Complete Genome Sequence of Virulence-Enhancing Siphophage VHS1 from Vibrio harveyi

ABSTRACTVibrio harveyisiphophage 1 (VHS1) is a tailed phage with an icosahedral head of approximately 66 nm in diameter and an unornamented, flexible tail of approximately 153 nm in length. WhenVibrio harveyi1114GL is lysogenized with VHS1, its virulence for the black tiger shrimp (Penaeus monodon) increases by more than 100 times, and this coincides with production of a toxin(s) associated with shrimp hemocyte agglutination. Curiously, the lysogen does not show increased virulence for the whiteleg shrimp (Penaeus[Litopenaeus]vannamei). Here we present and annotate the complete, circular genome of VHS1 (81,509 kbp; GenBank accession numberJF713456). By software analysis, the genome contains 125 putative open reading frames (ORFs), all of which appear to be located on the same DNA strand, similar to the case for many other bacteriophages. Most of the putative ORFs show no significant homology to known sequences in GenBank. Notable exceptions are ORFs for a putative DNA polymerase and putative phage structural proteins, including a portal protein, a phage tail tape measure protein, and a phage head protein. The last protein was identified as a component of the species-specific toxin mixture described above as being associated with agglutination of hemocytes fromP. monodon.

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Opposing Roles for Two Molecular Forms of Replication Protein A in Rad51-Rad54-Mediated DNA Recombination in Plasmodium falciparum

mBio ◽

10.1128/mbio.00252-13 ◽

2013 ◽

Vol 4 (3) ◽

Cited By ~ 23

Author(s):

Anusha M. Gopalakrishnan ◽

Nirbhay Kumar

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Antigenic Variation ◽

Protein A ◽

Dna Recombination ◽

Strand Exchange ◽

Content Type ◽

Dna Strand Exchange ◽

Dna Strand

ABSTRACT The bacterial RecA protein and its eukaryotic homologue Rad51 play a central role in the homologous DNA strand exchange reaction during recombination and DNA repair. Previously, our lab has shown that PfRad51, the Plasmodium falciparum homologue of Rad51, exhibited ATPase activity and promoted DNA strand exchange in vitro. In this study, we evaluated the catalytic functions of PfRad51 in the presence of putative interacting partners, especially P. falciparum homologues of Rad54 and replication protein A. PfRad54 accelerated PfRad51-mediated pairing between single-stranded DNA (ssDNA) and its homologous linear double-stranded DNA (dsDNA) in the presence of 0.5 mM CaCl2. We also present evidence that recombinant PfRPA1L protein serves the function of the bacterial homologue single-stranded binding protein (SSB) in initiating homologous pairing and strand exchange activity. More importantly, the function of PfRPA1L was negatively regulated in a dose-dependent manner by PfRPA1S, another RPA homologue in P. falciparum. Finally, we present in vivo evidence through comet assays for methyl methane sulfonate-induced DNA damage in malaria parasites and accompanying upregulation of PfRad51, PfRad54, PfRPA1L, and PfRPA1S at the level of transcript and protein needed to repair DNA damage. This study provides new insights into the role of putative Rad51-interacting proteins involved in homologous recombination and emphasizes the physiological role of DNA damage repair during the growth of parasites. IMPORTANCE Homologous recombination plays a major role in chromosomal rearrangement, and Rad51 protein, aided by several other proteins, plays a central role in DNA strand exchange reaction during recombination and DNA repair. This study reports on the characterization of the role of P. falciparum Rad51 in homologous strand exchange and DNA repair and evaluates the functional contribution of PfRad54 and PfRPA1 proteins. Data presented here provide mechanistic insights into DNA recombination and DNA damage repair mechanisms in this parasite. The importance of these research findings in future work will be to investigate if Rad51-dependent mechanisms are involved in chromosomal rearrangements during antigenic variation in P. falciparum. A prominent determinant of antigenic variation, the extraordinary ability of the parasite to rapidly change its surface molecules, is associated with var genes, and antigenic variation presents a major challenge to vaccine development.

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Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

Applied and Environmental Microbiology ◽

10.1128/aem.00518-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3724-3733 ◽

Cited By ~ 103

Author(s):

Frank O. Aylward ◽

Bradon R. McDonald ◽

Sandra M. Adams ◽

Alejandra Valenzuela ◽

Rebeccah A. Schmidt ◽

...

