Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction–modification systems

Microbiology ◽  
2003 ◽  
Vol 149 (11) ◽  
pp. 3311-3319 ◽  
Author(s):  
Monika Adamczyk-Popławska ◽  
Aneta Kondrzycka ◽  
Katarzyna Urbanek ◽  
Andrzej Piekarowicz
Keyword(s):  
Amino Acid ◽  
Tandem Repeats ◽  
Molecular Evidence ◽  
Type I ◽  
High Identity ◽  
E Coli ◽  
Wide Range ◽  
Type Ia ◽  
Restriction Modification

All known type I restriction and modification (R–M) systems of Escherichia coli and Salmonella enterica belong to one of four discrete families: type IA, IB, IC or ID. The classification of type I systems from a wide range of other genera is mainly based on complementation and molecular evidence derived from the comparison of the amino acid similarity of the corresponding subunits. This affiliation was seldom based on the strictest requirement for membership of a family, which depends on relatedness as demonstrated by complementation tests. This paper presents data indicating that the type I NgoAV R–M system from Neisseria gonorrhoeae, despite the very high identity of HsdM and HsdR subunits with members of the type IC family, does not show complementation with E. coli type IC R–M systems. Sequence analysis of the HsdS subunit of several different potential type IC R–M systems shows that the presence of different tetra-amino-acid sequence repeats, e.g. TAEL, LEAT, SEAL, TSEL, is characteristic for type IC R–M systems encoded by distantly related bacteria. The other regions of the HsdS subunits potentially responsible for subunit interaction are also different between a group of distantly related bacteria, but show high similarity within these bacteria. Complementation between the NgoAV R–M system and members of the EcoR124 R–M family can be restored by changing the tetra-amino-acid repeat within the HsdS subunit. The authors propose that the type IC family of R–M systems could consist of several complementation subgroups whose specificity would depend on differences in the conserved regions of the HsdS polypeptide.

scholarly journals A Single Adaptive Mutation in Sodium Taurocholate Cotransporting Polypeptide Induced by Hepadnaviruses Determines Virus Species Specificity

2018 ◽  
Vol 93 (5) ◽  
Author(s):  
Junko S. Takeuchi ◽  
Kento Fukano ◽  
Masashi Iwamoto ◽  
Senko Tsukuda ◽  
Ryosuke Suzuki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Virus Infection ◽  
Positive Selection ◽  
Sodium Taurocholate ◽  
Arms Race ◽  
Adaptive Mutation ◽  
Molecular Evidence ◽  
Adaptive Mutations ◽  
Wide Range ◽  
Coevolutionary Arms Race

ABSTRACTHepatitis B virus (HBV) and its hepadnavirus relatives infect a wide range of vertebrates, from fish to human. Hepadnaviruses and their hosts have a long history of acquiring adaptive mutations. However, there are no reports providing direct molecular evidence for such a coevolutionary “arms race” between hepadnaviruses and their hosts. Here, we present evidence suggesting that the adaptive evolution of the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, has been influenced by virus infection. Evolutionary analysis of the NTCP-encoding genes from 20 mammals showed that most NTCP residues are highly conserved among species, exhibiting evolution under negative selection (dN/dSratio [ratio of nonsynonymous to synonymous evolutionary changes] of <1); this observation implies that the evolution of NTCP is restricted by maintaining its original protein function. However, 0.7% of NTCP amino acid residues exhibit rapid evolution under positive selection (dN/dSratio of >1). Notably, a substitution at amino acid (aa) 158, a positively selected residue, converting the human NTCP to a monkey-type sequence abrogated the capacity to support HBV infection; conversely, a substitution at this residue converting the monkey Ntcp to the human sequence was sufficient to confer HBV susceptibility. Together, these observations suggested a close association of the aa 158 positive selection with the pressure by virus infection. Moreover, the aa 158 sequence determined attachment of the HBV envelope protein to the host cell, demonstrating the mechanism whereby HBV infection would create positive selection at this NTCP residue. In summary, we provide the first evidence in agreement with the function of hepadnavirus as a driver for inducing adaptive mutation in host receptor.IMPORTANCEHBV and its hepadnavirus relatives infect a wide range of vertebrates, with a long infectious history (hundreds of millions of years). Such a long history generally allows adaptive mutations in hosts to escape from infection while simultaneously allowing adaptive mutations in viruses to overcome host barriers. However, there is no published molecular evidence for such a coevolutionary arms race between hepadnaviruses and hosts. In the present study, we performed coevolutionary phylogenetic analysis between hepadnaviruses and the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, combined with virological experimental assays for investigating the biological significance of NTCP sequence variation. Our data provide the first molecular evidence supporting that HBV-related hepadnaviruses drive adaptive evolution in the NTCP sequence, including a mechanistic explanation of how NTCP mutations determine host viral susceptibility. Our novel insights enhance our understanding of how hepadnaviruses evolved with their hosts, permitting the acquisition of strong species specificity.

