scholarly journals Comparative Genomics of Streptococcus thermophilus Phage Species Supports a Modular Evolution Theory

1999 ◽  
Vol 73 (10) ◽  
pp. 8647-8656 ◽  
Author(s):  
Sacha Lucchini ◽  
Frank Desiere ◽  
Harald Brüssow
Keyword(s):  
Dna Recombination ◽  
Point Mutations ◽  
Streptococcus Thermophilus ◽  
Tail Fiber ◽  
Dna Repeats ◽  
Modular Evolution ◽  
Fiber Protein ◽  
Variable Domains ◽  
Replication Region ◽  
Fiber Gene

ABSTRACT The comparative analysis of five completely sequencedStreptococcus thermophilus bacteriophage genomes demonstrated that their diversification was achieved by a combination of DNA recombination events and an accumulation of point mutations. The five phages included lytic and temperate phages, both pacsite and cos site, from three distinct geographical areas. The units of genetic exchange were either large, comprising the entire morphogenesis gene cluster, excluding the putative tail fiber genes, or small, consisting of one or maximally two genes or even segments of a gene. Many indels were flanked by DNA repeats. Differences in a single putative tail fiber gene correlated with the host ranges of the phages. The predicted tail fiber protein consisted of highly conserved domains containing conspicuous glycine repeats interspersed with highly variable domains. As in the T-even coliphage adhesins, the glycine-containing domains were recombinational hot spots. Downstream of a highly conserved DNA replication region, all lytic phages showed a short duplication; in three isolates the origin of replication was repeated. The lytic phages could conceivably be derived from the temperate phages by deletion and multiple rearrangement events in the lysogeny module, giving rise to occasional selfish phages that defy the superinfection control systems of the corresponding temperate phages.

scholarly journals DNA Inversion in the Tail Fiber Gene Alters the Host Range Specificity of Carotovoricin Er, a Phage-Tail-Like Bacteriocin of Phytopathogenic Erwinia carotovora subsp.carotovora Er

2001 ◽  
Vol 183 (21) ◽  
pp. 6274-6281 ◽  
Author(s):  
Hoa Anh Nguyen ◽  
Toshio Tomita ◽  
Morihiko Hirota ◽  
Jun Kaneko ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Host Range ◽  
Erwinia Carotovora ◽  
Tail Fiber ◽  
Chromosomal Dna ◽  
Tail Fiber Protein ◽  
Dna Inversion ◽  
Phage Tail ◽  
Fiber Protein ◽  
Invertase Gene ◽  
Fiber Gene

ABSTRACT Carotovoricin Er is a phage-tail-like bacteriocin produced byErwinia carotovora subsp. carotovorastrain Er, a causative agent for soft rot disease in plants. Here we studied binding and killing spectra of carotovoricin Er preparations for various strains of the bacterium (strains 645Ar, EC-2, N786, and P7) and found that the preparations contain two types of carotovoricin Er with different host specificities; carotovoricin Era possessing a tail fiber protein of 68 kDa killed strains 645Ar and EC-2, while carotovoricin Erb with a tail fiber protein of 76 kDa killed strains N786 and P7. The tail fiber proteins of 68 and 76 kDa had identical N-terminal amino acid sequences for at least 11 residues. A search of the carotovoricin Er region in the chromosome of strain Er indicated the occurrence of a DNA inversion system for the tail fiber protein consisting of (i) two 26-bp inverted repeats inside and downstream of the tail fiber gene that flank a 790-bp fragment and (ii) a putative DNA invertase gene with a 90-bp recombinational enhancer sequence. In fact, when a 1,400-bp region containing the 790-bp fragment was amplified by a PCR using the chromosomal DNA of strain Er as the template, both the forward and the reverse nucleotide sequences of the 790-bp fragment were detected. DNA inversion of the 790-bp fragment also occurred in Escherichia coli DH5α when two compatible plasmids carrying either the 790-bp fragment or the invertase gene were cotransformed into the bacterium. Furthermore, hybrid carotovoricin CGE possessing the tail fiber protein of 68 or 76 kDa exhibited a host range specificity corresponding to that of carotovoricin Era or Erb, respectively. Thus, a DNA inversion altered the C-terminal part of the tail fiber protein of carotovoricin Er, altering the host range specificity of the bacteriocin.