Keyword(s):

Nutrient Cycling ◽

Genomic Analysis ◽

Amino Acid Identity ◽

Open Reading Frames ◽

Glycoside Hydrolases ◽

Content Type ◽

Metabolic Versatility ◽

Plasmid Recombination ◽

Environmental Adaptations ◽

Species Specific

ABSTRACTSphingomonads comprise a physiologically versatile group within theAlphaproteobacteriathat includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm thatSphingomonas,Sphingobium,Sphingopyxis, andNovosphingobiumare well-resolved monophyletic groups with the exception ofSphingomonassp. strain SKA58, which we propose belongs to the genusSphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.

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Outer Membrane Protein A of Bovine and Ovine Isolates of Mannheimia haemolytica Is Surface Exposed and Contains Host Species-Specific Epitopes

Infection and Immunity ◽

10.1128/iai.05469-11 ◽

2011 ◽

Vol 79 (11) ◽

pp. 4332-4341 ◽

Cited By ~ 17

Author(s):

Jonathan D. A. Hounsome ◽

Susan Baillie ◽

Mojtaba Noofeli ◽

Alan Riboldi-Tunnicliffe ◽

Richard J. S. Burchmore ◽

...

Keyword(s):

Transmembrane Domain ◽

Protein A ◽

Growth Conditions ◽

Mannheimia Haemolytica ◽

Immunogold Electron Microscopy ◽

Content Type ◽

Polysaccharide Capsule ◽

Ompa Protein ◽

Species Specific ◽

Cattle And Sheep

ABSTRACTMannheimia haemolyticais the etiological agent of pneumonic pasteurellosis of cattle and sheep; two different OmpA subclasses, OmpA1 and OmpA2, are associated with bovine and ovine isolates, respectively. These proteins differ at the distal ends of four external loops, are involved in adherence, and are likely to play important roles in host adaptation.M. haemolyticais surrounded by a polysaccharide capsule, and the degree of OmpA surface exposure is unknown. To investigate surface exposure and immune specificity of OmpA among bovine and ovineM. haemolyticaisolates, recombinant proteins representing the transmembrane domain of OmpA from a bovine serotype A1 isolate (rOmpA1) and an ovine serotype A2 isolate (rOmpA2) were overexpressed, purified, and used to generate anti-rOmpA1 and anti-rOmpA2 antibodies, respectively. Immunogold electron microscopy and immunofluorescence techniques demonstrated that OmpA1 and OmpA2 are surface exposed, and are not masked by the polysaccharide capsule, in a selection ofM. haemolyticaisolates of various serotypes and grown under different growth conditions. To explore epitope specificity, anti-rOmpA1 and anti-rOmpA2 antibodies were cross-absorbed with the heterologous isolate to remove cross-reacting antibodies. These cross-absorbed antibodies were highly specific and recognized only the OmpA protein of the homologous isolate in Western blot assays. A wider examination of the binding specificities of these antibodies forM. haemolyticaisolates representing different OmpA subclasses revealed that cross-absorbed anti-rOmpA1 antibodies recognized OmpA1-type proteins but not OmpA2-type proteins; conversely, cross-absorbed anti-rOmpA2 antibodies recognized OmpA2-type proteins but not OmpA1-type proteins. Our results demonstrate that OmpA1 and OmpA2 are surface exposed and could potentially bind to different receptors in cattle and sheep.

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Complete Genome Sequence of a Jumbo Bacteriophage, vB_pir03, against Vibrio harveyi

Microbiology Resource Announcements ◽

10.1128/mra.00910-20 ◽

2020 ◽

Vol 9 (44) ◽

Cited By ~ 1

Author(s):

Gerald N. Misol ◽

Constantinta Kokkari ◽

Pantelis Katharios

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Vibrio Harveyi ◽

Disease Outbreaks ◽

Open Reading Frames ◽

Content Type ◽

Reading Frames

ABSTRACT Vibrio harveyi is a persistent pathogen responsible for disease outbreaks in aquaculture. We have sequenced the genome of a jumbo Vibrio phage, vB_pir03, isolated in Greece. Here, we present the complete genome of vB_pir03, which consists of 286,284 bp and 336 open reading frames.

