Bioinformatic analysis reveals that some bacteria may aid SARS–CoV-2 spread and entry into host cells

The Type VI Secretion System (T6SS) has important roles relating to bacterial antagonism, subversion of host cells, and niche colonisation. Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis worldwide and is a commensal coloniser of birds. Although recently discovered, the T6SS biological functions and identities of its effectors are still poorly defined in C. jejuni. Here, we perform a comprehensive bioinformatic analysis of the C. jejuni T6SS by investigating the prevalence and genetic architecture of the T6SS in 513 publicly available genomes using C. jejuni 488 strain as reference. A unique and conserved T6SS cluster associated with the Campylobacter jejuni Integrated Element 3 (CJIE3) was identified in the genomes of 117 strains. Analyses of the T6SS-positive 488 strain against the T6SS-negative C. jejuni RM1221 strain and the T6SS-positive plasmid pCJDM202 carried by C. jejuni WP2-202 strain defined the “T6SS-containing CJIE3” as a pathogenicity island, thus renamed as Campylobacter jejuni Pathogenicity Island-1 (CJPI-1). Analysis of CJPI-1 revealed two canonical VgrG homologues, CJ488_0978 and CJ488_0998, harbouring distinct C-termini in a genetically variable region downstream of the T6SS operon. CJPI-1 was also found to carry a putative DinJ-YafQ Type II toxin-antitoxin (TA) module, conserved across pCJDM202 and the genomic island CJIE3, as well as several open reading frames functionally predicted to encode for nucleases, lipases, and peptidoglycan hydrolases. This comprehensive in silico study provides a framework for experimental characterisation of T6SS-related effectors and TA modules in C. jejuni.

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ORF4 of the Temperate Archaeal Virus SNJ1 Governs the Lysis-Lysogeny Switch and Superinfection Immunity

Journal of Virology ◽

10.1128/jvi.00841-20 ◽

2020 ◽

Vol 94 (16) ◽

Author(s):

Beibei Chen ◽

Zhao Chen ◽

Yuchen Wang ◽

Han Gong ◽

Linshan Sima ◽

...

Keyword(s):

Life Cycle ◽

Bioinformatic Analysis ◽

Model System ◽

Life Cycles ◽

Host Cells ◽

Biological Functions ◽

Mechanistic Studies ◽

Cultivation Conditions ◽

Archaeal Virus ◽

Archaeal Viruses

ABSTRACT Recent environmental and metagenomic studies have considerably increased the repertoire of archaeal viruses and suggested that they play important roles in nutrient cycling in the biosphere. However, very little is known about how they regulate their life cycles and interact with their hosts. Here, we report that the life cycle of the temperate haloarchaeal virus SNJ1 is controlled by the product ORF4, a small protein belonging to the antitoxin MazE superfamily. We show that ORF4 controls the lysis-lysogeny switch of SNJ1 and mediates superinfection immunity by repression of genomic DNA replication of the superinfecting viruses. Bioinformatic analysis shows that ORF4 is highly conserved in two SNJ1-like proviruses, suggesting that the mechanisms for lysis-lysogeny switch and superinfection immunity are conserved in this group of viruses. As the lysis-lysogeny switch and superinfection immunity of archaeal viruses have been poorly studied, we suggest that SNJ1 could serve as a model system to study these processes. IMPORTANCE Archaeal viruses are important parts of the virosphere. Understanding how they regulate their life cycles and interact with host cells provide crucial insights into their biological functions and the evolutionary histories of viruses. However, mechanistic studies of the life cycle of archaeal viruses are scarce due to a lack of genetic tools and demanding cultivation conditions. Here, we discover that the temperate haloarchaeal virus SNJ1, which infects Natrinema sp. strain J7, employs a lysis-lysogeny switch and establishes superinfection immunity like bacteriophages. We show that its ORF4 is critical for both processes and acts as a repressor of the replication of SNJ1. These results establish ORF4 as a master regulator of SNJ1 life cycle and provides novel insights on the regulation of life cycles by temperate archaeal viruses and on their interactions with host cells.