Nonlytic Recombinant Phage Tail Fiber Protein for Specific Recognition of Pseudomonas aeruginosa

2018 ◽  
Vol 90 (24) ◽  
pp. 14462-14468 ◽  
Author(s):  
Yong He ◽  
Yanli Shi ◽  
Mengli Liu ◽  
Yingran Wang ◽  
Lin Wang ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Tail Fiber ◽  
Tail Fiber Protein ◽  
Recombinant Phage ◽  
Specific Recognition ◽  
Phage Tail ◽  
Fiber Protein

scholarly journals Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract

2020 ◽  
Author(s):  
Sabrina I. Green ◽  
Carmen Gu Liu ◽  
Xue Yu ◽  
Shelley Gibson ◽  
Wilhem Salmen ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Chemical Properties ◽  
Protein Product ◽  
Lytic Cycle ◽  
Tail Fiber ◽  
Bacterial Host ◽  
Intestinal Mucus ◽  
Mucosal Surfaces ◽  
Epithelial Cell Surface ◽  
Fiber Gene

AbstractThe human mucosal surface consists of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. Bacteriophage parasitize the prokaryotes but are not known to associate with eukaryotic cells. In the gastrointestinal tract, the interaction of these two domains influences the health of the host, especially colonization with invasive pathobionts. Antibiotics may be used but they also kill protective commensals and lack the physio-chemical properties to be specifically and optimally active in this complex milieu. Here, we report a novel phage whose lytic cycle is enhanced in intestinal environments. The enhanced activity is encoded in its tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, thereby positioning it near its bacterial host, a type of locational targeting mechanism. This finding offers the prospect of developing epithelial-targeting phage to selectively remove invasive pathobiont species from mucosal surfaces.Graphical AbstractModel showing (1) mucins from the intestinal mucus layer inhibit phage infection, (2) phage ES17 can bind to mucin and utilize other intestinal glycans as a receptor to infect and kill mucus-coated bacteria, and (3) phages like ES17 can be utilized to coat the intestinal epithelium by binding heparan sulfate glycans to protect from invasive pathogen infection.

scholarly journals Uncoupling of the apyrimidinic/apurinic endonucleolytic and 3′→5′ exonucleolytic activities of the Nfo protein of Mycoplasma pneumoniae through mutation of specific amino acid residues

Microbiology ◽  
2014 ◽  
Vol 160 (6) ◽  
pp. 1087-1100 ◽  
Author(s):  
Silvia Estevão ◽  
Pieternella E. van der Spek ◽  
Annemarie M. C. van Rossum ◽  
Cornelis Vink
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Divalent Cations ◽  
Single Point ◽  
Dna Recombination ◽  
Point Mutations ◽  
Mycoplasma Genitalium ◽  
Amino Acid Residues ◽  
Specific Amino Acid ◽  
Cleavage Activity ◽  
Ap Sites

The DNA recombination and repair machineries of Mycoplasma pneumoniae and Mycoplasma genitalium were predicted to consist of a set of ~11 proteins. The function of one of these proteins was inferred from its homology with proteins belonging to the Endo IV enzyme family. The members of this family function in the repair of apyrimidinic/apurinic (AP) sites in DNA. As such activity may be crucial in the mycoplasmal life cycle, we set out to study the Endo IV-like proteins encoded by M. pneumoniae and M. genitalium. Both proteins, termed Nfo Mpn and Nfo Mge , respectively, were assessed for their ability to interact with damaged and undamaged DNA. In the absence of divalent cations, both proteins exhibited specific cleavage of AP sites. Surprisingly, the proteins also recognized and cleaved cholesteryl-bound deoxyribose moieties in DNA, showing that these Nfo proteins may also function in repair of large DNA adducts. In the presence of Mg2+, Nfo Mpn and Nfo Mge also showed 3′→5′ exonucleolytic activity. By introduction of 13 single point mutations at highly conserved positions within Nfo Mpn , two major types of mutants could be distinguished: (i) mutants that showed no, or limited, AP cleavage activity in the presence of EDTA, but displayed significant levels of AP cleavage activity in the presence of Mg2+; these mutants displayed no, or very low, exonucleolytic activity; and (ii) mutants that only demonstrated marginal levels of AP site cleavage activity in the presence of Mg2+ and did not show exonucleolytic activity. Together, these results indicated that the AP endonucleolytic activity of the Nfo Mpn protein can be uncoupled from its 3′→5′ exonucleolytic activity.

scholarly journals Molecular dissection of pheromone selectivity in the competence signaling system ComRS of streptococci

