| 1. |
- Balasubramaniam, Sasitharan, et al.
(författare)
-
Exploiting bacterial properties for multi-hop nanonetworks
- 2014
-
Ingår i: IEEE Communications Magazine. - Piscataway, NJ, USA : IEEE Press. - 0163-6804 .- 1558-1896. ; 52:7, s. 184-191
-
Tidskriftsartikel (refereegranskat)abstract
- Molecular communication is a relatively new communication paradigm for nanomachines where the communication is realized by utilizing existing biological components found in nature. In recent years researchers have proposed using bacteria to realize molecular communication because the bacteria have the ability to swim and migrate between locations, carry DNA contents (i.e. plasmids) that could be utilized for information storage, and interact and transfer plasmids to other bacteria (one of these processes is known as bacterial conjugation). However, current proposals for bacterial nanonetworks have not considered the internal structures of the nanomachines that can facilitate the use of bacteria as an information carrier. This article presents the types and functionalities of nanomachines that can be utilized in bacterial nanonetworks. A particular focus is placed on the bacterial conjugation and its support for multihop communication between nanomachines. Simulations of the communication process have also been evaluated, to analyze the quantity of bits received as well as the delay performances. Wet lab experiments have also been conducted to validate the bacterial conjugation process. The article also discusses potential applications of bacterial nanonetworks for cancer monitoring and therapy. © 2014 IEEE.
|
|
| 2. |
- El Mouali, Youssef, et al.
(författare)
-
Stand-alone EAL domain proteins form a distinct subclass of EAL proteins involved in regulation of cell motility and biofilm formation in enterobacteria
- 2017
-
Ingår i: Journal of Bacteriology. - : American Society for Microbiology. - 0021-9193 .- 1098-5530. ; 199:18
-
Tidskriftsartikel (refereegranskat)abstract
- The second messenger cyclic dimeric GMP (c-di-GMP) is almost ubiquitous among bacteria as are the c-di-GMP turnover proteins, which mediate the transition between motility and sessility. EAL domain proteins have been characterized as c-di-GMP-specific phosphodiesterases. While most EAL domain proteins contain additional, usually N-terminal, domains, there is a distinct family of proteins with stand-alone EAL domains, exemplified by Salmonella enterica serovar Typhimurium proteins STM3611 (YhjH/PdeH), a c-di-GMP-specific phosphodiesterase, and the enzymatically inactive STM1344 (YdiV/CdgR) and STM1697, which regulate bacterial motility through interaction with the flagellar master regulator, FlhDC. We have analyzed the phylogenetic distribution of EAL-only proteins and their potential functions. Genes encoding EAL-only proteins were found in various bacterial phyla, although most of them were seen in proteobacteria, particularly enterobacteria. Based on the conservation of the active site residues, nearly all stand-alone EAL domains encoded by genomes from phyla other than proteobacteria appear to represent functional phosphodiesterases. Within enterobacteria, EAL-only proteins were found to cluster either with YhjH or with one of the subfamilies of YdiV-related proteins. EAL-only proteins from Shigella flexneri, Klebsiella pneumoniae, and Yersinia enterocolitica were tested for their ability to regulate swimming and swarming motility and formation of the red, dry, and rough (rdar) biofilm morphotype. In these tests, YhjH-related proteins S4210, KPN_01159, KPN_03274, and YE4063 displayed properties typical of enzymatically active phosphodiesterases, whereas S1641 and YE1324 behaved like members of the YdiV/STM1697 subfamily, with Yersinia enterocolitica protein YE1324 shown to downregulate motility in its native host. Of two closely related EAL-only proteins, YE2225 is an active phosphodiesterase, while YE1324 appears to interact with FlhD. These results suggest that in FlhDC-harboring beta-and gammaproteobacteria, some EAL-only proteins evolved to become catalytically inactive and regulate motility and biofilm formation by interacting with FlhDC. IMPORTANCE The EAL domain superfamily consists mainly of proteins with cyclic dimeric GMP-specific phosphodiesterase activity, but individual domains have been classified in three classes according to their functions and conserved amino acid signatures. Proteins that consist solely of stand-alone EAL domains cannot rely on other domains to form catalytically active dimers, and most of them fall into one of two distinct classes: catalytically active phosphodiesterases with well-conserved residues of the active site and the dimerization loop, and catalytically inactive YdiV/CdgR-like proteins that regulate bacterial motility by binding to the flagellar master regulator, FlhDC, and are found primarily in enterobacteria. The presence of apparently inactive EAL-only proteins in the bacteria that do not express FlhD suggests the existence of additional EAL interaction partners.
|
|
| 3. |
|
|
| 4. |
- Forsum, Urban, 1946-, et al.
