scholarly journals Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C

2017 ◽  
Author(s):  
Maria A Prostova ◽  
Andrei A Deviatkin ◽  
Irina O Tcelykh ◽  
Alexander N Lukashev ◽  
Anatoly P Gmyl
Keyword(s):  
Amino Acid ◽  
Genome Stability ◽  
Rna Binding ◽  
Apical Region ◽  
Reading Frame ◽  
Loop Region ◽  
Binding Partners ◽  
D Loop ◽  
The One ◽  
Species Specific

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.

scholarly journals Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C

2017 ◽  
Author(s):  
Maria A Prostova ◽  
Andrei A Deviatkin ◽  
Irina O Tcelykh ◽  
Alexander N Lukashev ◽  
Anatoly P Gmyl
Keyword(s):  
Amino Acid ◽  
Genome Stability ◽  
Rna Binding ◽  
Apical Region ◽  
Reading Frame ◽  
Loop Region ◽  
Binding Partners ◽  
D Loop ◽  
The One ◽  
Species Specific

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.

scholarly journals Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C

2017 ◽  
Author(s):  
Maria A Prostova ◽  
Andrey A Deviatkin ◽  
Irina O Tcelykh ◽  
Alexander N Lukashev ◽  
Anatoly P Gmyl
Keyword(s):  
Amino Acid ◽  
Genome Stability ◽  
Rna Binding ◽  
Apical Region ◽  
Reading Frame ◽  
Loop Region ◽  
Binding Partners ◽  
D Loop ◽  
The One ◽  
Species Specific

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity that allows virus to adapt to changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides) that were present in the NCBI database on February 2017 and analyzed variety and abundance of sequences in domain d of replicative element oriL and in the protein 3C. Results. A total of 2842 full genome sequences were analyzed. Majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). Putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion. Despite RNA-binding tripeptide is suggested to interact with apical region of domain d, they evolve independently in nature. Together, our data indicates plastic evolution of both interplayers of 3C-oriL recognition.

scholarly journals Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3896 ◽  
Author(s):  
Maria A. Prostova ◽  
Andrei A. Deviatkin ◽  
Irina O. Tcelykh ◽  
Alexander N. Lukashev ◽  
Anatoly P. Gmyl
Keyword(s):  
Amino Acid ◽  
Genome Stability ◽  
Rna Binding ◽  
Virus Protein ◽  
Apical Region ◽  
Reading Frame ◽  
Loop Region ◽  
Binding Partners ◽  
D Loop ◽  
Species Specific

BackgroundEnteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein.MethodsTo evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6, 400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C.ResultsA total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y = U/C, N = any nucleotide, H = A/C/U). The putative RNA-binding tripeptide 154–156 (Enterovirus C3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.DiscussionDespite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.

scholarly journals Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

scholarly journals Species-Specific Recognition of Sulfolobales Mediated by UV-Inducible Pili and S-Layer Glycosylation Patterns

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Marleen van Wolferen ◽  
Asif Shajahan ◽  
Kristina Heinrich ◽  
Susanne Brenzinger ◽  
Ian M. Black ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Genome Stability ◽  
Binding Pocket ◽  
Dna Double Strand Breaks ◽  
Content Type ◽  
Strand Breaks ◽  
Type Iv ◽  
Self Recognition ◽  
The One ◽  
Species Specific

ABSTRACT The UV-inducible pili system of Sulfolobales (Ups) mediates the formation of species-specific cellular aggregates. Within these aggregates, cells exchange DNA to repair DNA double-strand breaks via homologous recombination. Substitution of the Sulfolobus acidocaldarius pilin subunits UpsA and UpsB with their homologs from Sulfolobus tokodaii showed that these subunits facilitate species-specific aggregation. A region of low conservation within the UpsA homologs is primarily important for this specificity. Aggregation assays in the presence of different sugars showed the importance of N-glycosylation in the recognition process. In addition, the N-glycan decorating the S-layer of S. tokodaii is different from the one of S. acidocaldarius. Therefore, each Sulfolobus species seems to have developed a unique UpsA binding pocket and unique N-glycan composition to ensure aggregation and, consequently, also DNA exchange with cells from only the same species, which is essential for DNA repair by homologous recombination. IMPORTANCE Type IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The UV-inducible pili system of Sulfolobales (Ups) pili from the crenarchaeal Sulfolobales species are essential in establishing species-specific mating partners, thereby assisting in genome stability. With this work, we show that different Sulfolobus species have specific regions in their Ups pili subunits, which allow them to interact only with cells from the same species. Additionally, different Sulfolobus species have unique surface-layer N-glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.