2020 ◽  
Vol 117 (14) ◽  
pp. 7745-7754
Author(s):  
Laura Ledesma-Garcia ◽  
Jordhan Thuillier ◽  
Armando Guzman-Espinola ◽  
Imke Ensinck ◽  
Inès Li de la Sierra-Gallay ◽  
...  
Keyword(s):  
Biomedical Applications ◽  
Rational Design ◽  
Mutational Analysis ◽  
Point Mutations ◽  
Streptococcus Thermophilus ◽  
Activation Mechanism ◽  
Toggle Switch ◽  
Exogenous Dna ◽  
C Terminus ◽  
Molecular Determinants

Competence allows bacteria to internalize exogenous DNA fragments for the acquisition of new phenotypes such as antibiotic resistance or virulence traits. In most streptococci, competence is regulated by ComRS signaling, a system based on the mature ComS pheromone (XIP), which is internalized to activate the (R)RNPP-type ComR sensor by triggering dimerization and DNA binding. Cross-talk analyses demonstrated major differences of selectivity between ComRS systems and raised questions concerning the mechanism of pheromone-sensor recognition and coevolution. Here, we decipher the molecular determinants of selectivity of the closely related ComRS systems fromStreptococcus thermophilusandStreptococcus vestibularis. Despite high similarity, we show that the divergence in ComR-XIP interaction does not allow reciprocal activation. We perform the structural analysis of the ComRS system fromS. vestibularis.Comparison with its ortholog fromS. thermophilusreveals an activation mechanism based on a toggle switch involving the recruitment of a key loop by the XIP C terminus. Together with a broad mutational analysis, we identify essential residues directly involved in peptide binding. Notably, we generate a ComR mutant that displays a fully reversed selectivity toward the heterologous pheromone with only five point mutations, as well as other ComR variants featuring XIP bispecificity and/or neofunctionalization for hybrid XIP peptides. We also reveal that a single XIP mutation relaxes the strictness of ComR activation, suggesting fast adaptability of molecular communication phenotypes. Overall, this study is paving the way toward the rational design or directed evolution of artificial ComRS systems for a range of biotechnological and biomedical applications.

Tail Fiber Protein-Immobilized Magnetic Nanoparticle-Based Affinity Approaches for Detection of Acinetobacter baumannii

2019 ◽  
Vol 91 (15) ◽  
pp. 10335-10342 ◽  
Author(s):  
Yi-Ling Bai ◽  
Md. Shahed-Al-Mahmud ◽  
Karuppuchamy Selvaprakash ◽  
Nien-Tsung Lin ◽  
Yu-Chie Chen
Keyword(s):  
Acinetobacter Baumannii ◽  
Magnetic Nanoparticle ◽  
Tail Fiber ◽  
Tail Fiber Protein ◽  
Fiber Protein

scholarly journals Characterization of Streptococcus thermophilus Host Range Phage Mutants

2006 ◽  
Vol 72 (4) ◽  
pp. 3036-3041 ◽  
Author(s):  
Martin Duplessis ◽  
Céline M. Lévesque ◽  
Sylvain Moineau
Keyword(s):  
Host Range ◽  
Point Mutations ◽  
Streptococcus Thermophilus ◽  
Structural Proteins ◽  
Laser Desorption Ionization ◽  
Wild Type ◽  
Ionization Time ◽  
Host Interactions ◽  
Flight Mass Spectrometry

ABSTRACT To investigate phage-host interactions in Streptococcus thermophilus, a phage-resistant derivative (SMQ-301R) was obtained by challenging a Tn917 library of phage-sensitive strain S. thermophilus SMQ-301 with virulent phage DT1. Mutants of phages DT1 and MD2 capable of infecting SMQ-301 and SMQ-301R were isolated at a frequency of 10−6. Four host range phage mutants were analyzed further and compared to the two wild-type phages. Altogether, three genes (orf15, orf17, and orf18) contained point mutations leading to amino acid substitutions and were responsible for the expanded host range. These three proteins were also identified in both phages by N-terminal sequencing and/or matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. The results suggest that at least three phage structural proteins may be involved in phage-host interactions in S. thermophilus.

scholarly journals Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34

Viruses ◽  
2017 ◽  
Vol 9 (7) ◽  
pp. 168 ◽  
Author(s):  
Meritxell Granell ◽  
Mikiyoshi Namura ◽  
Sara Alvira ◽  
Shuji Kanamaru ◽  
Mark van Raaij
Keyword(s):  
Crystal Structure ◽  
Bacteriophage T4 ◽  
Terminal Region ◽  
Tail Fiber ◽  
Tail Fiber Protein ◽  
Long Tail ◽  
Fiber Protein ◽  
Carboxy Terminal Region ◽  
Carboxy Terminal
Sign in / Sign up

Export Citation Format

Share Document