scholarly journals The Moraxella catarrhalis Immunoglobulin D-Binding Protein MID Has Conserved Sequences and Is Regulated by a Mechanism Corresponding to Phase Variation

2003 ◽  
Vol 185 (7) ◽  
pp. 2285-2295 ◽  
Author(s):  
Andrea Möllenkvist ◽  
Therése Nordström ◽  
Christer Halldén ◽  
Jens Jørgen Christensen ◽  
Arne Forsgren ◽  
...  
Keyword(s):  
Moraxella Catarrhalis ◽  
Point Mutations ◽  
Phase Variation ◽  
The United States ◽  
Open Reading Frames ◽  
Peptide Sequence ◽  
Transcriptional Level ◽  
Signal Peptide Sequence ◽  
Immunoglobulin D ◽  
Reading Frames

ABSTRACT The prevalence of the Moraxella catarrhalis immunoglobulin D (IgD)-binding outer membrane protein MID and its gene was determined in 91 clinical isolates and in 7 culture collection strains. Eighty-four percent of the clinical Moraxella strains expressed MID-dependent IgD binding. The mid gene was detected in all strains as revealed by homology of the signal peptide sequence and a conserved area in the 3′ end of the gene. When MID proteins from five different strains were compared, an identity of 65.3 to 85.0% and a similarity of 71.2 to 89.1% were detected. Gene analyses showed several amino acid repeat motifs in the open reading frames, and MID could be called a putative autotransport protein. Interestingly, homopolymeric {polyguanine [poly(G)]} tracts were detected at the 5′ ends within the open reading frames. By flow cytometry, using human IgD and fluorescein isothiocyanate-conjugated anti-IgD polyclonal antibodies, most strains showed two peaks: one high- and one low-intensity peak. All isolates expressing high levels of MID had 1, 2, or 3 triplets of G's in their poly(G) tracts, while strains not expressing MID had 4, 7, 8, or 10 G’s in their poly(G) tracts or point mutations causing a putative preterminated translation. Northern blot analysis revealed that the mid gene was regulated at the transcriptional level. Experiments with nonclumping variants of M. catarrhalis proved that bacteria lost their MID expression by removing a G in their poly(G) tracts. Moraxella strains isolated from the nasopharynx or from blood and sputum specimens expressed MID at approximately the same frequency. In addition, no variation was observed between strains of different geographical origins (Australia, Europe, Japan, or the United States). MID and the mid gene were found solely in M. catarrhalis, whereas related Neisseria and Moraxella species did not express MID. Taken together, MID appears to be a conserved protein that can be found in essentially all M. catarrhalis strains. Furthermore, MID is governed by poly(G) tracts when bacteria undergo phase variation.

scholarly journals Genome Data of Four Pythium insidiosum Strains from the Phylogenetically-Distinct Clades I, II, and III

2021 ◽  
Author(s):  
Theerapong Krajaejun ◽  
Weerayuth Kittichotirat ◽  
Preecha Patumcharoenpol ◽  
Thidarat Rujirawat ◽  
Tassanee Lohnoo ◽  
...  
Keyword(s):  
The United States ◽  
Open Reading Frames ◽  
Genome Database ◽  
Pythium Insidiosum ◽  
Data Description ◽  
Genome Data ◽  
Serious Infection ◽  
Gdna Sample ◽  
Different Strains ◽  
Reading Frames