(författare)
-
Methods in molecular biology
- 2004
-
Bok (övrigt vetenskapligt/konstnärligt)abstract
- An accessible introduction to how genomics has and will provide novel methods for bacterial investigation and advance our understanding and knowledge of bacterial pathogenicity. The authors critically evaluate the applications of genomics to diagnostic bacteriology, highlighting both current and likely future uses, describing real-time PCR methods, and outlining the promise of microarrays in clinical bacteriology. Their discussion examines in detail genomic approaches to antibacterial discovery, the nature of pathogenicity, the discovery of new pathogens, the exploration of the concept of clonality in bacteria, and bacterial taxonomics.
|
|
| 5. |
- Happonen, Lotta J., et al.
(författare)
-
BtuB-dependent infection of the T5-like Yersinia phage φr2-01
- 2021
-
Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 13:11, s. 1-18
-
Tidskriftsartikel (refereegranskat)abstract
- Yersinia enterocolitica is a food-borne Gram-negative pathogen responsible for several gastrointestinal disorders. Host-specific lytic bacteriophages have been increasingly used recently as an alternative or complementary treatment to combat bacterial infections, especially when antibiotics fail. Here, we describe the proteogenomic characterization and host receptor identification of the siphovirus vB_YenS_φR2-01 (in short, φR2-01) that infects strains of several Yersinia enterocolitica serotypes. The φR2-01 genome contains 154 predicted genes, 117 of which encode products that are homologous to those of Escherichia bacteriophage T5. The φR2-01 and T5 genomes are largely syntenic, with the major differences residing in areas encoding hypothetical φR2-01 proteins. Label-free massspectrometry-based proteomics confirmed the expression of 90 of the φR2-01 genes, with 88 of these being either phage particle structural or phage-particle-associated proteins. In vitro transposon-based host mutagenesis and φR2-01 adsorption experiments identified the outer membrane vitamin B12 receptor BtuB as the host receptor. This study provides a proteogenomic characterization of a T5-type bacteriophage and identifies specific Y. enterocolitica strains sensitive to infection with possible future applications of φR2-01 as a food biocontrol or phage therapy agent.
|
|
| 6. |
- Ho, Derek K., et al.
(författare)
-
Functional Recruitment of the Human Complement Inhibitor C4BP to Yersinia pseudotuberculosis Outer Membrane Protein Ail
- 2012
-
Ingår i: Journal of Immunology. - : The American Association of Immunologists. - 1550-6606 .- 0022-1767. ; 188:9, s. 4450-4459
-
Tidskriftsartikel (refereegranskat)abstract
- All is a 17-kDa chromosomally encoded outer membrane protein that mediates serum resistance (complement resistance) in the pathogenic Yersiniae (Yersinia pestis, Y. enterocolitica, and Y. pseudotuberculosis). In this article, we demonstrate that Y pseudotuberculosis Ail from strains PB1, 2812/79, and YPIII/pIB1 (serotypes O:1a, O:1b, and O:3, respectively) can bind the inhibitor of the classical and lectin pathways of complement, C4b-binding protein (C4BP). Binding was observed irrespective of serotype tested and independently of YadA, which is the primary C4BP receptor of Y. enterocolitica. Disruption of the a gene in Y. pseudotuberculosis resulted in loss of C4BP binding. Cofactor assays revealed that bound C4BP is functional, because bound C4BP in the presence of factor I cleaved C4b. In the absence of YadA, Ail conferred serum resistance to strains PB1 and YPIII, whereas serum resistance was observed in strain 2812/79 in the absence of both YadA and Ail, suggesting additional serum resistance factors. Ail from strain YPIII/pIB1 alone can mediate serum resistance and C4BP binding, because its expression in a serum-sensitive laboratory strain of Escherichia coli conferred both of these phenotypes. Using a panel of C4BP mutants, each deficient in a single complement control protein domain, we observed that complement control protein domains 6-8 are important for binding to Ail. Binding of C4BP was unaffected by increasing heparin or salt concentrations, suggesting primarily nonionic interactions. These results indicate that Y. pseudotuberculosis Ail recruits C4BP in a functional manner, facilitating resistance to attack from complement. The Journal of Immunology, 2012, 188: 4450-4459.
|
|
| 7. |
- Ho, Derek K., et al.