scholarly journals Methylation by multiple type I restriction modification systems avoids influencing gene regulation in uropathogenic Escherichia coli

2021 ◽  
Author(s):  
Kurosh S Mehershahi ◽  
Swaine Chen
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Dna Methylation ◽  
Gene Regulation ◽  
Detectable Effect ◽  
Epigenetic Mark ◽  
Type I ◽  
E Coli ◽  
Restriction Modification ◽  
Restriction Modification Systems

DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life, extending also to bacterial virulence. Both orphan methyltransferases and those from restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. However, the potential regulatory role of DNA methylation mediated by archetypal Type I systems in Escherichia coli has never been studied. We demonstrated that removal of DNA methylated mediated by three different Escherichia coli Type I RMSs in three distinct E. coli strains had no detectable effect on gene expression or growth in a screen of 1190 conditions. Additionally, deletion of the Type I RMS EcoUTI in UTI89, a prototypical cystitis strain of E. coli , which led to loss of methylation at >750 sites across the genome, had no detectable effect on virulence in a murine model of ascending urinary tract infection (UTI). Finally, introduction of two heterologous Type I RMSs into UTI89 also resulted in no detectable change in gene expression or growth phenotypes. These results stand in sharp contrast with many reports of RMSs regulating gene expression in other bacteria, leading us to propose the concept of “regulation avoidance” for these E. coli Type I RMSs. We hypothesize that regulation avoidance is a consequence of evolutionary adaptation of both the RMSs and the E. coli genome. Our results provide a clear and (currently) rare example of regulation avoidance for Type I RMSs in multiple strains of E. coli , further study of which may provide deeper insights into the evolution of gene regulation and horizontal gene transfer.

scholarly journals Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses

2021 ◽  
Author(s):  
Winnie Thabisa Ramaloko ◽  
John Osei Sekyere
Keyword(s):  
Bacterial Infections ◽  
One Health ◽  
Phylogenetic Analyses ◽  
Restriction Enzymes ◽  
Type I ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli ◽  
Meta Analyses ◽  
Restriction Modification

Gram-negative bacteria (GNB) continue to develop resistance against important antibiotics including last-resort ones such as carbapenems and polymyxins. An analysis of GNB with co-resistance to carbapenems and polymyxins from a One Health perspective is presented. Data of species name, country, source of isolation, resistance genes (ARGs), plasmid type, clones, and mobile genetic elements (MGEs) were deduced from 129 articles from January 2016 to March 2021. Available genomes and plasmids were obtained from PATRIC and NCBI. Resistomes and methylomes were analysed using BAcWGSTdb and REBASE whilst Kaptive was used to predict capsule typing. Plasmids and other MEGs were identified using MGE Finder and ResFinder. Phylogenetic analyses were done using RAxML and annotated with MEGA 7. A total of 877 isolates, 32 genomes and 44 plasmid sequences were analysed. Most of these isolates were reported in Asian countries and were isolated from clinical, animal, and environmental sources. Colistin resistance was mostly mediated by mgrB inactivation, while OXA-48/181 was the most reported carbapenemase. IncX and IncI were the most common plasmids hosting carbapenemases and mcr genes. The isolates were co-resistant to other antibiotics, with floR (chloramphenicol) and fosA3 (fosfomycin) being common; E. coli ST156 and K. pneumoniae ST258 strains were common globally. Virulence genes and capsular KL-types were also detected. Type I, II, III and IV restriction modification systems were detected, comprising various MTases and restriction enzymes. The escalation of highly resistant isolates drains the economy due to untreatable bacterial infections, which leads to increasing global mortality rates and healthcare costs.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

2006 ◽  
Vol 24 (3) ◽  
pp. 181-190 ◽  
Author(s):  
Fangqing Zhao ◽  
Xiaowen Zhang ◽  
Chengwei Liang ◽  
Jinyu Wu ◽  
Qiyu Bao ◽  
...  
Keyword(s):  
Positive Selection ◽  
Draft Genome ◽  
Gene Clusters ◽  
Pcr Analysis ◽  
Type I ◽  
Type Ii ◽  
Filamentous Cyanobacteria ◽  
Modification System ◽  
Wide Range ◽  
Restriction Modification

