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1.
J Virol ; 93(5)2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30541839

RESUMO

The 240-kb Salmonella phage SPN3US genome encodes 264 gene products, many of which are functionally uncharacterized. We have previously used mass spectrometry to define the proteomes of wild-type and mutant forms of the SPN3US virion. In this study, we sought to determine whether this technique was suitable for the characterization of the SPN3US proteome during liquid infection. Mass spectrometry of SPN3US-infected cells identified 232 SPN3US and 1,994 Salmonella proteins. SPN3US proteins with related functions, such as proteins with roles in DNA replication, transcription, and virion formation, were coordinately expressed in a temporal manner. Mass spectral counts showed the four most abundant SPN3US proteins to be the major capsid protein, two head ejection proteins, and the functionally unassigned protein gp22. This high abundance of gp22 in infected bacteria contrasted with its absence from mature virions, suggesting that it might be the scaffold protein, an essential head morphogenesis protein yet to be identified in giant phages. We identified homologs to SPN3US gp22 in 45 related giant phages, including ϕKZ, whose counterpart is also abundant in infected bacteria but absent in the virion. We determined the ϕKZ counterpart to be cleaved in vitro by its prohead protease, an event that has been observed to promote head maturation of some other phages. Our findings are consistent with a scaffold protein assignment for SPN3US gp22, although direct evidence is required for its confirmation. These studies demonstrate the power of mass spectral analyses for facilitating the acquisition of new knowledge into the molecular events of viral infection.IMPORTANCE "Giant" phages with genomes >200 kb are being isolated in increasing numbers from a range of environments. With hosts such as Salmonella enterica, Pseudomonas aeruginosa, and Erwinia amylovora, these phages are of interest for phage therapy of multidrug-resistant pathogens. However, our understanding of how these complex phages interact with their hosts is impeded by the proportion (∼80%) of their gene products that are functionally uncharacterized. To develop the repertoire of techniques for analysis of phages, we analyzed a liquid infection of Salmonella phage SPN3US (240-kb genome) using third-generation mass spectrometry. We observed the temporal production of phage proteins whose genes collectively represent 96% of the SPN3US genome. These findings demonstrate the sensitivity of mass spectrometry for global proteomic profiling of virus-infected cells, and the identification of a candidate for a major head morphogenesis protein will facilitate further studies into giant phage head assembly.


Assuntos
Vírus Gigantes/genética , Glicoproteínas/genética , Proteoma/análise , Fagos de Salmonella/genética , Salmonella typhimurium/virologia , Proteínas Virais/genética , DNA Viral/genética , Perfilação da Expressão Gênica , Genoma Viral/genética , Espectrometria de Massas , Pseudomonas aeruginosa/virologia
2.
J Virol ; 90(22): 10284-10298, 2016 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-27605673

RESUMO

Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241, which encodes an RNA polymerase ß subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a "missing" ß' subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. IMPORTANCE: In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and phage therapy applications. Our understanding of the biology of these phages is limited, as a large proportion of their proteins have not been characterized and/or have been deemed putative without any experimental verification. In this study, we analyzed Salmonella phage SPN3US using a combination of genomics, genetics, and proteomics and in doing so revealed new information regarding giant phage head structure and assembly and virion RNA polymerase composition. Our findings demonstrate the suitability of SPN3US as a model phage for the growing group of phages related to ϕKZ.


Assuntos
Genes Essenciais/genética , Fagos de Salmonella/genética , Proteínas Virais/genética , RNA Polimerases Dirigidas por DNA/genética , Genoma Viral/genética , Vírion/genética
3.
J Virol ; 87(15): 8713-25, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23740980

RESUMO

Pseudomonas aeruginosa myovirus KZ has a 270-kb genome within a T=27 icosahedral capsid that contains a large, unusual, and structurally well-defined protein cylindrical inner body (IB) spanning its interior. Proteolysis forms a pivotal stage in KZ head and IB morphogenesis, with the protease gp175 cleaving at least 19 of 49 different head proteins, including the major capsid protein and five major structural IB proteins. Here we show that the purified mature form of gp175 is active and cleaves purified IB structural proteins gp93 and gp89. Expression vector synthesis and purification of the zymogen/precursor yielded an active, mature-length protease, showing independent C-terminal gp175 self-cleavage autoactivation. Mutation of either the predicted catalytic serine or histidine inactivated mature gp175, supporting its classification as a serine protease and representing the first such direct biochemical demonstration with purified protease and substrate proteins for any phage protease. These mutations also blocked self-cleavage of the precursor while allowing intermolecular gp175 processing. To confirm the cleavage specificity of gp175, we mutated three cleavage sites in gp93, which blocked proteolysis at these sites. The N-terminal propeptide of gp93 was shown to undergo more extensive proteolysis than previously identified. We found that proteolysis in gp93 progressed from the N to C terminus, while blocking cleavage sites slowed but did not eliminate downstream proteolysis. These findings were shown by informatics to be relevant to the head morphogenesis of numbers of other related IB-containing giant phages as well as to T4 and herpesviruses, which have homologous proteases.