(författare)
-
Yersinia pestis Ail recruitment of C4b-binding protein leads to factor I- mediated inactivation of covalently and noncovalently bound C4b
- 2014
-
Ingår i: European Journal of Immunology. - : Wiley. - 1521-4141 .- 0014-2980. ; 44:3, s. 742-751
-
Tidskriftsartikel (refereegranskat)abstract
- The outer membrane protein Ail of Yersinia pestis mediates several virulence functions, including serum resistance. Here, we demonstrate that Ail binds C4b-binding protein (C4BP), the primary fluid-phase regulator of the classical and lectin pathways. Non-covalent binding of C4 and C4b to Ail was also observed. C4BP bound to Ail can act as a cofactor to the serine protease factor I (fI) in the cleavage of fluid-phase C4b. Employing a panel of C4BP alpha-chain mutants, we observed that the absence of complement control protein domain 6 and 8 reduced binding to Ail. Immunoblot analysis of normal human serum (NHS)-treated bacteria revealed minimal C4b alpha'-chain complexes with bacterial outer membrane targets. Addition of the anti-C4BP monoclonal antibody MK104 to NHS restored C4b-alpha' chain target complexes, suggesting that C4b binds covalently to targets on the Y. pestis surface. C4b bound to Ail noncovalently was also cleaved in a C4BP and fI-dependent manner, leaving the C4c fragment bound to Ail. MK104 also prevented the cleavage of noncovalently bound C4b. Collectively, these data suggest that when C4BP is bound to Ail, fI can cleave and inactivate C4b that has bound covalently to bacterial surface structures as well as C4b bound noncovalently to Ail.
|
|
| 8. |
- Kirjavainen, Vesa, et al.
(författare)
-
Yersinia enterocolitica serum resistance proteins YadA and Ail bind the complement regulator C4b-binding protein
- 2008
-
Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 4:8
-
Tidskriftsartikel (refereegranskat)abstract
- Many pathogens are equipped with factors providing resistance against the bactericidal action of complement. Yersinia enterocolitica, a Gram-negative enteric pathogen with invasive properties, efficiently resists the deleterious action of human complement. The major Y. enterocolitica serum resistance determinants include outer membrane proteins YadA and Ail. Lipopolysaccharide (LPS) O-antigen (O-ag) and outer core (OC) do not contribute directly to complement resistance. The aim of this study was to analyze a possible mechanism whereby Y. enterocolitica could inhibit the antibody-mediated classical pathway of complement activation. We show that Y. enterocolitica serotypes O:3, O:8, and O:9 bind C4b-binding protein (C4bp), an inhibitor of both the classical and lectin pathways of complement. To identify the C4bp receptors on Y. enterocolitica serotype O:3 surface, a set of mutants expressing YadA, Ail, O-ag, and OC in different combinations was tested for the ability to bind C4bp. The studies showed that both YadA and Ail acted as C4bp receptors. Ail-mediated C4bp binding, however, was blocked by the O-ag and OC, and could be observed only with mutants lacking these LPS structures. C4bp bound to Y. enterocolitica was functionally active and participated in the factor I-mediated degradation of C4b. These findings show that Y. enterocolitica uses two proteins, YadA and Ail, to bind C4bp. Binding of C4bp could help Y. enterocolitica to evade complement-mediated clearance in the human host.
|
|
| 9. |
- Leon-Velarde, Carlos G., et al.
(författare)
-
Yersinia enterocolitica-specific infection by bacteriophages TG1 and φR1-RT is dependent on temperature-regulated expression of the phage host receptor OmpF
- 2016
-
Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 82:17, s. 5340-5353
-
Tidskriftsartikel (refereegranskat)abstract
- Bacteriophages present huge potential both as a resource for developing novel tools for bacterial diagnostics and for use in phage therapy. This potential is also valid for bacteriophages specific for Yersinia enterocolitica. To increase our knowledge of Y. enterocolitica- specific phages, we characterized two novel yersiniophages. The genomes of the bacteriophages vB_YenM_TG1 (TG1) and vB_YenM_φR1-RT (φR1-RT), isolated from pig manure in Canada and from sewage in Finland, consist of linear double-stranded DNA of 162,101 and 168,809 bp, respectively. Their genomes comprise 262 putative coding sequences and 4 tRNA genes and share 91% overall nucleotide identity. Based on phylogenetic analyses of their whole-genome sequences and large terminase subunit protein sequences, a genus named Tg1virus within the family Myoviridae is proposed, with TG1 and φR1-RT (R1RT in the ICTV database) as member species. These bacteriophages exhibit a host range restricted to Y. enterocolitica and display lytic activity against the epidemiologically significant serotypes O:3, O:5,27, and O:9 at and below 25°C. Adsorption analyses of lipopolysaccharide (LPS) and OmpF mutants demonstrate that these phages use both the LPS inner core heptosyl residues and the outer membrane protein OmpF as phage receptors. Based on RNA sequencing and quantitative proteomics, we also demonstrate that temperature-dependent infection is due to strong repression of OmpF at 37°C. In addition, φR1-RT was shown to be able to enter into a pseudolysogenic state. Together, this work provides further insight into phage-host cell interactions by highlighting the importance of understanding underlying factors which may affect the abundance of phage host receptors on the cell surface.
