one transcription start site located downstream of the first putative −10 region was identified. An inverted repeat structure with ΔG of −64.8 kJ/mol was found downstream of the PepT-encoding region.

scholarly journals Evolution of the Major Pilus Gene Cluster ofHaemophilus influenzae

1998 ◽  
Vol 180 (17) ◽  
pp. 4693-4703 ◽  
Author(s):  
Tendai Mhlanga-Mutangadura ◽  
Gregory Morlin ◽  
Arnold L. Smith ◽  
Abraham Eisenstark ◽  
Miriam Golomb
Keyword(s):  
Insertion Site ◽  
Data Bank ◽  
Open Reading Frames ◽  
Direct Repeats ◽  
Chromosomal Locus ◽  
Human Respiratory Tract ◽  
Small Proteins ◽  
Ofhaemophilus Influenzae ◽  
Hypothetical Ancestor ◽  
Reading Frames

ABSTRACT Haemophilus influenzae is a ubiquitous colonizer of the human respiratory tract and causes diseases ranging from otitis media to meningitis. Many H. influenzae isolates express pili (fimbriae), which mediate adherence to epithelial cells and facilitate colonization. The pilus gene (hif) cluster of H. influenzae type b maps between purE andpepN and resembles a pathogenicity island: it is present in invasive strains, absent from the nonpathogenic Rd strain, and flanked by direct repeats of sequence at the insertion site. To investigate the evolution and role in pathogenesis of the hif cluster, we compared the purE-pepN regions of various H. influenzae laboratory strains and clinical isolates. Unlike Rd, most strains had an insert at this site, which usually was the only chromosomal locus of hif DNA. The inserts are diverse in length and organization: among 20 strains, nine different arrangements were found. Several nontypeable isolates lack hif genes but have two conserved open reading frames (hicA andhicB) upstream of purE; their inferred products are small proteins with no data bank homologs. Other isolates havehif genes but lack hic DNA or have combinations of hif and hic genes. By comparing these arrangements, we have reconstructed a hypothetical ancestral genotype, the extended hif cluster. The hif region of INT1, an invasive nontypeable isolate, resembles the hypothetical ancestor. We propose that a progenitor strain acquired the extended cluster by horizontal transfer and that other variants arose as deletions. The structure of the hif cluster may correlate with colonization site or pathogenicity.

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