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Identification of a Hypervariable Region Containing New Legionella pneumophila Icm/Dot Translocated Substrates by Using the Conserved icmQ Regulatory Signature

Infection and Immunity ◽

10.1128/iai.00337-08 ◽

2008 ◽

Vol 76 (10) ◽

pp. 4581-4591 ◽

Cited By ~ 26

Author(s):

Tal Zusman ◽

Elena Degtyar ◽

Gil Segal

Keyword(s):

Legionella Pneumophila ◽

Regulatory Element ◽

Hypervariable Region ◽

Genomic Analysis ◽

Bioinformatic Analysis ◽

Genomic Region ◽

Host Cells ◽

Regulatory Sequence ◽

Dependent Manner ◽

Genomic Regions

ABSTRACT Legionella pneumophila is an intracellular pathogen that has been shown to utilize the Icm/Dot type IV secretion system for pathogenesis. This system was shown to be composed of Icm/Dot complex components, accessory proteins, and a large number of translocated substrates. In this study, comparison of the icmQ regulatory regions from many Legionella species revealed a conserved regulatory sequence that includes the icmQ −10 promoter element. Mutagenesis of this conserved regulatory element indicated that each of the nucleotides in it affects the level of expression of the icmQ gene but not in a uniform fashion. A genomic analysis discovered that four additional genes in L. pneumophila contain this conserved regulatory sequence, which was found to function similarly in these genes as well. Examination of these four genes indicated that they are dispensable for intracellular growth, but two of them were found to encode new Icm/Dot translocated substrates (IDTS). Comparison of the genomic regions encoding these two IDTS among the four available L. pneumophila genomic sequences indicated that one of these genes is located in a hypervariable genomic region, which was shown before to contain an IDTS-encoding gene. Translocation analysis that was performed for nine proteins encoded from this hypervariable genomic region indicated that six of them are new IDTS which are translocated into host cells in an Icm/Dot-dependent manner. Furthermore, a bioinformatic analysis indicated that additional L. pneumophila genomic regions that contain several neighboring IDTS-encoding genes are hypervariable in gene content.

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The molecular basis of loss of smell in 2019-nCoV infected individuals

10.31219/osf.io/cmfsp ◽

2020 ◽

Cited By ~ 3

Author(s):

Krishan Gupta ◽

Sanjay Kumar Mohanty ◽

Siddhant Kalra ◽

Aayushi Mittal ◽

Tripti Mishra ◽

...

Keyword(s):

Clinical Symptoms ◽

Expression Profiles ◽

Mammalian Species ◽

Expression Patterns ◽

Cell Types ◽

Bioinformatic Analysis ◽

Tissue Level ◽

Olfactory Mucosa ◽

Host Cells ◽

Sustentacular Cells

Among the prominent clinical symptoms such as fatigue, shortness of breath, fever, and cough, 2019-nCoV infected individuals often experience hyposmia/anosmia (decrease or loss of sense of smell). Angiotensin I Converting Enzyme 2 (ACE2), a key host receptor has now been established as an important moiety for the entry of 2019-nCoV into the host cells. A multitude of studies estimated the expression of ACE2 in multiple organs including heart, kidney, intestine, lungs, buccal cavity, etc. The ongoing medical examinations and the autopsy reports of the diseased individuals strongly corroborate these organ/tissue-level molecular insights. Olfactory mucosa harbors multiple functionally distinct cell types. Zeroing in on the cell lineages that underpin infection associated loss of olfaction may provide new leads for diagnostics/clinical management of 2019-nCoV infected individuals. Our pointed bioinformatic analysis of single-cell expression profiles underscored selective expression of ACE2 in a subset of sustentacular cells (SUSs), Olfactory Stem cells (HBCs and GBCs), and Bowman’s gland cells of the olfactory mucosa in humans. Co-expression analysis of ACE2 and TMPRSS2 (protease), two host-specific moieties indispensable for 2019-nCoV entry into the host cell revealed the highest infection susceptibility for the sustentacular cells. Additionally, an inspection of the ACE2 and TMPRSS2 levels in the olfactory mucosa of 4 additional mammalian species revealed comparable expression patterns, indicating the potential risk of olfactory dysfunction in these species. In summary, our findings pinpoint the molecular rationale of loss of smell in 2019-nCoV infected patients.

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SAG3 Toxoplasma gondii cloning reveals unexpected fivefold infection in the blood of feral cats in the Mexican Caribbean

BMC Veterinary Research ◽

10.1186/s12917-021-03129-9 ◽

2022 ◽

Vol 18 (1) ◽

Author(s):

Luis Fernando Valenzuela-Moreno ◽

Sara Teresa Méndez-Cruz ◽

Claudia Patricia Rico-Torres ◽

Carlos Cedillo-Peláez ◽

Dolores Correa ◽

...