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F420H2Is Required for Phthiocerol Dimycocerosate Synthesis in Mycobacteria

Journal of Bacteriology ◽

10.1128/jb.01035-15 ◽

2016 ◽

Vol 198 (15) ◽

pp. 2020-2028 ◽

Cited By ~ 8

Author(s):

Endang Purwantini ◽

Lacy Daniels ◽

Biswarup Mukhopadhyay

Keyword(s):

Mycobacterium Tuberculosis ◽

Protein A ◽

Mycobacterium Leprae ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Hydroxyl Group ◽

Host Immune System ◽

Content Type ◽

Glucose 6 Phosphate Dehydrogenase ◽

Phthiocerol Dimycocerosates

ABSTRACTPhthiocerol dimycocerosates (PDIM) are a group of cell surface-associated apolar lipids ofMycobacterium tuberculosisand closely related mycobacteria, such asMycobacterium bovisandMycobacterium leprae. A characteristic methoxy group of these lipids is generated from the methylation of a hydroxyl group of the direct precursors, the phthiotriols. The precursors arise from the reduction of phthiodiolones, the keto intermediates, by a ketoreductase. The putative phthiodiolone ketoreductase (PKR) is encoded by Rv2951c inM. tuberculosisand BCG_2972c inM. bovisBCG, and these open reading frames (ORFs) encode identical amino acid sequences. We investigated the cofactor requirement of the BCG_2972c protein. A comparative analysis based on the crystallographic structures of similar enzymes identified structural elements for binding of coenzyme F420and hydrophobic phthiodiolones in PKR. Coenzyme F420is a deazaflavin coenzyme that serves several key functions in pathogenic and nonpathogenic mycobacteria. We found that anM. bovisBCG mutant lacking F420-dependent glucose-6-phosphate dehydrogenase (Fgd), which generates F420H2(glucose-6-phosphate + F420→ 6-phosphogluconate + F420H2), was devoid of phthiocerols and accumulated phthiodiolones. When the mutant was provided with F420H2, a broken-cell slurry of the mutant converted accumulated phthiodiolones to phthiocerols; F420H2was generatedin situfrom F420and glucose-6-phosphate by the action of Fgd. Thus, the reaction mixture was competent in reducing phthiodiolones to phthiotriols (phthiodiolones + F420H2→ phthiotriols + F420), which were then methylated to phthiocerols. These results established the mycobacterialphthiodioloneketoreductase as anF420H2-dependent enzyme (fPKR). A phylogenetic analysis of close homologs of fPKR revealed potential F420-dependent lipid-modifying enzymes in a broad range of mycobacteria.IMPORTANCEMycobacterium tuberculosisis the causative agent of tuberculosis, and phthiocerol dimycocerosates (PDIM) protect this pathogen from the early innate immune response of an infected host. Thus, the PDIM synthesis system is a potential target for the development of effective treatments for tuberculosis. The current study shows that a PDIM synthesis enzyme is dependent on the coenzyme F420. F420is universally present in mycobacteria and absent in humans. This finding expands the number of experimentally validated F420-dependent enzymes inM. tuberculosisto six, each of which helps the pathogen to evade killing by the host immune system, and one of which activates an antituberculosis drug, PA-824. This work also has relevance to leprosy, since similar waxy lipids are found inMycobacterium leprae.

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Vibrio harveyi virulence gene expression in vitro and in vivo during infection in black tiger shrimp Penaeus monodon

Diseases of Aquatic Organisms ◽

10.3354/dao03475 ◽

2020 ◽

Vol 139 ◽

pp. 153-160

Author(s):

S Peeralil ◽

TC Joseph ◽

V Murugadas ◽

PG Akhilnath ◽

VN Sreejith ◽

...