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e.g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

scholarly journals Elements of secondary structure in a human epithelial mucin core peptide fragment

1990 ◽  
Vol 267 (3) ◽  
pp. 733-737 ◽  
Author(s):  
S J B Tendler
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Tandem Repeats ◽  
Type I ◽  
Peptide Fragment ◽  
Trans Form ◽  
Beta Turn ◽  
Acid Fragment ◽  
Core Peptide ◽  
Turn Region

The protein core of human epithelial mucin has previously been shown to consist of tandem repeats of a 20-amino-acid sequence that carries the epitopes for a number of tumour-marking monoclonal antibodies. High-field n.m.r. studies have now been undertaken on an 11-amino-acid fragment of this sequence dissolved in dimethyl sulphoxide. The studies reveal elements of secondary structure to be present: a type I beta-turn has been identified from Asp2 to Arg4 of this peptide, and this turn is extended by Pro5 being in the trans form. The observed turn region extends into the known epitopes for the antibodies C595 and NCRC-11 and may form the basis for how the antibodies recognize these peptides.

scholarly journals Cloning, Expression, and Characterization of a Novel Thermophilic Monofunctional Catalase fromGeobacillussp. CHB1

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Xianbo Jia ◽  
Jichen Chen ◽  
Chenqiang Lin ◽  
Xinjian Lin
Keyword(s):  
Amino Acid ◽  
Specific Activity ◽  
Fermentation Broth ◽  
Residual Activity ◽  
Industrial Applications ◽  
Activity Level ◽  
High Yield ◽  
E Coli ◽  
Wide Range ◽  
Clone And Express

Catalases are widely used in many scientific areas. A catalase gene (Kat) fromGeobacillussp. CHB1 encoding a monofunctional catalase was cloned and recombinant expressed inEscherichia coli(E. coli), which was the first time to clone and express this type of catalase ofgenus Geobacillusstrains as far as we know. ThisKatgene was 1,467 bp in length and encoded a catalase with 488 amino acid residuals, which is only 81% similar to the previously studiedBacillussp. catalase in terms of amino acid sequence. Recombinant catalase was highly soluble inE. coliand made up 30% of the totalE. coliprotein. Fermentation broth of the recombinantE. colishowed a high catalase activity level up to 35,831 U/mL which was only lower than recombinantBacillussp. WSHDZ-01 among the reported catalase production strains. The purified recombinant catalase had a specific activity of 40,526 U/mg andKmof 51.1 mM. The optimal reaction temperature of this recombinant enzyme was 60°C to 70°C, and it exhibited high activity over a wide range of reaction temperatures, ranging from 10°C to 90°C. The enzyme retained 94.7% of its residual activity after incubation at 60°C for 1 hour. High yield and excellent thermophilic properties are valuable features for this catalase in industrial applications.

Diversity within the Campylobacter jejuni type I restriction–modification loci

Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 337-351 ◽  
Author(s):  
William G. Miller ◽  
Bruce M. Pearson ◽  
Jerry M. Wells ◽  
Craig T. Parker ◽  
Vladimir V. Kapitonov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Campylobacter Jejuni ◽  
Gene Organization ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Type I ◽  
New Genes ◽  
Or Gene ◽  
H Pylori ◽  
Restriction Modification

The type I restriction–modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA–H (R-linked ORF) and mloA–B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R–M systems are assigned to one of three families: ‘IAB’, ‘IC’ or ‘IF’. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The ‘IC’ hsd loci are >99 % identical at the nucleotide level, as are the ‘IF’ hsd loci. Additionally, whereas the nucleotide sequences of the ‘IAB’ hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the ‘IAB’ hsdS and rlo genes vary considerably. This diversity suggests that recombination between ‘IAB’ hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R–M systems is discussed.

scholarly journals Pseudohypoparathyroidism: Diagnosis and Treatment

2011 ◽  
Vol 96 (10) ◽  
pp. 3020-3030 ◽  
Author(s):  
Giovanna Mantovani
Keyword(s):  
Evidence Synthesis ◽  
Diagnostic Procedures ◽  
Type I ◽  
Epigenetic Alterations ◽  
Molecular Alterations ◽  
Gnas Gene ◽  
Type Ia ◽  
Pubmed Search ◽  
Actual Classification