Abstract Objectives: We employed the Illumina NGS platform to sequence genomes of 4 different strains of Pythium insidiosum, an oomycete that causes a serious infection, called pythiosis, in humans and animals. These strains were isolated from humans in Thailand (n=3) and the United States (n=1), and phylogenetically classified into clade-I, -II, and -III. Our study augmented the completeness of the P. insidiosum genome database for exploration of the biology, evolution, and pathogenesis of the pathogen. Data description: Each gDNA sample from the P. insidiosum strains ATCC20026 (clade-I), Pi19 (clade-II), MCC18 (clade-II), and SIMI4763 (clade-III) was processed to prepare one paired-end library (180-bp insert) for whole-genome sequencing by Illumina HiSeq2000/HiSeq2500 NGS platform. A range of 28.4-59.4 million raw reads, accounted for 3.0-7.3 Gb, were obtained and assembled into the genome sizes of 47.1 Mb (15,153 contigs; 85% completeness; 19,329 open reading frames [ORFs]) for strain ATCC20026, 35.4 Mb (14,576 contigs; 83% completeness; 13,895 ORFs) for strain Pi19, 34.5 Mb (11,084 contigs; 84% completeness; 13,249 ORFs) for strain MCC18, and 47.1 Mb (15,162 contigs; 85% completeness; 19,340 ORFs) for strain SIMI4763. The genome data can be downloaded from the NCBI/DDBJ databases under the accessions BCFN00000000.1 (ATCC20026), BCFS00000000.1 (Pi19), BCFT00000000.1 (MCC18), and BCFU00000000.1 (SIMI4763).

scholarly journals Complete Genome Sequence of a Renamed Isolate, Trichoplusia ni Ascovirus 6b, from the United States

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Yuan-Yuan Liu ◽  
Wen-Fei Xian ◽  
Jin Xue ◽  
Yong-Lu Wei ◽  
Xiao-Wen Cheng ◽  
...  
Keyword(s):  
United States ◽  
Phylogenetic Relationship ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Trichoplusia Ni ◽  
The United States ◽  
Open Reading Frames ◽  
First Time ◽  
Reading Frames

ABSTRACT The complete genome of Trichoplusia ni ascovirus 6b (TnAV-6b) was sequenced for the first time. The TnAV-6b isolate, which has its closest phylogenetic relationship with the TnAV-6a isolate, has a circular genome of 185,664 bp, with a G+C content of 46.0% and 178 predicted open reading frames.

scholarly journals Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

2008 ◽  
Vol 89 (5) ◽  
pp. 1202-1211 ◽  
Author(s):  
José Luiz Caldas Wolff ◽  
Fernando Hercos Valicente ◽  
Renata Martins ◽  
Juliana Velasco de Castro Oliveira ◽  
Paolo Marinho de Andrade Zanotto
Keyword(s):  
Spodoptera Frugiperda ◽  
Point Mutations ◽  
Open Reading Frames ◽  
Temporal Organization ◽  
Agrotis Segetum ◽  
Gene Gain ◽  
Physical Maps ◽  
Polyadenylation Sites ◽  
Group Ii ◽  
Reading Frames

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-19), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-19 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-19 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-19 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group II NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group II had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60 % of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

scholarly journals Genome data of four Pythium insidiosum strains from the phylogenetically-distinct clades I, II, and III

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Theerapong Krajaejun ◽  
Weerayuth Kittichotirat ◽  
Preecha Patumcharoenpol ◽  
Thidarat Rujirawat ◽  
Tassanee Lohnoo ◽  
...  
Keyword(s):  
The United States ◽  
Open Reading Frames ◽  
Whole Genome ◽  
Genome Database ◽  
Pythium Insidiosum ◽  
Data Description ◽  
Genome Data ◽  
Gdna Sample ◽  
Different Strains ◽  
Reading Frames

Abstract Objectives We employed the Illumina NGS platform to sequence genomes of 4 different strains of the pathogenic oomycete Pythium insidiosum, the causative agent of pythiosis. These strains were isolated from humans in Thailand (n = 3) and the United States (n = 1), and phylogenetically classified into clade-I, -II, and -III. Our study augmented the completeness of the P. insidiosum genome database for exploration of the biology, evolution, and pathogenesis of the pathogen. Data description One paired-end library (180-bp insert) was prepared from a gDNA sample of P. insidiosum strains ATCC200269 (clade-I), Pi19 (clade-II), MCC18 (clade-II), and SIMI4763 (clade-III) for whole-genome sequencing by Illumina HiSeq2000/HiSeq2500 NGS platform. A range of 28.4–59.4 million raw reads, accounted for 3.0–7.3 Gb, were obtained and assembled into the genome sizes of 47.1 Mb (15,153 contigs; 85% completeness; 19,329 open reading frames [ORFs]) for strain ATCC200269, 35.4 Mb (14,576 contigs; 83% completeness; 13,895 ORFs) for strain Pi19, 34.5 Mb (11,084 contigs; 84% completeness; 13,249 ORFs) for strain MCC18, and 47.1 Mb (15,162 contigs; 85% completeness; 19,340 ORFs) for strain SIMI4763. The genome data can be downloaded from the NCBI/DDBJ databases under the accessions BCFN00000000.1 (ATCC200269), BCFS00000000.1 (Pi19), BCFT00000000.1 (MCC18), and BCFU00000000.1 (SIMI4763).