|
|
| 10. |
- Nilsson, Anna, 1986-
(författare)
-
Characterization of Campylobacter jejuni and Campylobacter coli water isolates
- 2018
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Campylobacter jejuni and C. coli are together the most common cause of bacterial gastroenteritis in the European Union. Campylobacter can be transmitted to humans via contaminated water, but it is largely unknown how these bacteria survive in water.The aim of this thesis was to better understand the water survival strategies and pathogenic potential of Campylobacter water isolates. For this purpose, C. jejuni and C. coli, originally isolated from incoming water at surface water plants, were characterized using whole genome sequencing, phenotypical assays, water survival experiments and an in vitro infection model.C. jejuni water isolates included both common and uncommon sequence types for human pathogens, whereas C. coli isolates were assigned to clades 2 and 3, associated with environmental sources. For C. jejuni, comparative genomics revealed genes involved in oxidative and aerobic stress response. In C. coli, various carbon metabolism-related sequences were identified in clade 2 isolates and in clade 3 isolates, oxidative stress and putative virulence genes were detected. All water isolates were motile and the majority of C. jejuni isolates, but none of C. coli isolates, were able to form biofilm. C. jejuni survived better than C. coli in untreated well and lake water. Furthermore, in contrast to C. coli, a seasonal difference in survival was observed for C. jejuni with better survival in lake water collected during autumn than in spring. When tested in an in vitro infection model, all water isolates adhered to and induced IL-8 response in HT-29 cells indicating pathogenic potential. However, C. coli clade 3 isolates demonstrated a strong cytotoxic effect on human HT-29 cells leading to rapid cell death. This novel phenomenon was not observed for C. coli clade 2 or C. jejuni isolates.This is, to the best of our knowledge, the first study on Campylobacter water isolates characterized using genomic, phenotypical and in vitro infection analyses. These findings suggest that some Campylobacter isolates might survive better than others in water and water survival patterns shown here help us further understand the seasonality and predominance of water-related C. jejuni infections.
|
|
| 11. |
- Skurnik, Mikael, et al.
(författare)
-
Bacteriophages fEV-1 and fD1 Infect Yersinia pestis
- 2021
-
Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 13:7
-
Tidskriftsartikel (refereegranskat)abstract
- Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using Yersinia pestis strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for Y. pestis. The host range of fEV-1 was restricted strictly to Y. pestis strains, while that of fD1 also included other members of Enterobacterales such as Escherichia coli and Yersinia pseudotuberculosis. In this study, we present the life cycles, genomes, and proteomes of two Yersinia myoviruses, fEV-1 and fD1.
|
|
| 12. |
- Skurnik, Mikael, et al.
(författare)
-
Characterization of the genome, proteome, and structure of yersiniophage φR1-37
- 2012
-
Ingår i: Journal of Virology. - 0022-538X. ; 86:23, s. 12625-12642
-
Tidskriftsartikel (refereegranskat)abstract
- The bacteriophage vB_YecM-φR1-37 (φR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage φR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of φR1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the φR1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage φKZ. The tail of φR1-37 has a contractile sheath. We conclude that phage φR1-37 is a representative of a novel phage type that carries the dU-containing genome in a φKZ-like head.
|
|
| 13. |
- Zhang, Shu-sheng, et al.
(författare)
-
Plasminogen activator Pla of Yersinia pestis utilizes murine DEC-205 (CD205) as a receptor to promote dissemination
- 2008
-
Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 283:46, s. 31511-21
-
Tidskriftsartikel (refereegranskat)abstract
- Yersinia pestis, a Gram-negative bacterium that causes bubonic and pneumonic plague, is able to rapidly disseminate to other parts of its mammalian hosts. Y. pestis expresses plasminogen activator (PLA) on its surface, which has been suggested to play a role in bacterial dissemination. It has been speculated that Y. pestis hijacks antigen-presenting cells, such as macrophages (MPhis) and dendritic cells, to be delivered to lymph nodes to initiate dissemination and infection. Both alveolar MPhis and pulmonary dendritic cells express a C-type lectin receptor, DEC-205 (CD205), which mediates antigen uptake and presentation. However, no ligand has been identified for DEC-205. In this study, we show that the invasion of alveolar MPhisby Y. pestis depends both in vitro and in vivo on the expression of PLA. DEC-205-expressing MPhis and transfectants, but not their negative counterparts, phagocytosed PLA-expressing Y. pestis and Escherichia coli K12 more efficiently than PLA-negative controls. The interactions between PLA-expressing bacteria and DEC-205-expressing transfectants or alveolar MPhis could be inhibited by an anti-DEC-205 antibody. Importantly, the blockage of the PLA-DEC-205 interaction reduced the dissemination of Y. pestis in mice. In conclusion, murine DEC-205 is a receptor for PLA of Y. pestis, and this host-pathogen interaction appears to play a key role in promoting bacterial dissemination.
|
|
