scholarly journals Molecular characterization of lengthy mitochondrial DNA duplications from the parasitic nematode Romanomermis culicivorax.

Genetics ◽  
1993 ◽  
Vol 133 (4) ◽  
pp. 933-942
Author(s):  
J L Azevedo ◽  
B C Hyman
Keyword(s):  
Mitochondrial Dna ◽  
Repeat Unit ◽  
Nucleotide Sequences ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Mermithid Nematode ◽  
And Inversion ◽  
Coding Potential ◽  
Reading Frames

Abstract Complete nucleotide sequences, precise endpoints and coding potential of several 3.0-kilobase mitochondrial DNA (mtDNA) repeating units derived from two isofemale lineages of the mermithid nematode Romanomermis culicivorax have been determined. Endpoint analysis has allowed us to infer deletion and inversion events that most likely generated the present day repeat configuration. Each amplified unit contains the genes for NADH dehydrogenase subunits 3 and 6 (ND3 and ND6), an open reading frame (ORF 1) that represents a cytochrome P450-like gene, and three additional unidentified open reading frames. The primary nucleotide sequences of the R. culicivorax mt-repeat copies within individual haplotypes are highly conserved; three nearly complete copies of the repeat unit vary by 0.01% at the nucleotide level. These observations suggest that concerted evolution mechanisms may be active, resulting in sequence homogenation of these lengthy duplications.

Molecular characterization of the genome of a partitivirus from the basidiomycete Rhizoctonia solani

Microbiology ◽  
2000 ◽  
Vol 81 (2) ◽  
pp. 549-555 ◽  
Author(s):  
Ethan E. Strauss ◽  
Dilip K. Lakshman ◽  
Stellos M. Tavantzis
Keyword(s):  
Rhizoctonia Solani ◽  
Molecular Mass ◽  
Rna Virus ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Subgenomic Rna ◽  
Atkinsonella Hypoxylon ◽  
Coding Potential ◽  
Reading Frames

The bisegmented genome of a double-stranded (ds) RNA virus from the fungus Rhizoctonia solani isolate Rhs 717 was characterized. The larger segment, dsRNA 1, is 2363 bases long whereas the smaller segment, dsRNA 2, has 2206 bases. The 5′ ends of the coding strands of dsRNA 1 and dsRNA 2 are highly conserved (100% identity over 47 bases), and contain inverted repeats capable of forming stable stem–loop structures. Analysis of the coding potential of each of the two segments showed that dsRNAs 1 and 2 could code for polypeptides of 730 aa (bases 86–2275; molecular mass 86 kDa) and 683 aa (bases 79–2130; molecular mass 76 kDa), respectively. The 86 kDa polypeptide has all the motifs of dsRNA RNA-dependent RNA polymerases (RDRP), and has significant homology with putative RDRPs of partitiviruses from Fusarium poae and Atkinsonella hypoxylon. The 76 kDa protein shows homology with the putative capsid proteins (CP) of the same viruses. Northern blot analysis revealed no subgenomic RNA species, consistent with the fact that the long open reading frames encoding the putative RDRP and CP cover the entire length of the respective dsRNAs.

scholarly journals Characterization of a Cytosolic NiFe-Hydrogenase from the Hyperthermophilic Archaeon Thermococcus kodakaraensis KOD1

2003 ◽  
Vol 185 (5) ◽  
pp. 1705-1711 ◽  
Author(s):  
Tamotsu Kanai ◽  
Sota Ito ◽  
Tadayuki Imanaka
Keyword(s):  
Polyclonal Antibodies ◽  
Open Reading Frames ◽  
Hydrogenase Activity ◽  
Putative Open Reading Frame ◽  
Electron Carrier ◽  
Reading Frame ◽  
Hyperthermophilic Archaeon ◽  
Acid Labile ◽  
Reading Frames

ABSTRACT We have identified an NiFe-hydrogenase exclusively localized in the cytoplasm of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (T. kodakaraensis hydrogenase). A gene cluster encoding T. kodakaraensis hydrogenase was composed of four open reading frames (hyhBGSLTk ), where the hyhSTk and hyhLTk gene products corresponded to the small and the large subunits of NiFe-hydrogenase, respectively. A putative open reading frame for hydrogenase-specific maturation endopeptidase (hybDTk ) was found downstream of the cluster. Polyclonal antibodies raised against recombinant HyhL Tk were used for immunoaffinity purification of T. kodakaraensis hydrogenase, leading to a 259-fold concentration of hydrogenase activity. The purified T. kodakaraensis hydrogenase was composed of four subunits (β, γ, δ, and α), corresponding to the products of hyhBGSLTk , respectively. Each αβγδ unit contained 0.8 mol of Ni, 22.3 mol of Fe, 21.1 mol of acid-labile sulfide, and 1.01 mol of flavin adenine dinucleotide. The optimal temperature for the T. kodakaraensis hydrogenase was 95°C for H2 uptake and 90°C for H2 production with methyl viologen as the electron carrier. We found that NADP+ and NADPH promoted high levels of uptake and evolution of H2, respectively, suggesting that the molecule is the electron carrier for the T. kodakaraensis hydrogenase.