Keyword(s):

Genetic Diversity ◽

Toxoplasma Gondii ◽

Bioinformatic Analysis ◽

Restriction Pattern ◽

Host Cells ◽

Tropical Region ◽

High Genetic Diversity ◽

Feral Cats ◽

Mexican Caribbean ◽

Pcr Rflp

Abstract Background Currently, more than 300 genotypes of Toxoplasma gondii (T. gondii) have been described throughout the world, demonstrating its wide genetic diversity. The SAG3 locus is one of the genes included in the genotyping panel of this parasite. It is associated with its virulence since it participates during the invasion process of the host cells. Therefore, cloning, sequencing, and bioinformatic analysis were used to deepen the understanding of the SAG3 locus genetic diversity of T. gondii in blood samples from feral cats. Results Six different SAG3 sequences were detected, five of which were detected in one feline. Three sequences were first reported here; one of them was an intragenic recombinant. In the cladogram, four out of ten SAG3 sequences did not share nodes with others reported worldwide. Conclusions Cloning and sequencing of samples with more than one restriction pattern by PCR-RFLP were very helpful tools to demonstrate the presence of more than three genotypes of T. gondii in the blood of feral cats from southeastern Mexico. This suggests a potential mixed infection of multiple T. gondii strains and high genetic diversity of the parasites in felines in this tropical region of Mexico.

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Composition, Acquisition, and Distribution of the Vi Exopolysaccharide-Encoding Salmonella enterica Pathogenicity Island SPI-7

Journal of Bacteriology ◽

10.1128/jb.185.17.5055-5065.2003 ◽

2003 ◽

Vol 185 (17) ◽

pp. 5055-5065 ◽

Cited By ~ 82

Author(s):

Derek Pickard ◽

John Wain ◽

Stephen Baker ◽

Alexandra Line ◽

Sonia Chohan ◽

...

Keyword(s):

Salmonella Enterica ◽

Sequence Variation ◽

Capsular Polysaccharide ◽

Mobile Element ◽

Pathogenicity Island ◽

Bioinformatic Analysis ◽

Host Cells ◽

Sequence Identity ◽

Type Iv ◽

Vi Capsular Polysaccharide

ABSTRACT Vi capsular polysaccharide production is encoded by the viaB locus, which has a limited distribution in Salmonella enterica serovars. In S. enterica serovar Typhi, viaB is encoded on a 134-kb pathogenicity island known as SPI-7 that is located between partially duplicated tRNA pheU sites. Functional and bioinformatic analysis suggests that SPI-7 has a mosaic structure and may have evolved as a consequence of several independent insertion events. Analysis of viaB-associated DNA in Vi-positive S. enterica serovar Paratyphi C and S. enterica serovar Dublin isolates revealed the presence of similar SPI-7 islands. In S. enterica serovars Paratyphi C and Dublin, the SopE bacteriophage and a 15-kb fragment adjacent to the intact tRNA pheU site were absent. In S. enterica serovar Paratyphi C only, a region encoding a type IV pilus involved in the adherence of S. enterica serovar Typhi to host cells was missing. The remainder of the SPI-7 islands investigated exhibited over 99% DNA sequence identity in the three serovars. Of 30 other Salmonella serovars examined, 24 contained no insertions at the equivalent tRNA pheU site, 2 had a 3.7-kb insertion, and 4 showed sequence variation at the tRNA pheU -phoN junction, which was not analyzed further. Sequence analysis of the SPI-7 region from S. enterica serovar Typhi strain CT18 revealed significant synteny with clusters of genes from a variety of saprophytic bacteria and phytobacteria, including Pseudomonas aeruginosa and Xanthomonas axonopodis pv. citri. This analysis suggested that SPI-7 may be a mobile element, such as a conjugative transposon or an integrated plasmid remnant.

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Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy Against the Phytopathogen Ralstonia solanacearum

10.20944/preprints202112.0049.v1 ◽

2021 ◽

Author(s):

Elena G. Biosca ◽

José F. Català-Senent ◽

Àngela Figàs-Segura ◽

Edson Bertolini ◽

María M. López ◽

...

Keyword(s):

Biological Control ◽

Ralstonia Solanacearum ◽

Control Strategies ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Bioinformatic Analysis ◽

Environmental Water ◽

Plant Diseases ◽

Host Cells ◽

Genomic Characterization

Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plant were isolated from river water in Europe but not fully characterized, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.