scholarly journals Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

2009 ◽  
Vol 75 (24) ◽  
pp. 7663-7673 ◽  
Author(s):  
Pilar García ◽  
Beatriz Martínez ◽  
José María Obeso ◽  
Rob Lavigne ◽  
Rudi Lurz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Recombination ◽  
Point Mutations ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Functional Genomic Analysis ◽  
Replication Point ◽  
Terminal Amino ◽  
Functional Analyses ◽  
Reading Frames

ABSTRACT The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the S. aureus-infecting phages.

scholarly journals Genetic Structures at the Origin of Acquisition of the β-Lactamase blaKPC Gene

2008 ◽  
Vol 52 (4) ◽  
pp. 1257-1263 ◽  
Author(s):  
Thierry Naas ◽  
Gaelle Cuzon ◽  
Maria-Virginia Villegas ◽  
Marie-Frédérique Lartigue ◽  
John P. Quinn ◽  
...  
Keyword(s):  
United States ◽  
Pseudomonas Aeruginosa ◽  
The United States ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Transposase Gene ◽  
Repeat Sequences ◽  
Class A ◽  
Genetic Structures ◽  
Reading Frames

ABSTRACT Genetic structures surrounding the carbapenem-hydrolyzing Ambler class A bla KPC gene were characterized in several KPC-positive Klebsiella pneumoniae and Pseudomonas aeruginosa strains isolated from the United States, Colombia, and Greece. The bla KPC genes were associated in all cases with transposon-related structures. In the K. pneumoniae YC isolate from the United States, the β-lactamase bla KPC-2 gene was located on a novel Tn3-based transposon, Tn4401. Tn4401 was 10 kb in size, was delimited by two 39-bp imperfect inverted repeat sequences, and harbored, in addition to the β-lactamase bla KPC-2 gene, a transposase gene, a resolvase gene, and two novel insertion sequences, ISKpn6 and ISKpn7. Tn4401 has been identified in all isolates. However, two isoforms of this transposon were found: Tn4401a was found in K. pneumoniae YC and K. pneumoniae GR from the United States and Greece, respectively, and differed by a 100-bp deletion, located just upstream of the bla KPC-2 gene, compared to the sequence of Tn4401b, which was found in the Colombian isolates. In all isolates tested, Tn4401 was flanked by a 5-bp target site duplication, the signature of a recent transposition event, and was inserted in different open reading frames located on plasmids that varied in size and nature. Tn4401 is likely at the origin of carbapenem-hydrolyzing β-lactamase KPC mobilization to plasmids and its further insertion into various-sized plasmids identified in nonclonally related K. pneumoniae and P. aeruginosa isolates.

scholarly journals Detection of novel divergent arenaviruses in boid snakes with inclusion body disease in The Netherlands

2013 ◽  
Vol 94 (6) ◽  
pp. 1206-1210 ◽  
Author(s):  
R. Bodewes ◽  
M. J. L. Kik ◽  
V. Stalin Raj ◽  
C. M. E. Schapendonk ◽  
B. L. Haagmans ◽  
...  
Keyword(s):  
The Netherlands ◽  
Inclusion Body ◽  
The United States ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Golden Gate ◽  
Inclusion Body Disease ◽  
A New Species ◽  
Generation Sequencing ◽  
Reading Frames

Arenaviruses are bi-segmented negative-stranded RNA viruses, which were until recently only detected in rodents and humans. Now highly divergent arenaviruses have been identified in boid snakes with inclusion body disease (IBD). Here, we describe the identification of a new species and variants of the highly divergent arenaviruses, which were detected in tissues of captive boid snakes with IBD in The Netherlands by next-generation sequencing. Phylogenetic analysis of the complete sequence of the open reading frames of the four predicted proteins of one of the detected viruses revealed that this virus was most closely related to the recently identified Golden Gate virus, while considerable sequence differences were observed between the highly divergent arenaviruses detected in this study. These findings add to the recent identification of the highly divergent arenaviruses in boid snakes with IBD in the United States and indicate that these viruses also circulate among boid snakes in Europe.

