scholarly journals Characterization of SepL of EnterohemorrhagicEscherichia coli

2000 ◽  
Vol 182 (22) ◽  
pp. 6490-6498 ◽  
Author(s):  
Andreas U. Kresse ◽  
Fabrizio Beltrametti ◽  
Astrid Müller ◽  
Frank Ebel ◽  
Carlos A. Guzmán
Keyword(s):  
Protein Localization ◽  
Open Reading Frames ◽  
Start Codon ◽  
Exponential Growth Phase ◽  
Promoter Sequences ◽  
Enterocyte Effacement ◽  
Extension Analysis ◽  
Reading Frames

ABSTRACT The sepL gene is expressed in the locus of enterocyte effacement and therefore is most likely implicated in the attaching and effacing process, as are the products encoded by open reading frames located up- and downstream of this gene. In this study, thesepL gene of the enterohemorrhagic Escherichia coli (EHEC) strain EDL933 was analyzed and the corresponding polypeptide was characterized. We found that sepL is transcribed monocistronically and independently from theesp operon located downstream, which codes for the secreted proteins EspA, -D, and -B. Primer extension analysis allowed us to identify a single start of transcription 83 bp upstream of thesepL start codon. The analysis of the upstream regions led to the identification of canonical promoter sequences between positions −5 and −36. Translational fusions using lacZ as a reporter gene demonstrated that sepL is activated in the exponential growth phase by stimuli that are characteristic for the intestinal niche, e.g., a temperature of 37°C, a nutrient-rich environment, high osmolarity, and the presence of Mn2+. Protein localization studies showed that SepL was present in the cytoplasm and associated with the bacterial membrane fraction. To analyze the functional role of the SepL protein during infection of eukaryotic cells, an in-frame deletion mutant was generated. ThissepL mutant was strongly impaired in its ability to attach to HeLa cells and induce a local accumulation of actin. These defects were partially restored by providing the sepL gene intrans. The EDL933ΔsepL mutant also exhibited an impaired secretion but not biosynthesis of Esp proteins, which was fully complemented by providing sepL in trans. These results demonstrate the crucial role played by SepL in the biological cycle of EHEC.

scholarly journals Characterization of Baculovirus Repeated Open Reading Frames (bro) in Bombyx moriNucleopolyhedrovirus

1999 ◽  
Vol 73 (12) ◽  
pp. 10339-10345 ◽  
Author(s):  
Wonkyung Kang ◽  
Masataka Suzuki ◽  
Evgueni Zemskov ◽  
Keiju Okano ◽  
Susumu Maeda
Keyword(s):  
Immunohistochemical Analysis ◽  
Immunoblot Analysis ◽  
Open Reading Frames ◽  
Start Codon ◽  
Sequence Analyses ◽  
Reverse Transcription Pcr ◽  
Double Deletion ◽  
Viral Factor ◽  
Reading Frames

ABSTRACT The baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV) contains five related open reading frames (ORFs). Recent sequence analyses of several other baculovirus genomes reveal that these ORFs belong to a unique multigene family called the baculovirus repeated ORFs (bro) family. Here we have characterized these five genes from BmNPV at the transcriptional and translational levels. Reverse transcription-PCR and primer extension analyses indicated that transcription of all bro genes occurs by 2 to 4 h postinfection (p.i.) and reaches maximal levels between at 8 and 12 h p.i. Transcription of all genes is initiated between 50 and 70 nucleotides upstream of the start codon, at a characteristic C(T)AGT motif. Expression of a cat reporter gene under the control of each bro promoter provides evidence that a viral factor(s) is required for the transcription of all brogenes. Immunoblot analysis indicated that a population of BRO proteins is produced vigorously between at 8 and 14 h p.i. Immunohistochemical analysis by confocal microscopy showed that BRO proteins are localized in both the nucleus and the cytoplasm at 8 h p.i. Four BmNPV mutants, in which the bro-a,bro-b, bro-c, and bro-e genes were individually inactivated, were successfully isolated. However, exhaustive efforts failed to isolate a bro-d-deficient mutant. Similarly, it was not possible to isolate a double-deletionbro-a bro-c mutant. The bro-d gene may play an irreplaceable functional role(s) during viral infection, whilebro-a and bro-c may functionally complement each other.

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

scholarly journals Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Chaitanya Erady ◽  
Adam Boxall ◽  
Shraddha Puntambekar ◽  
N. Suhas Jagannathan ◽  
Ruchi Chauhan ◽  
...  
Keyword(s):  
Transcript Level ◽  
Open Reading Frames ◽  
The Cancer Genome Atlas ◽  
Small Subset ◽  
Cancer Tissue ◽  
Post Translational Modifications ◽  
Cancer Genome Atlas ◽  
Systematic Identification ◽  
Reading Frames

AbstractUncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.

scholarly journals Characterization of Chlamydia trachomatis Plasmid-Encoded Open Reading Frames

2013 ◽  
Vol 195 (17) ◽  
pp. 3819-3826 ◽  
Author(s):  
S. Gong ◽  
Z. Yang ◽  
L. Lei ◽  
L. Shen ◽  
G. Zhong
Keyword(s):  
Chlamydia Trachomatis ◽  
Open Reading Frames ◽  
Reading Frames

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

2021 ◽  
Author(s):  
Yang Sun ◽  
Yan qiong Li ◽  
Wen han Dong ◽  
Ai li Sun ◽  
Ning wei Chen ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Open Reading Frames ◽  
The Family ◽  
Significant Amino Acid Sequence ◽  
Overlapping Open Reading Frames ◽  
Significant Amino Acid ◽  
Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

scholarly journals DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

2008 ◽  
Vol 190 (6) ◽  
pp. 2231-2238 ◽  
Author(s):  
Melanie Zaparty ◽  
Alexander Zaigler ◽  
Claudia Stamme ◽  
Jörg Soppa ◽  
Reinhard Hensel ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Dna Microarray ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Heterotrophic Growth ◽  
Thermoproteus Tenax ◽  
Central Carbohydrate Metabolism ◽  
Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

scholarly journals Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon Pyrococcus furiosus

2007 ◽  
Vol 74 (4) ◽  
pp. 1281-1283 ◽  
Author(s):  
Donald A. Comfort ◽  
Chung-Jung Chou ◽  
Shannon B. Conners ◽  
Amy L. VanFossen ◽  
Robert M. Kelly
Keyword(s):  
Glycoside Hydrolase ◽  
Bioinformatics Analysis ◽  
Pyrococcus Furiosus ◽  
Transcriptional Response ◽  
Open Reading Frames ◽  
Processing Enzymes ◽  
Response Information ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.

scholarly journals Characterization of Endogenous Retroviruses in Sheep

2003 ◽  
Vol 77 (20) ◽  
pp. 11268-11273 ◽  
Author(s):  
Nikolai Klymiuk ◽  
Mathias Müller ◽  
Gottfried Brem ◽  
Bernhard Aigner
Keyword(s):  
Endogenous Retrovirus ◽  
Ovis Aries ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
In Vivo Experiments ◽  
Pregnant Sheep ◽  
Reading Frames

ABSTRACT Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV β families and nine OERV γ families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV β family and two OERV γ families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.

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