scholarly journals Structure and function of the region of the replication origin of theBacillus subtilischromosome. IV. Transcription of theoriCregion and expression of DNA gyrase genes and other open reading frames

1985 ◽  
Vol 13 (7) ◽  
pp. 2267-2279 ◽  
Author(s):  
Naotake Ogasawara ◽  
Shigeki Moriya ◽  
Hiroshi Yoshikawa
Keyword(s):  
Replication Origin ◽  
Dna Gyrase ◽  
Structure And Function ◽  
Open Reading Frames ◽  
And Function ◽  
Reading Frames

scholarly journals Functional analysis of cT-DNAs in naturally transformed plants, recent findings and general considerations

2016 ◽  
Vol 14 (4) ◽  
pp. 26
Author(s):  
Léon Otten
Keyword(s):  
Structure And Function ◽  
Open Reading Frames ◽  
Biologically Active ◽  
Rolc Gene ◽  
Origin And Evolution ◽  
Transformed Plants ◽  
Growth Changes ◽  
And Function ◽  
Very High ◽  
Reading Frames

Several cases have been reported of naturally transformed plant species. These plants contain cellular T-DNAs (cT-DNAs) derived from ancient infections by Agrobacterium. We have determined the structure of 4 different cT-DNAs in N. tomentosiformis, the paternal ancestor of N. tabacum, and found several intact open reading frames. Among these, TB-mas2’ and TA-rolC were tested for activity. TB-mas2’ encodes desoxyfructosylglutamine (DFG) synthesis. Some N. tabacum cultivars show very high TB-mas2’ expression and produce DFG in their roots. The TA-rolC gene is biologically active and when expressed under strong constitutive promoter control, generates growth changes in N. tabacum. Based on these first data on the structure and function of cT-DNAs I present a theoretical model on the origin and evolution of naturally transformed plants, which may serve as a basis for further research in this field.

scholarly journals Peptide-Induced Amyloid-Like Conformational Transitions in Proteins

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Vladimir Egorov ◽  
Natalia Grudinina ◽  
Andrey Vasin ◽  
Dmitry Lebedev
Keyword(s):  
Protein Conformation ◽  
Conformational Transitions ◽  
Structural Features ◽  
Open Reading Frames ◽  
Short Peptides ◽  
Disease Pathogenesis ◽  
Conformational Diseases ◽  
Physiological Processes ◽  
And Function ◽  
Reading Frames

Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function.

scholarly journals Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8356
Author(s):  
Darrin T. Schultz ◽  
Jordan M. Eizenga ◽  
Russell B. Corbett-Detig ◽  
Warren R. Francis ◽  
Lynne M. Christianson ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Hypothesis Test ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Intergenic Sequence ◽  
Computational Tools ◽  
Protein Coding ◽  
Bayesian Hypothesis Test ◽  
And Function ◽  
Reading Frames

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

Prediction and functional analysis of the replication origin of the linear plasmid pSCL2 inStreptomyces clavuligerus

2006 ◽  
Vol 52 (4) ◽  
pp. 293-300 ◽  
Author(s):  
Wei Wu ◽  
Shannon K. D Leblanc ◽  
James Piktel ◽  
Susan E Jensen ◽  
Kenneth L Roy
Keyword(s):  
Amino Acids ◽  
Functional Analysis ◽  
Replication Origin ◽  
Streptomyces Clavuligerus ◽  
Replication Initiation ◽  
Open Reading Frames ◽  
Linear Plasmid ◽  
Replication Proteins ◽  
Bacterial Plasmid ◽  
Reading Frames

pSCL2 (120 kb), one of the linear plasmids found in Streptomyces clavuligerus NRRL3585, was isolated and partially sequenced. Computational analysis of the central region of pSCL2 revealed the presence of two open reading frames that appear to encode proteins highly homologous to RepL1 and RepL2, replication proteins from pSLA2-L, the large linear plasmid in Streptomyces rochei. The S. clavuligerus open reading frames were designated repC1 and repC2, encoding the proteins RepC1 (150 amino acids) and RepC2 (102 amino acids), respectively. The RepC and RepL proteins have identical translation features and very similar predicted secondary and tertiary structures. Functional analysis confirmed that RepC1 is essential for replication initiation of pSCL2, whereas RepC2 is dispensable but may play a role in copy number control. The RepC and RepL proteins do not show similarity to any other bacterial plasmid replication proteins. Three regions of DNA sequence, Box 1 (1050–850 bp), Box 2 (723–606 bp), and Box 3 (224–168 bp), located upstream of repC1, were also shown to be essential or very important for replication of pSCL2.Key words: pSCL2, Streptomyces clavuligerus, replication origin.

scholarly journals New Small, Acid-Soluble Proteins Unique to Spores ofBacillus subtilis: Identification of the Coding Genes and Regulation and Function of Two of These Genes

1998 ◽  
Vol 180 (24) ◽  
pp. 6704-6712 ◽  
Author(s):  
Irina Bagyan ◽  
Barbara Setlow ◽  
Peter Setlow
Keyword(s):  
Rna Polymerase ◽  
Mother Cell ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Soluble Proteins ◽  
Open Reading Frames ◽  
Coding Regions ◽  
Spore Outgrowth ◽  
And Function ◽  
Reading Frames

ABSTRACT Eleven small, acid-soluble proteins (SASP) which are present in spores but not in growing cells of Bacillus subtilis were identified by sequence analysis of proteins separated by acrylamide gel electrophoresis of acid extracts from spores which lack the three major SASP (α, β, and γ). Six of these proteins are encoded by open reading frames identified previously or by analysis of the complete sequence of the B. subtilis genome, including two minor α/β-type SASP (SspC and SspD) and a putative spore coat protein (CotK). Five proteins are encoded by short open reading frames that were not identified as coding regions in the analysis of the completeB. subtilis genomic sequence. Studies of the regulation of two of the latter genes, termed sspG and sspJ, showed that both are expressed only in sporulation. ThesspG gene is transcribed in the mother cell compartment by RNA polymerase with the mother cell-specific sigma factor for RNA polymerase, ςK, and is cotranscribed with a downstream gene, yurS; sspG transcription also requires the DNA binding protein GerE. In contrast, sspJ is transcribed in the forespore compartment by RNA polymerase with the forespore-specific ςG and appears to give a monocistronic transcript. A mutation eliminating SspG had no effect on sporulation or spore properties, while loss of SspJ caused a slight decrease in the rate of spore outgrowth in an otherwise wild-type background.

scholarly journals Structure and Function of the Campylobacter jejuni Chromosome Replication Origin

2018 ◽  
Vol 9 ◽  
Author(s):  
Pawel Jaworski ◽  
Rafal Donczew ◽  
Thorsten Mielke ◽  
Christoph Weigel ◽  
Kerstin Stingl ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Replication Origin ◽  
Chromosome Replication ◽  
Structure And Function ◽  
And Function
Sign in / Sign up

Export Citation Format

Share Document