Assuntos
Myoviridae/enzimologia , Fagos de Pseudomonas/enzimologia , Serina Proteases/genética , Serina Proteases/metabolismo , Proteínas não Estruturais Virais/genética , Proteínas não Estruturais Virais/metabolismo , Análise Mutacional de DNA , Proteínas Mutantes/genética , Proteínas Mutantes/isolamento & purificação , Proteínas Mutantes/metabolismo , Myoviridae/genética , Fagos de Pseudomonas/genética , Pseudomonas aeruginosa/virologia , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Serina Proteases/isolamento & purificação , Proteínas não Estruturais Virais/isolamento & purificação
4.
Viruses ; 16(2)2024 01 26.
Artigo em Inglês | MEDLINE | ID: mdl-38399968

RESUMO

In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.


Assuntos
Bacteriófago T4 , DNA Viral , DNA Viral/metabolismo , Bacteriófago T4/genética , Fluorescência , Montagem de Vírus , Empacotamento do DNA , Endodesoxirribonucleases/metabolismo
5.
Micromachines (Basel) ; 15(3)2024 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-38542616

RESUMO

Bacteriophage therapy presents a promising avenue for combating antibiotic-resistant bacterial infections. Yet, challenges exist, particularly, the lack of a straightforward purification pipeline suitable for widespread application to many phage types, as some phages are known to undergo significant titer loss when purified via current techniques. Electrokinetic methods offer a potential solution to this hurdle, with nonlinear electrophoresis emerging as a particularly appealing approach due to its ability to discern both the size and shape of the target phage particles. Presented herein is the electrokinetic characterization of the mobility of nonlinear electrophoresis for two phages (SPN3US and ϕKZ) and three types of polystyrene nanoparticles. The latter served as controls and were selected based on their sizes and surface charge magnitude. Particle tracking velocimetry experiments were conducted to characterize the mobility of all five particles included in this study. The results indicated that the selected nanoparticles effectively replicate the migration behavior of the two phages under electric fields. Further, it was found that there is a significant difference in the nonlinear electrophoretic response of phages and that of host cells, as first characterized in a previous report, illustrating that electrokinetic-based separations are feasible. The findings from this work are the first characterization of the behavior of phages under nonlinear electrophoresis effects and illustrate the potential for the development of electrokinetic-based phage purification techniques that could aid the advancement of bacteriophage therapy.

6.
Mol Microbiol ; 84(2): 324-39, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22429790

RESUMO

Encased within the 280 kb genome in the capsid of the giant myovirus φKZ is an unusual cylindrical proteinaceous 'inner body' of highly ordered structure. We present here mass spectrometry, bioinformatic and biochemical studies that reveal novel information about the φKZ head and the complex inner body. The identification of 39 cleavage sites in 19 φKZ head proteins indicates cleavage of many prohead proteins forms a major morphogenetic step in φKZ head maturation. The φKZ head protease, gp175, is newly identified here by a bioinformatics approach, as confirmed by a protein expression assay. Gp175 is distantly related to T4 gp21 and recognizes and cleaves head precursors at related but distinct S/A/G-X-E recognition sites. Within the φKZ head there are six high-copy-number proteins that are probable major components of the inner body. The molecular weights of five of these proteins are reduced 35-65% by cleavages making their mature form similar (26-31 kDa), while their precursors are dissimilar (36-88 kDa). Together the six abundant proteins sum to the estimated mass of the inner body (15-20 MDa). The identification of these proteins is important for future studies on the composition and function of the inner body.


Assuntos
Peptídeo Hidrolases/metabolismo , Fagos de Pseudomonas/enzimologia , Fagos de Pseudomonas/fisiologia , Proteínas Virais/metabolismo , Montagem de Vírus , Espectrometria de Massas , Peso Molecular , Myoviridae/química , Myoviridae/enzimologia , Myoviridae/fisiologia , Proteólise , Fagos de Pseudomonas/química , Pseudomonas aeruginosa/virologia
7.
Viruses ; 15(3)2023 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-36992431

RESUMO

Salmonella myovirus SPN3US has a T = 27 capsid composed of >50 different gene products, including many that are packaged along with the 240 kb genome and ejected into the host cell. Recently, we showed that an essential phage-encoded prohead protease gp245 is responsible for cleavage of proteins during SPN3US head assembly. This proteolytic maturation step induces major changes in precursor head particles, enabling them to expand and undergo genome packaging. To comprehensively define the composition of the mature SPN3US head and elucidate how it is modified by proteolysis during assembly, we conducted tandem mass spectrometry analysis of purified virions and tailless heads. Fourteen protease cleavage sites were identified in nine proteins, including eight sites not previously identified in head proteins in vivo. Among these was the maturation cleavage site of gp245 which was identical to the autocleavage site we had previously identified in purified recombinant gp245. Our findings underscore the value of employing multiple mass spectrometry-based experimental strategies as a way to enhance the detection of head protein cleavage sites in tailed phages. In addition, our results have identified a conserved set of head proteins in related giant phages that are similarly cleaved by their respective prohead proteases, suggesting that these proteins have important roles in governing the formation and function of large icosahedral capsids.