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Resistance towards monensin is proposed to be acquired in a Toxoplasma gondii model by reduced invasion and egress activities, in addition to increased intracellular replication

Parasitology ◽

10.1017/s0031182017001512 ◽

2017 ◽

Vol 145 (3) ◽

pp. 313-325 ◽

Cited By ~ 3

Author(s):

AHMED THABET ◽

JOHANNES SCHMIDT ◽

SVEN BAUMANN ◽

WALTHER HONSCHA ◽

MARTIN VON BERGEN ◽

...

Keyword(s):

Mass Spectrometry ◽

Toxoplasma Gondii ◽

Metal Ion ◽

Bioinformatic Analysis ◽

Resistance Mechanisms ◽

Host Cells ◽

Intracellular Replication ◽

Metal Ion Binding ◽

Stable Isotope Labelling

SUMMARYMonensin (Mon) is an anticoccidial polyether ionophore widely used to control coccidiosis. The extensive use of polyether ionophores on poultry farms resulted in widespread resistance, but the underlying resistance mechanisms are unknown in detail. For analysing the mode of action by which resistance against polyether ionophores is obtained, we induced in vitro Mon resistance in Toxoplasma gondii-RH strain (MonR-RH) and compared it with the sensitive parental strain (Sen-RH). The proteome assessment of MonR-RH and Sen-RH strains was obtained after isotopic labelling using stable isotope labelling by amino acid in cell culture. Relative proteomic quantification between resistant and sensitive strains was performed using liquid chromatography-mass spectrometry/mass spectrometry. Overall, 1024 proteins were quantified and 52 proteins of them were regulated. The bioinformatic analysis revealed regulation of cytoskeletal and transmembrane proteins being involved in transport mechanisms, metal ion-binding and invasion. During invasion, actin and microneme protein 8 (MIC8) are seem to be important for conoid extrusion and forming moving junction with host cells, respectively. Actin was significantly upregulated, while MIC8 was downregulated, which indicate an invasion reduction in the resistant strain. Resistance against Mon is not a simple process but it involves reduced invasion and egress activity of T. gondii tachyzoites while intracellular replication is enhanced.

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Characterization of a Hyaluronic Acid Utilization Locus and Identification of Two Hyaluronate Lyases in a Marine Bacterium Vibrio alginolyticus LWW-9

Frontiers in Microbiology ◽

10.3389/fmicb.2021.696096 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaoyi Wang ◽

Ziwei Wei ◽

Hao Wu ◽

Yujiao Li ◽

Feng Han ◽

...

Keyword(s):

Hyaluronic Acid ◽

Pathogenic Bacteria ◽

Marine Bacterium ◽

Opportunistic Pathogen ◽

Bioinformatic Analysis ◽

Industrial Applications ◽

Biochemical Properties ◽

Vibrio Alginolyticus ◽

Host Cells ◽

Marine Animals

Hyaluronic acid (HA) is a negatively charged and linear polysaccharide existing in the tissues and body fluids of all vertebrates. Some pathogenic bacteria target hyaluronic acid for adhesion and/or infection to host cells. Vibrio alginolyticus is an opportunistic pathogen related to infections of humans and marine animals, and the hyaluronic acid-degrading potential of Vibrio spp. has been well-demonstrated. However, little is known about how Vibrio spp. utilize hyaluronic acid. In this study, a marine bacterium V. alginolyticus LWW-9 capable of degrading hyaluronic acid has been isolated. Genetic and bioinformatic analysis showed that V. alginolyticus LWW-9 harbors a gene cluster involved in the degradation, transport, and metabolism of hyaluronic acid. Two novel PL8 family hyaluronate lyases, VaHly8A and VaHly8B, are the key enzymes for the degradation of hyaluronic acid. VaHly8A and VaHly8B have distinct biochemical properties, reflecting the adaptation of the strain to the changing parameters of the aquatic habitats and hosts. Based on genomic and functional analysis, we propose a model for the complete degradation of hyaluronic acid by V. alginolyticus LWW-9. Overall, our study expands our knowledge of the HA utilization paradigm within the Proteobacteria, and the two novel hyaluronate lyases are excellent candidates for industrial applications.

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Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy against the Phytopathogen Ralstonia solanacearum

Viruses ◽

10.3390/v13122539 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2539

Author(s):

Elena G. Biosca ◽

José Francisco Català-Senent ◽

Àngela Figàs-Segura ◽

Edson Bertolini ◽

María M. López ◽

...

Keyword(s):

Biological Control ◽

Ralstonia Solanacearum ◽

Control Strategies ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Bioinformatic Analysis ◽

Environmental Water ◽

Plant Diseases ◽

Host Cells ◽

Genomic Characterization

Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plants were isolated from river water in Europe but not fully analysed, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.

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