Identification and characterization of BrxR as a regulatory gene in the BREX phage restriction system

Bacteriophage exclusion (BREX) phage restriction systems are found in a wide range of bacteria. Various BREX systems encode unique combinations of proteins that usually include a site-specific methyltransferase; none appear to contain a nuclease. Here we describe the identification and characterization of a Type I BREX system from Acinetobacter and the effect of deleting each BREX ORF on growth, methylation and phage restriction. The analysis identified a previously uncharacterized gene at the 5-prime end of the BREX operon that is dispensable for methylation but involved in restriction. Biochemical and crystallographic analyses of this factor, which we term BrxR (BREX Regulator), demonstrate that it forms a homodimer and specifically binds a pseudo-palindromic DNA target site upstream of its transcription start site. Precise deletion of the BrxR gene causes cell toxicity, reduces phage restriction, and significantly increases the expression of BrxC. In contrast, the introduction of a premature stop codon into the BrxR gene has little effect, implying that the BrxR coding sequence and BrxR protein have independent functional roles in BREX regulation. We speculate that the BrxR coding sequence is involved in cis regulation of BREX activity and that the BrxR protein may play an additional regulatory role, perhaps during horizontal transfer of the system.

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Ectopic Transcript Analysis Indicates that Allelic Exclusion is an Important Cause of Type I Protein C Deficiency in Patients with Nonsense and Frameshift Mutations in the PROC Gene

Thrombosis and Haemostasis ◽

10.1055/s-0038-1650386 ◽

1996 ◽

Vol 75 (06) ◽

pp. 870-876 ◽

Cited By ~ 4

Author(s):

José Manuel Soria ◽

Lutz-Peter Berg ◽

Jordi Fontcuberta ◽

Vijay V Kakkar ◽

Xavier Estivill ◽

...

Keyword(s):

Splice Site ◽

Protein C ◽

Stop Codon ◽

Premature Stop Codon ◽

Allelic Exclusion ◽

Polymorphism Analysis ◽

Type I ◽

Protein C Deficiency ◽

Nonsense Mutations ◽

Stop Codons

SummaryNonsense mutations, deletions and splice site mutations are a common cause of type I protein C deficiency. Either directly or indirectly by altering the reading frame, these' lesions generate or may generate premature stop codons and could therefore be expected to result in premature termination of translation. In this study, the possibility that such mutations could instead exert their pathological effects at an earlier stage in the expression pathway, through “allelic exclusion” at the RNA level, was investigated. Protein C (PROC) mRNA was analysed in seven Spanish type I protein C deficient patients heterozygous for two nonsense mutations, a 7bp deletion, a 2bp insertion and three splice site mutations. Ectopic RNA transcripts from patient and control lymphocytes were analysed by RT-PCR and direct sequencing of amplified PROC cDNA fragments. The nonsense mutations and the deletion were absent from the cDNAs indicating that only mRNA derived from the normal allele had been expressed. Similarly for the splice site mutations, only normal PROC cDNAs were obtained. In one case, exclusion of the mutated allele could be confirmed by polymorphism analysis. In contrast to these six mutations, the 2 bp insertion was not associated with loss of mRNA from the mutated allele. In this case, cDNA analysis revealed the absence of 19 bases from the PROC mRNA consistent with the generation and utilization of a cryptic splice site 3’ to the site of mutation, which would result in a frameshift and a premature stop codon. It is concluded that allelic exclusion is a common causative mechanism in those cases of type I protein C deficiency which result from mutations that introduce premature stop codons

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Transcriptome-wide Identification and Characterization of microRNAs and Their Targets in a Highly Adaptable Conifer Platycladus orientalis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs05091-21 ◽

2022 ◽

Vol 147 (1) ◽

pp. 7-17

Author(s):

Ying Yang ◽

Xian-Ge Hu ◽

Bingsong Zheng ◽

Yue Li ◽

Tongli Wang ◽

...

