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 smORFer: a modular algorithm to detect small ORFs in prokaryotes

2020 ◽  
Author(s):  
Alexander Bartholomäus ◽  
Baban Kolte ◽  
Ayten Mustafayeva ◽  
Ingrid Goebel ◽  
Stephan Fuchs ◽  
...  
Keyword(s):  
Integrated Approach ◽  
Structural Features ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Data Sets ◽  
Physiological Processes ◽  
Small Proteins ◽  
Prokaryotic Genomes ◽  
Modular Algorithm ◽  
Reading Frames

ABSTRACTEmerging evidence places small proteins (≤ 50 amino acids) more centrally in physiological processes. Yet, the identification of functional small proteins and the systematic genome annotation of their cognate small open reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. Yet, they have difficulties evaluating prokaryotic genomes due to the unique architecture of prokaryotic genomes (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present our new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting smORFs. The unique feature of smORFer is that it uses integrated approach and considers structural features of the genetic sequence along with in-register translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way and dependent on the data available for a particular organism allows using different modules for smORF search.

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.

scholarly journals Genetic locus for the biosynthesis of the variable portion of Neisseria gonorrhoeae lipooligosaccharide.

1994 ◽  
Vol 180 (6) ◽  
pp. 2181-2190 ◽  
Author(s):  
E C Gotschlich
Keyword(s):  
Inner Core ◽  
Genetic Locus ◽  
Structural Features ◽  
Open Reading Frames ◽  
Gene Deletions ◽  
Reading Frame ◽  
Glycosyl Transferases ◽  
Strong Homology ◽  
Gonococcal Strain ◽  
Reading Frames

A locus involved in the biosynthesis of gonococcal lipooligosaccharide (LOS) has been cloned from gonococcal strain F62. The locus contains five open reading frames. The first and second reading frames are homologous, but not identical, to the fourth and fifth reading frames, respectively. Interposed is an additional reading frame which has distant homology to the Escherichia coli rfaI and rfaI genes, both glucosyl transferases involved in lipopolysaccharide core biosynthesis. The second and fifth reading frames show strong homology to the lex-1 or lic2A gene of Haemophilus influenzae, but do not contain the CAAT repeats found in this gene. Deletions of each of these five genes, of combinations of genes, and of the entire locus were constructed and introduced into parental gonococcal strain F62 by transformation. The LOS phenotypes were then analyzed by SDS-PAGE and reactivity with monoclonal antibodies. Analysis of the gonococcal mutants indicates that four of these genes are the glycosyl transferases that add GalNAc beta 1-->3Gal beta 1-->4GlcNAc beta 1-->3 Gal beta 1--4 to the substrate Glc beta 1-->4Hep--R of the inner core region. The gene with homology to E. coli rfaI/rfaI is involved with the addition of the alpha-linked galactose residue in the biosynthesis of the alternative LOS structure Gal alpha 1-->4Gal beta 1-->4Glc beta 1-->4Hep-->R. Since these genes encode LOS glycosyl transferases they have been named lgtA, lgtB, lgtC, lgtD, and lgtE. The DNA sequence analysis revealed that lgtA, lgtC, and lgtD contained poly-G tracts, which, in strain F62 were, respectively, 17, 10, and 11 bp. Thus, three of the LOS biosynthetic enzymes are potentially susceptible to premature termination by reading frame changes. It is likely that these structural features are responsible for the high-frequency genetic variation of gonococcal LOS.

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 Bacteriophage and Phenotypic Variation in Pseudomonas aeruginosa Biofilm Development

2004 ◽  
Vol 186 (23) ◽  
pp. 8066-8073 ◽  
Author(s):  
Jeremy S. Webb ◽  
Mathew Lau ◽  
Staffan Kjelleberg
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Phenotypic Variation ◽  
Open Reading Frames ◽  
Agar Media ◽  
Small Colony ◽  
Biofilm Development ◽  
And Function ◽  
Postsegregational Killing ◽  
Reading Frames ◽  
A Current

ABSTRACT A current question in biofilm research is whether biofilm-specific genetic processes can lead to differentiation in physiology and function among biofilm cells. In Pseudomonas aeruginosa, phenotypic variants which exhibit a small-colony phenotype on agar media and a markedly accelerated pattern of biofilm development compared to that of the parental strain are often isolated from biofilms. We grew P. aeruginosa biofilms in glass flow cell reactors and observed that the emergence of small-colony variants (SCVs) in the effluent runoff from the biofilms correlated with the emergence of plaque-forming Pf1-like filamentous phage (designated Pf4) from the biofilm. Because several recent studies have shown that bacteriophage genes are among the most highly upregulated groups of genes during biofilm development, we investigated whether Pf4 plays a role in SCV formation during P. aeruginosa biofilm development. We carried out immunoelectron microscopy using anti-Pf4 antibodies and observed that SCV cells, but not parental-type cells, exhibited high densities of Pf4 filaments on the cell surface and that these filaments were often tightly interwoven into complex latticeworks surrounding the cells. Moreover, infection of P. aeruginosa planktonic cultures with Pf4 caused the emergence of SCVs within the culture. These SCVs exhibited enhanced attachment, accelerated biofilm development, and large regions of dead and lysed cells inside microcolonies in a manner identical to that of SCVs obtained from biofilms. We concluded that Pf4 can mediate phenotypic variation in P. aeruginosa biofilms. We also performed partial sequencing and analysis of the Pf4 replicative form and identified a number of open reading frames not previously recognized in the genome of P. aeruginosa, including a putative postsegregational killing operon.