Keyword(s):

Gene Expression ◽

Virulence Genes ◽

Vibrio Harveyi ◽

Penaeus Monodon ◽

Challenge Test ◽

Virulence Gene ◽

Economic Losses ◽

Virulence Gene Expression

Luminescent Vibrio harveyi is common in sea and estuarine waters. It produces several virulence factors and negatively affects larval penaeid shrimp in hatcheries, resulting in severe economic losses to shrimp aquaculture. Although V. harveyi is an important pathogen of shrimp, its pathogenicity mechanisms have yet to be completely elucidated. In the present study, isolates of V. harveyi were isolated and characterized from diseased Penaeus monodon postlarvae from hatcheries in Kerala, India, from September to December 2016. All 23 tested isolates were positive for lipase, phospholipase, caseinase, gelatinase and chitinase activity, and 3 of the isolates (MFB32, MFB71 and MFB68) showed potential for significant biofilm formation. Based on the presence of virulence genes, the isolates of V. harveyi were grouped into 6 genotypes, predominated by vhpA+ flaB+ ser+ vhh1- luxR+ vopD- vcrD+ vscN-. One isolate from each genotype was randomly selected for in vivo virulence experiments, and the LD50 ranged from 1.7 ± 0.5 × 103 to 4.1 ± 0.1 × 105 CFU ml-1. The expression of genes during the infection in postlarvae was high in 2 of the isolates (MFB12 and MFB32), consistent with the result of the challenge test. However, in MFB19, even though all genes tested were present, their expression level was very low and likely contributed to its lack of virulence. Because of the significant variation in gene expression, the presence of virulence genes alone cannot be used as a marker for pathogenicity of V. harveyi.

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Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00423-13 ◽

2013 ◽

Vol 57 (8) ◽

pp. 3775-3782 ◽

Cited By ~ 48

Author(s):

Jianhui Xiong ◽

David C. Alexander ◽

Jennifer H. Ma ◽

Maxime Déraspe ◽

Donald E. Low ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Carbapenem Resistance ◽

Complete Sequence ◽

Open Reading Frames ◽

Content Type ◽

Conserved Sequence ◽

Carbapenem Resistant ◽

Class 1 ◽

Usage Analysis ◽

Type 3

ABSTRACTPseudomonas aeruginosa96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Whole-genome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G+C content of 57%. Of the 618 predicted open reading frames, 65% encode hypothetical proteins. The pOZ176 backbone is not closely related to any plasmids thus far sequenced, but some similarity to pQBR103 ofPseudomonas fluorescensSBW25 was observed. Two multiresistant class 1 integrons and several insertion sequences were identified. TheblaIMP-9-carrying integron containedaacA4→blaIMP-9→aacA4, flanked upstream by Tn21 tnpMRAand downstream by a completetnioperon of Tn402and amermodule, named Tn6016. The second integron carriedaacA4→catB8a→blaOXA-10and was flanked by Tn1403-liketnpRAand asul1-type 3′ conserved sequence (3′-CS), named Tn6217. Other features include three resistance genes similar to those of Tn5, a tellurite resistance operon, and twopiloperons. The replication and maintenance systems exhibit similarity to a genomic island ofRalstonia solanacearumGM1000. Codon usage analysis suggests the recent acquisition ofblaIMP-9. The origins of the integrons on pOZ176 indicated separate horizontal gene transfer events driven by antibiotic selection. The novel mosaic structure of pOZ176 suggests that it is derived from environmental bacteria.

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CD4 T Cell Antigens from Staphylococcus aureus Newman Strain Identified following Immunization with Heat-Killed Bacteria

Clinical and Vaccine Immunology ◽

10.1128/cvi.05642-11 ◽

2012 ◽

Vol 19 (4) ◽

pp. 477-489 ◽

Cited By ~ 9

Author(s):

Paulraj K. Lawrence ◽

Bachra Rokbi ◽

Nadège Arnaud-Barbe ◽

Eric L. Sutten ◽

Junzo Norimine ◽

...

Keyword(s):