Involvement of upstream open reading frames in regulation of rat V1b vasopressin receptor expression

2001 ◽  
Vol 280 (5) ◽  
pp. E780-E787 ◽  
Author(s):  
Atsushi Nomura ◽  
Yasumasa Iwasaki ◽  
Masayuki Saito ◽  
Yoshiaki Aoki ◽  
Etsuko Yamamori ◽  
...  
Keyword(s):  
Receptor Gene ◽  
Suppressive Effect ◽  
Open Reading Frames ◽  
Receptor Expression ◽  
Luciferase Reporter ◽  
Transcriptional Level ◽  
Vasopressin Receptor ◽  
Start Site ◽  
Upstream Open Reading Frames ◽  
Reading Frames

The V1b vasopressin receptor, expressed mainly in the corticotroph of the anterior pituitary, mediates the stimulatory effect of vasopressin on ACTH release. To clarify the regulation of receptor expression, we cloned, sequenced (up to ∼5 kb from the translation start site), and characterized the 5′-flanking region of the rat V1b receptor gene. We identified the transcription start site by amplification of cDNA ends and found a new intron within the 5′-untranslated region (5′-UTR) by comparing the sequence with that of cDNA. We then confirmed that the obtained promoter indeed has transcriptional activity by use of the luciferase reporter in AtT-20 mouse corticotroph cells. Interestingly, there were five short upstream open reading frames (uORFs) located within the 5′-UTR that were found to suppress V1b expression. Subsequent mutational analyses showed that the two downstream uORFs have an inhibitory effect on expression in both homologous and heterologous contexts. Furthermore, the inhibition did not accompany a parallel decrease in mRNA, suggesting that the suppressive effect occurs at a level downstream of transcription. Taken together, our data strongly suggest that the expression of the V1b receptor is regulated at the posttranscriptional as well as transcriptional level through uORFs within the 5′-UTR region of the mRNA. Whether the uORF-mediated regulation of V1b expression is functionally linked to any intracellular and/or extracellular factor(s) awaits further research.

The signal peptide sequence of a lytic transglycosylase of Neisseria meningitidis is involved in regulation of gene expression

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1427-1437 ◽  
Author(s):  
Davide Serruto ◽  
Cesira L. Galeotti
Keyword(s):  
Secondary Structure ◽  
Neisseria Meningitidis ◽  
Signal Peptide ◽  
Regulation Of Gene Expression ◽  
Peptide Sequence ◽  
Deletion Mutants ◽  
Transcriptional Level ◽  
Signal Peptide Sequence ◽  
Synonymous Mutations ◽  
Lytic Transglycosylase

The 60 nucleotides encoding the signal peptide of the Neisseria meningitidis membrane-bound lytic transglycosylase (MltA) homologue GNA33 were found to exert a negative regulatory effect on expression of GNA33 from either a T7- or a Plac-driven system in Escherichia coli. Down-regulation was observed to occur at the transcriptional/post-transcriptional level and could possibly be ascribed to the formation of a stem–loop secondary structure within the signal peptide sequence. Slowing down the transcription rate through inhibition/titration of the RNA polymerase resulted in a considerable increase in mRNA accumulation, suggesting that a better coupling of translation to transcription would impede the formation of the putative secondary structure. Screening of synonymous mutations in the signal peptide sequence that showed high-level expression of an in-frame fusion to a reporter resulted in the isolation of several deletion mutants lacking most of the sequence participating in the putative secondary structure. Interestingly, the increase in the steady-state mRNA level observed in deletion mutants was higher, reaching a 300-fold increment, than that found in substitution mutants. Our results support the hypothesis that the rate of transcription controls the formation of a secondary structure in the region of the GNA33 transcript corresponding to the signal peptide sequence and this, when formed, negatively regulates expression.

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