scholarly journals Synthesis, Stability, and Function of Cytadhesin P1 and Accessory Protein B/C Complex of Mycoplasma pneumoniae

2006 ◽  
Vol 188 (2) ◽  
pp. 569-575 ◽  
Author(s):  
Robert H. Waldo ◽  
Duncan C. Krause
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Frameshift Mutation ◽  
Open Reading Frames ◽  
Transcriptional Unit ◽  
Multiprotein Complex ◽  
Wild Type ◽  
C Proteins ◽  
C Complex ◽  
And Function ◽  
Reading Frames

ABSTRACT The genes MPN141 and MPN142 encode the major adhesin P1 and the cytadherence-related B/C proteins (P90/P40), respectively, in Mycoplasma pneumoniae. Using reverse transcriptase PCR we found open reading frames MPN140 to MPN142 constitute a polycistronic transcriptional unit. Cytadherence mutant IV-22 has a frameshift mutation in MPN141 and lacks the P1, B, or C proteins. Recombinant MPN141 and/or MPN142 were introduced into mutant IV-22 by transposon delivery in several configurations, and the levels of the P1, B, and C proteins were assessed by immunoblotting. MPN142 in mutant IV-22 has a wild-type nucleotide sequence, yet the introduction of recombinant MPN141 alone to mutant IV-22, although it restored P1 levels, failed to restore levels of B or C. In contrast, recombinant MPN141 and MPN142 delivered in cis or in trans were sufficient to restore all three proteins. Taken together, our data indicated that some but not all synthesis of B or C is dependent on coupling to the translation of P1 immediately upstream of MPN142 and demonstrated that proteins B and C are not stable in the absence of P1. The linkage of MPN141 and MPN142 at the levels of transcription, translation, and protein stability, in addition to their previously demonstrated colocalization and the requirement of B and/or C for P1 function, reinforces the conclusion that these proteins constitute a multiprotein complex that functions in receptor binding.

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 Comparative Genome Analysis of Four Magnetotactic Bacteria Reveals a Complex Set of Group-Specific Genes Implicated in Magnetosome Biomineralization and Function

2007 ◽  
Vol 189 (13) ◽  
pp. 4899-4910 ◽  
Author(s):  
Michael Richter ◽  
Michael Kube ◽  
Dennis A. Bazylinski ◽  
Thierry Lombardot ◽  
Frank Oliver Glöckner ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Complete Genome ◽  
Core Genome ◽  
Magnetotactic Bacteria ◽  
Open Reading Frames ◽  
Field Lines ◽  
And Function ◽  
Magnetospirillum Magnetotacticum ◽  
Magnetospirillum Magneticum ◽  
Reading Frames

ABSTRACT Magnetotactic bacteria (MTB) are a heterogeneous group of aquatic prokaryotes with a unique intracellular organelle, the magnetosome, which orients the cell along magnetic field lines. Magnetotaxis is a complex phenotype, which depends on the coordinate synthesis of magnetosomes and the ability to swim and orient along the direction caused by the interaction with the Earth's magnetic field. Although a number of putative magnetotaxis genes were recently identified within a conserved genomic magnetosome island (MAI) of several MTB, their functions have remained mostly unknown, and it was speculated that additional genes located outside the MAI might be involved in magnetosome formation and magnetotaxis. In order to identify genes specifically associated with the magnetotactic phenotype, we conducted comparisons between four sequenced magnetotactic Alphaproteobacteria including the nearly complete genome of Magnetospirillum gryphiswaldense strain MSR-1, the complete genome of Magnetospirillum magneticum strain AMB-1, the complete genome of the magnetic coccus MC-1, and the comparative-ready preliminary genome assembly of Magnetospirillum magnetotacticum strain MS-1 against an in-house database comprising 426 complete bacterial and archaeal genome sequences. A magnetobacterial core genome of about 891 genes was found shared by all four MTB. In addition to a set of approximately 152 genus-specific genes shared by the three Magnetospirillum strains, we identified 28 genes as group specific, i.e., which occur in all four analyzed MTB but exhibit no (MTB-specific genes) or only remote (MTB-related genes) similarity to any genes from nonmagnetotactic organisms and which besides various novel genes include nearly all mam and mms genes previously shown to control magnetosome formation. The MTB-specific and MTB-related genes to a large extent display synteny, partially encode previously unrecognized magnetosome membrane proteins, and are either located within (18 genes) or outside (10 genes) the MAI of M. gryphiswaldense. These genes, which represent less than 1% of the 4,268 open reading frames of the MSR-1 genome, as yet are mostly of unknown functions but are likely to be specifically involved in magnetotaxis and, thus, represent prime targets for future experimental analysis.

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