Keyword(s):

Stress Tolerance ◽

Leucine Zipper ◽

Class Iii ◽

Conifer Species ◽

Essential Information ◽

Sequencing Platform ◽

Platycladus Orientalis ◽

Wide Range ◽

Identification And Characterization

MicroRNAs (miRNAs) are short noncoding RNAs (20–25 nucleotides) that regulate gene expression posttranscriptionally. However, identification and characterization of miRNAs remain limited for conifer species. In this study, we applied transcriptome-wide miRNAs sequencing to a conifer species Platycladus orientalis, which is highly adaptable to a wide range of environmental adversities, including drought, barren soil, and mild salinity. A total of 17,181,542 raw reads were obtained from the Illumina sequencing platform; 31 conserved and 91 novel miRNAs were identified, and their unique characteristics were further analyzed. Ten randomly selected miRNAs were validated by quantificational real-time polymerase chain reaction. Through miRNA target predictions based on psRNATarget, 2331 unique mRNAs were predicted to be targets of P. orientalis miRNAs that involved in 187 metabolic pathways in KEGG database. These targets included not only important transcription factors (e.g., class III homeodomain leucine zipper targeted by por-miR166d) but also indispensable nontranscriptional factor proteins (i.e., por-miR482a-3p regulated nucleotide-binding site leucine-rich repeat protein). Interestingly, six miRNAs (por-miR16, -miR44, -miR60-5p, -miR69–3p, -miR166b-5p, and -miR395c) were found in adaptation-related pathways (e.g., drought), indicating their possible involved in this species’ stress-tolerance characteristics. The present study provided essential information for understanding the regulatory role of miRNAs in P. orientalis and sheds light on their possible use in tree improvement for stress tolerance.

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Molecular and Cellular Characterization of a New α-Thalassemia Mutation (HBA2:c.94A>C) Generating an Alternative Splice Site and a Premature Stop Codon

Hemoglobin ◽

10.3109/03630269.2012.670683 ◽

2012 ◽

Vol 36 (3) ◽

pp. 244-252 ◽

Cited By ~ 3

Author(s):

Talal Qadah ◽

Jill Finlayson ◽

Christopher Newbound ◽

Nicole Pell ◽

Michelle Pascoe ◽

...

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Stop Codon ◽

Premature Stop Codon ◽

Alternative Splice Site ◽

Thalassemia Mutation

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Aminoglycoside-Induced Premature Stop Codon Read-Through of Mucopolysaccharidosis Type I Patient Q70X and W402X Mutations in Cultured Cells

JIMD Reports - JIMD Reports - Case and Research Reports, Volume 13 ◽

10.1007/8904_2013_270 ◽

2013 ◽

pp. 139-147 ◽

Cited By ~ 14

Author(s):

Makoto Kamei ◽

Karissa Kasperski ◽

Maria Fuller ◽

Emma J. Parkinson-Lawrence ◽

Litsa Karageorgos ◽

...

Keyword(s):

Cultured Cells ◽

Stop Codon ◽

Premature Stop Codon ◽

Type I ◽

Mucopolysaccharidosis Type ◽

Mucopolysaccharidosis Type I

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Genetic variability of spelt factor gene in Triticum and Aegilops species

BMC Plant Biology ◽

10.1186/s12870-020-02536-8 ◽

2020 ◽

Vol 20 (S1) ◽

Author(s):

Valeriya Vavilova ◽

Irina Konopatskaia ◽

Alexandr Blinov ◽

Elena Ya. Kondratenko ◽

Yuliya V. Kruchinina ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Chinese Spring ◽

Stop Codon ◽

Aegilops Tauschii ◽

Premature Stop Codon ◽

Gene Sequences ◽

D Genome ◽

Factor Gene ◽

Spike Shape ◽

Wide Range

Abstract Background Threshability, rachis fragility and spike shape are critical traits for the domestication and evolution of wheat, determining the crop yield and efficiency of the harvest. Spelt factor gene Q controls a wide range of domestication-related traits in polyploid wheats, including those mentioned above. The main goal of the present study was to characterise the Q gene for uninvestigated accessions of wheats, including four endemics, and Aegilops accessions, and to analyze the species evolution based on differences in Q gene sequences. Results We have studied the spike morphology for 15 accessions of wheat species, including four endemics, namely Triticum macha, T. tibetanum, T. aestivum ssp. petropavlovskyi and T. spelta ssp. yunnanense, and 24 Aegilops accessions, which are donors of B and D genomes for polyploid wheat. The Q-5A, q-5D and q-5S genes were investigated, and a novel allele of the Q-5A gene was found in accessions of T. tibetanum (KU510 and KU515). This allele was similar to the Q allele of T. aestivum cv. Chinese Spring but had an insertion 161 bp in length within exon 5. This insertion led to a frameshift and premature stop codon formation. Thus, the T. tibetanum have spelt spikes, which is probably determined by the gene Tg, rather than Q. We determined the variability within the q-5D genes among hexaploid wheat and their D genome donor Aegilops tauschii. Moreover, we studied the accessions C21–5129, KU-2074, and K-1100 of Ae. tauschii ssp. strangulata, which could be involved in the origin of hexaploid wheats. Conclusions The variability and phylogenetic relationships of the Q gene sequences studied allowed us to clarify the relationships between species of the genus Triticum and to predict the donor of the D genome among the Ae. tauschii accessions. Ae. tauschii ssp. strangulata accessions C21–5129, KU-2074 and K-1100 are the most interesting among the analysed accessions, since their partial sequence of q-5D is identical to the q-5D of T. aestivum cv. Chinese Spring. This result indicates that the donor is Ae. tauschii ssp. strangulata but not Ae. tauschii ssp. tauschii. Our analysis allowed us to clarify the phylogenetic relationships in the genus Triticum.