Abstract Context: The term pseudohypoparathyroidism (PHP) indicates a group of heterogeneous disorders whose common feature is represented by impaired signaling of various hormones (primarily PTH) that activate cAMP-dependent pathways via Gsα protein. The two main subtypes of PHP, PHP type Ia, and Ib (PHP-Ia, PHP-Ib) are caused by molecular alterations within or upstream of the imprinted GNAS gene, which encodes Gsα and other translated and untranslated products. Evidence acquisition: A PubMed search was used to identify the available studies (main query terms: pseudohypoparathyroidism; Albright hereditary osteodystrophy; GNAS; GNAS1; progressive osseous heteroplasia). The most relevant studies until February 2011 have been included in the review. Evidence synthesis and conclusions: Despite the first description of this disorder dates back to 1942, recent findings indicating complex epigenetic alterations beside classical mutations at the GNAS complex gene, pointed out the limitation of the actual classification of the disease, resulting in incorrect genetic counselling and diagnostic procedures, as well as the gap in our actual knowledge of the pathogenesis of these disorders. This review will focus on PHP type I, in particular its diagnosis, classification, treatment, and underlying molecular alterations.

scholarly journals Systematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors

2018 ◽  
Author(s):  
Ernest Mordret ◽  
Avia Yehonadav ◽  
Georgina D Barnabas ◽  
Jürgen Cox ◽  
Orna Dahan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Error Rates ◽  
Mass Spectrometry Data ◽  
Single Amino Acid ◽  
Post Translational Modification ◽  
E Coli ◽  
Wide Range ◽  
Proteome Level ◽  
Mechanistic Basis ◽  
Translation Errors

Translation errors limit the accuracy of information transmission from DNA to proteins. Selective pressures shape the way cells produce their proteins: the translation machinery and the mRNA sequences it decodes co-evolved to ensure that translation proceeds fast and accurately in a wide range of environmental conditions. Our understanding of the causes of amino acid misincorporations and of their effect on the evolution of protein sequences is largely hindered by the lack of experimental methods to observe errors at the full proteome level. Here, we systematically detect and quantify errors in entire proteomes from mass spectrometry data. Following HPLC MS-MS data acquisition, we identify E. coli and S. cerevisiae peptides whose mass and fragment ion spectrum are consistent with that of a peptide bearing a single amino acid substitution, and verify that such spectrum cannot result from a post-translational modification. Our analyses confirm that most substitutions occur due to codon-to-anticodon mispairing within the ribosome. Patterns of errors due to mispairing were similar in bacteria and yeast, suggesting that the error spectrum is chemically constrained. Treating E. coli cells with a drug known to affect ribosomal proofreading increased the error rates due to mispairing at the wobble codon position. Starving bacteria for serine resulted in specific patterns of substitutions reflecting the amino acid deficiency. Overall, translation errors tend to occur at positions that are less evolutionarily conserved, and that minimally affect protein energetic stability, indicating that they are selected against. Genome wide ribosome density data suggest that errors occur at sites where ribosome velocity is relatively high, supporting the notion of a trade-off between speed and accuracy as predicted by proofreading theories. Together our results reveal a mechanistic basis for ribosome errors in translation.

scholarly journals Functional characterization of the type I toxin Lpt from Lactobacillus rhamnosus by fluorescence and atomic force microscopy

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefano Maggi ◽  
Korotoum Yabre ◽  
Alberto Ferrari ◽  
Camilla Lazzi ◽  
Mitsuoki Kawano ◽  
...  
Keyword(s):  
Amino Acid ◽  
Surface Defects ◽  
Fluorescent Protein ◽  
Functional Characterization ◽  
Lactobacillus Rhamnosus ◽  
Type I ◽  
Force Microscopy ◽  
E Coli ◽  
Atomic Force ◽  
Α Helix

Abstract Lpt is a 29 amino acid long type I toxin identified in the plasmid DNA of wild Lactobacillus rhamnosus strains isolated from food. We previously reported that transcription of the encoding gene was upregulated under nutritional starvation conditions mimicking cheese ripening environment. The heterologous expression of the Lpt peptide in E. coli resulted in cell growth inhibition, nucleoid condensation and compromised integrity of the cell membrane. Fusion of the Lpt peptide with the fluorescent protein mCherry allowed to visualize the accumulation of the peptide into the membrane, while mutagenesis experiments showed that either the insertion of a negatively charged amino acid into the hydrophobic α-helix or deletion of the hydrophilic C-terminal region, leads to a non-toxic peptide. AFM imaging of Lpt expressing E. coli cells has revealed the presence of surface defects that are compatible with the loss of portions of the outer membrane bilayer. This observation provides support for the so-called “carpet” model, by which the Lpt peptide is supposed to destabilize the phospholipid packing through a detergent-like mechanism leading to the removal of small patches of bilayer through micellization.

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