scholarly journals Species-specific recognition of Sulfolobales mediated by UV-inducible pili and S-layer glycosylation patterns

2019 ◽  
Author(s):  
Marleen van Wolferen ◽  
Asif Shajahan ◽  
Kristina Heinrich ◽  
Susanne Brenzinger ◽  
Ian M. Black ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Genome Stability ◽  
Binding Pocket ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Type Iv ◽  
Self Recognition ◽  
The One ◽  
Species Specific ◽  
First Time

AbstractThe UV-inducible pili system of Sulfolobales (Ups) mediates the formation of species-specific cellular aggregates. Within these aggregates, cells exchange DNA in order to repair DNA double strand breaks via homologous recombination. Substitution of theS. acidocaldariuspilin subunits UpsA and UpsB with their homologs fromSulfolobus tokodaiishowed that these subunits facilitate species-specific aggregation. A region of low conservation within the UpsA homologs is primarily important for this specificity. Aggregation assays in the presence of different sugars showed the importance ofN-glycosylation in the recognition process. In addition, theN-glycan decorating the S-layer ofS. tokodaiiis different from the one ofS. acidocaldarius. Therefore, eachSulfolobusspecies seems to have developed a unique UpsA binding pocket and uniqueN-glycan composition to ensure aggregation and consequently also DNA exchange with cells from only the same species, which is essential for DNA repair by homologous recombination.ImportanceType IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The Ups-pili from the crenarchaeal Sulfolobales species are essential in establishing species-specific mating partners, ensuring genome stability. With this work, we show that differentSulfolobusspecies have species-specific regions in their Ups-pilin subunits, which allow them to interact only with cells from the same species. Additionally, differentSulfolobusspecies all have unique S-layerN-glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.

scholarly journals Identification of Girella punctata and G. leonina by PCR-RFLP analysis

2006 ◽  
Vol 64 (2) ◽  
pp. 328-331 ◽  
Author(s):  
Shiro Itoi ◽  
Takashi Saito ◽  
Mai Shimojo ◽  
Sayaka Washio ◽  
Haruo Sugita
Keyword(s):  
Rflp Analysis ◽  
Morphological Identification ◽  
Similar Species ◽  
Sequencing Analysis ◽  
Electrophoretic Patterns ◽  
Loop Region ◽  
Site Mapping ◽  
Pcr Rflp ◽  
D Loop ◽  
Species Specific

Abstract Itoi, S., Saito, T., Shimojo, M., Washio, S., and Sugita, H. 2007. Identification of Girella punctata and G. leonina by PCR-RFLP analysis. – ICES Journal of Marine Science, 64: 328–331. Two Girella species, Girella punctata and G. leonina, are sympatric sister species with an extensive overlap in their respective distributions on shallow rocky reefs from Hong Kong to the south of the Japanese Islands. Juveniles of the two species cannot be discriminated easily on the basis of external characters. In this study, after morphological identification of the species, sequencing analysis was carried out for the partial 16S ribosomal RNA gene and for the D-loop region in mitochondrial DNA. A total of 109 specimens was examined. Restriction site mapping of the sequences suggested that the electrophoretic patterns of polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) analysis of the gene products would produce a species-specific banding pattern. Subsequently, the PCR-RFLP analysis showed that the method was as effective for separating the two morphologically similar species of the genus Girella as the sequencing analysis.

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