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 Alternative processing of RNA transcribed from NMYC.

1987 ◽  
Vol 7 (12) ◽  
pp. 4266-4272 ◽  
Author(s):  
L W Stanton ◽  
J M Bishop
Keyword(s):  
Alternative Splicing ◽  
Open Reading Frames ◽  
Structure And Stability ◽  
Alternative Processing ◽  
Coding Potential ◽  
Reading Frames

NMYC is a gene whose amplification and overexpression have been implicated in the generation of certain human malignancies. Little is known of how the expression of NMYC is normally controlled. We have therefore characterized transcription from the gene and the structure and stability of the resulting mRNAs. Transcription from NMYC is exceptionally complex: it initiates at numerous sites that may be grouped under the control of two promoters, and the multiplicity of initiation sites combines with alternative splicing to engender two forms of mRNA. The mRNAs have different 5' leader sequences (alternative first exons of the gene) but identical bodies (the second and third exons of the gene). Both forms of mRNA are unstable, with half-lives of ca. 15 min. Both encode the previously identified 65,000 and 67,000-dalton products of NMYC. However, the alternative first exons contain distinctive open reading frames that may diversify the coding potential of NMYC. The complexities in transcription of NMYC expand the means by which expression of the gene might be controlled.

scholarly journals Genomic Sequence of Rhesus Cytomegalovirus 180.92: Insights into the Coding Potential of Rhesus Cytomegalovirus

2006 ◽  
Vol 80 (8) ◽  
pp. 4179-4182 ◽  
Author(s):  
Pierre Rivailler ◽  
Amitinder Kaur ◽  
R. Paul Johnson ◽  
Fred Wang
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Rhesus Cytomegalovirus ◽  
Human Cmv ◽  
Coding Capacity ◽  
Coding Potential ◽  
Reading Frames ◽  
Genetic Rearrangements

ABSTRACT A pathogenic isolate of rhesus cytomegalovirus (rhCMV 180.92) was cloned, sequenced, and annotated. Comparisons with the published rhCMV 68.1 genome revealed 8 open reading frames (ORFs) in isolate 180.92 that are absent in 68.1, 10 ORFs in 68.1 that are absent in 180.92, and 34 additional ORFs that were not previously annotated. Most of the differences appear to be due to genetic rearrangements in both isolates from a region that is frequently altered in human CMV (hCMV) during in vitro passage. These results indicate that the rhCMV ORF repertoire is larger than previously recognized. Like hCMV, understanding of the complete coding capacity of rhCMV is complicated by genomic instability and may require comparisons with additional isolates in vitro and in vivo.

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

The positive regulatory function of the 5'-proximal open reading frames in GCN4 mRNA can be mimicked by heterologous, short coding sequences

1988 ◽  
Vol 8 (9) ◽  
pp. 3827-3836
Author(s):  
N P Williams ◽  
P P Mueller ◽  
A G Hinnebusch
Keyword(s):  
Translational Control ◽  
Normal Growth ◽  
Regulatory Elements ◽  
Growth Conditions ◽  
Open Reading Frames ◽  
Regulatory Function ◽  
Yeast Saccharomyces Cerevisiae ◽  
Reading Frame ◽  
Yeast Genes ◽  
Reading Frames

Translational control of GCN4 expression in the yeast Saccharomyces cerevisiae is mediated by multiple AUG codons present in the leader of GCN4 mRNA, each of which initiates a short open reading frame of only two or three codons. Upstream AUG codons 3 and 4 are required to repress GCN4 expression in normal growth conditions; AUG codons 1 and 2 are needed to overcome this repression in amino acid starvation conditions. We show that the regulatory function of AUG codons 1 and 2 can be qualitatively mimicked by the AUG codons of two heterologous upstream open reading frames (URFs) containing the initiation regions of the yeast genes PGK and TRP1. These AUG codons inhibit GCN4 expression when present singly in the mRNA leader; however, they stimulate GCN4 expression in derepressing conditions when inserted upstream from AUG codons 3 and 4. This finding supports the idea that AUG codons 1 and 2 function in the control mechanism as translation initiation sites and further suggests that suppression of the inhibitory effects of AUG codons 3 and 4 is a general consequence of the translation of URF 1 and 2 sequences upstream. Several observations suggest that AUG codons 3 and 4 are efficient initiation sites; however, these sequences do not act as positive regulatory elements when placed upstream from URF 1. This result suggests that efficient translation is only one of the important properties of the 5' proximal URFs in GCN4 mRNA. We propose that a second property is the ability to permit reinitiation following termination of translation and that URF 1 is optimized for this regulatory function.

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.

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