Staphylococcus Aureus ◽

T Cell ◽

Reverse Genetics ◽

Vaccine Development ◽

Protein A ◽

Cd4 T Cell ◽

Content Type ◽

Intramammary Infections ◽

T Cell Antigens ◽

Ifn Γ

ABSTRACTStaphylococcus aureusis a commensal bacterium associated with the skin and mucosal surfaces of humans and animals that can also cause chronic infection. The emergence of antibiotic-resistant strains such as methicillin-resistantS. aureus(MRSA) and strains causing chronic intramammary infections (IMI) in cows results in severe human and livestock infections. Conventional approaches to vaccine development have yielded only a few noneffective vaccines against MRSA or IMI strains, so there is a need for improved vaccine development. CD4 T lymphocytes are required for promoting gamma interferon (IFN-γ) mediated immunoglobulin isotype switching in B lymphocytes to produce high-affinity IgG antibodies and IFN-γ-mediated phagocyte activation for an effective resolution of bacterial infection. However, the lack of known CD4 T cell antigens fromS. aureushas made it difficult to design effective vaccines. The goal of this study was to identifyS. aureusproteins recognized by immune CD4 T cells. Using a reverse genetics approach, 43 antigens were selected from theS. aureusNewman strain. These included lipoproteins, proteases, transcription regulators, an alkaline shock protein, conserved-domain proteins, hemolysins, fibrinogen-binding protein, staphylokinase, exotoxin, enterotoxin, sortase, and protein A. Screening of expressed proteins for recall T cell responses in outbred, immune calves identified 13 proteins that share over 80% sequence identity among MRSA or IMI strains. These may be useful for inclusion in a broadly protective multiantigen vaccine against MRSA or IMI.

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Draft Genome Sequence of a Vibrio harveyi Strain Associated with Vibriosis in Pacific White Shrimp (Litopenaeus vannamei)

Genome Announcements ◽

10.1128/genomea.01662-16 ◽

2017 ◽

Vol 5 (7) ◽

Cited By ~ 5

Author(s):

Emille Moreno ◽

Marci Parks ◽

Lee J. Pinnell ◽

James J. Tallman ◽

Jeffrey W. Turner

Keyword(s):

Genome Sequence ◽

Litopenaeus Vannamei ◽

Vibrio Harveyi ◽

Draft Genome ◽

Penaeid Shrimp ◽

Pacific White Shrimp ◽

Draft Genome Sequence ◽

White Shrimp ◽

Content Type ◽

Future Studies

ABSTRACT Vibrio harveyi is a Gram-negative bacterium associated with vibriosis in penaeid shrimp. Here, we report the draft genome sequence of a V. harveyi strain isolated from Pacific white shrimp (Litopenaeus vannamei) during a vibriosis outbreak. The availability of this genome will aid future studies of vibriosis in shrimp aquaculture.

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Anaplasma phagocytophilum Outer Membrane Protein A Interacts with Sialylated Glycoproteins To Promote Infection of Mammalian Host Cells

Infection and Immunity ◽

10.1128/iai.00654-12 ◽

2012 ◽

Vol 80 (11) ◽

pp. 3748-3760 ◽

Cited By ~ 36

Author(s):

Nore Ojogun ◽

Amandeep Kahlon ◽

Stephanie A. Ragland ◽

Matthew J. Troese ◽

Juliana E. Mastronunzio ◽

...

Keyword(s):

Membrane Protein ◽

Outer Membrane ◽

Outer Membrane Protein ◽

Anaplasma Phagocytophilum ◽

Protein A ◽

Host Cells ◽

Mammalian Host ◽

Content Type ◽

Outer Membrane Protein A ◽

Sialylated Glycoproteins

ABSTRACTAnaplasma phagocytophilumis the tick-transmitted obligate intracellular bacterium that causes human granulocytic anaplasmosis (HGA).A. phagocytophilumbinding to sialyl Lewis x (sLex) and other sialylated glycans that decorate P selectin glycoprotein 1 (PSGL-1) and other glycoproteins is critical for infection of mammalian host cells. Here, we demonstrate the importance ofA. phagocytophilumouter membrane protein A (OmpA) APH_0338 in infection of mammalian host cells. OmpA is transcriptionally induced during transmission feeding ofA. phagocytophilum-infected ticks on mice and is upregulated during invasion of HL-60 cells. OmpA is presented on the pathogen's surface. Sera from HGA patients and experimentally infected mice recognize recombinant OmpA. Pretreatment ofA. phagocytophilumorganisms with OmpA antiserum reduces their abilities to infect HL-60 cells. The OmpA N-terminal region is predicted to contain the protein's extracellular domain. GlutathioneS-transferase (GST)-tagged versions of OmpA and OmpA amino acids 19 to 74 (OmpA19-74) but not OmpA75-205bind to, and competitively inhibitA. phagocytophiluminfection of, host cells. Pretreatment of host cells with sialidase or trypsin reduces or nearly eliminates, respectively, GST-OmpA adhesion. Therefore, OmpA interacts with sialylated glycoproteins. This study identifies the firstA. phagocytophilumadhesin-receptor pair and delineates the region of OmpA that is critical for infection.

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