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IDUA mutational profiling of a cohort of 102 European patients with mucopolysaccharidosis type I: identification and characterization of 35 novel α-L-iduronidase (IDUA) alleles

Human Mutation ◽

10.1002/humu.21479 ◽

2011 ◽

Vol 32 (6) ◽

pp. E2189-E2210 ◽

Cited By ~ 44

Author(s):

Francesca Bertola ◽

Mirella Filocamo ◽

Giorgio Casati ◽

Matthew Mort ◽

Camillo Rosano ◽

...

Keyword(s):

Type I ◽

Mucopolysaccharidosis Type ◽

Mucopolysaccharidosis Type I ◽

Mutational Profiling ◽

Identification And Characterization

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Noval Mutation in Four Saudi Families with Glanzmann Thrombasthenia

Blood ◽

10.1182/blood.v118.21.1136.1136 ◽

2011 ◽

Vol 118 (21) ◽

pp. 1136-1136

Author(s):

Tarek Owaidah ◽

Hala Abalkhail ◽

Abdulrahman Al Musa ◽

Hasan Mosmali ◽

Albanyan Abdulmajeed ◽

...

Keyword(s):

Conflicts Of Interest ◽

Stop Codon ◽

Direct Sequencing ◽

Family Members ◽

Premature Stop Codon ◽

Type I ◽

Bleeding Tendency ◽

Coding Region ◽

Glanzmann Thrombasthenia ◽

Exon 1

Abstract Abstract 1136 Introduction: Glanzmann thrombasthenia (GT) is a rare autosomal recessive inherited bleeding disorder characterized by an impaired platelet aggregation and variable bleeding tendency. Inherited genetic mutations in integrin alpha IIb and beta3 (ITGA2B, ITGB3) result in a heterogeneity of the thrombasthenia phenotypes. It is phenotypically expressed in homozygotes or compound heterozygotes, given that 50% of normal aIIbb3 is sufficient to guarantee unimpaired platelet function that result in asymptomatic carriers. Defects in ITGB3 result in failure of binding of B3 and alpha IIb. These defects had been reported in Arabs (Iraqi Jews). We are reporting some results of Saudi GT genotype project. Materials & Methods: In this study, we analyzed the entire coding region ITGB3 gene using polymerase chain reaction (PCR) and direct sequencing with primers specifically designed to amplify the coding region of exon 1–15 and exon /Intron boundaries in a cohort of 51 GT patients diagnosed and treated in our institute. Results: Out of 51 cases from 20 families had mutational screening of the ITGB3 gene with the aim to detect the causative pathogenic mutations to enable the pre-symptomatic diagnosis in at risk family members. In this study we detect 1 novel germline mutation c.2190delC (p.Ser703fs) in exon 13. The mutation is predicted to result in premature stop codon and protein truncation. The mutation was detected in 6 patients in homozygous stat (3 males and 3 females). Three tested samples from the patients family members detected the mutation in heterozygous state and all of them were asymptomatic with normal PFA and Intact expression of Platelet Glycoprotiens CD41(Gpllb), CD42a(GPIX), CD42b(GPlb), and CD61(Gpllla). All the GT patients with this mutation were type I GT with Prolonged PFA and complete absence of CD41(Gpllb) and CD61(Gpllla) glycoprotein. Conclusion: The result of this study represents the first Molecular analysis of ITGB3 gene in Saudi Arabia and displays the existence of novel pathogenic and possibly a founder effect in Saudi families. Disclosures: No relevant conflicts of interest to declare.

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