Assuntos
Capsídeo , Peptídeo Hidrolases , Capsídeo/metabolismo , Proteólise , Peptídeo Hidrolases/metabolismo , Proteínas do Capsídeo/química , Salmonella , Endopeptidases/genética , Endopeptidases/metabolismo
8.
J Biomol Tech ; 34(3)2023 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-37969874

RESUMO

Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation, data acquisition, and bioinformatics workflows have greatly contributed to progress in this field. In 2020, the Association of Biomolecular Research Facilities Proteome Informatics Research Group launched a collaborative study to assess the bioinformatics options available for metaproteomics research. The study was conducted in 2 phases. In the first phase, participants were provided with mass spectrometry data files and were asked to identify the taxonomic composition and relative taxa abundances in the samples without supplying any protein sequence databases. The most challenging question asked of the participants was to postulate the nature of any biological phenomena that may have taken place in the samples, such as interactions among taxonomic species. In the second phase, participants were provided a protein sequence database composed of the species present in the sample and were asked to answer the same set of questions as for phase 1. In this report, we summarize the data processing methods and tools used by participants, including database searching and software tools used for taxonomic and functional analysis. This study provides insights into the status of metaproteomics bioinformatics in participating laboratories and core facilities.


Assuntos
Proteoma , Proteômica , Humanos , Proteômica/métodos , Software , Biologia Computacional , Bases de Dados de Proteínas
9.
Appl Microbiol Biotechnol ; 94(6): 1609-17, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22562168

RESUMO

Pseudomonas aeruginosa is an important cause of infections, especially in patients with immunodeficiency or diabetes. Antibiotics are effective in preventing morbidity and mortality from Pseudomonas infection, but because of spreading multidrug-resistant bacterial strains, bacteriophages are being explored as an alternative therapy. Two newly purified broad host range Pseudomonas phages, named vB_Pae-Kakheti25 and vB_Pae-TbilisiM32, were characterized as candidates for use in phage therapy. Morphology, host range, growth properties, thermal stability, serology, genomic sequence, and virion composition are reported. When phages are used as bactericides, they are used in mixtures to overcome the development of resistance in the targeted bacterial population. These two phages are representative of diverse siphoviral and podoviral phage families, respectively, and hence have unrelated mechanisms of infection and no cross-antigenicity. Composing bactericidal phage mixtures with members of different phage families may decrease the incidence of developing resistance through a common mechanism.


Assuntos
Genoma Viral , Infecções por Pseudomonas/microbiologia , Fagos de Pseudomonas/fisiologia , Pseudomonas aeruginosa/virologia , Genômica , Dados de Sequência Molecular , Filogenia , Fagos de Pseudomonas/classificação , Fagos de Pseudomonas/genética , Fagos de Pseudomonas/isolamento & purificação , Pseudomonas aeruginosa/isolamento & purificação , Esgotos/virologia , Proteínas Virais/genética , Proteínas Virais/metabolismo , Vírion/classificação , Vírion/genética , Vírion/isolamento & purificação , Vírion/fisiologia
10.
Mol Cell Proteomics ; 9(5): 940-51, 2010 May.
Artigo em Inglês | MEDLINE | ID: mdl-20233846

RESUMO

Pseudomonas chlororaphis phage 201 phi 2-1 produces a large structurally complex virion, including the products of 89 phage genes. Many of these proteins are modified by proteolysis during virion maturation. To delineate the proteolytic maturation process, 46 slices from an SDS-polyacrylamide gel were subjected to tryptic digestion and then HPLC-electrospray ionization-tandem mass spectrometry analysis. The scale of the experiment allowed high sequence coverage and detection of mass spectra assigned to peptides with one end produced by trypsin and the other end derived from a maturation cleavage (semitryptic peptides). Nineteen cleavage sites were detected in this way. From these sites, a cleavage motif was defined and used to predict the remaining cleavages required to explain the gel mobility of the processed polypeptide species. Profiling the gel with spectrum counts for specific polypeptide regions was found to be helpful in deducing the patterns of proteolysis. A total of 29 cleaved polypeptides derived from 19 gene products were thus detected in the mature 201 phi 2-1 virion. When combined with bioinformatics analyses, these results revealed the presence of head protein-encoding gene modules. Most of the propeptides that were removed from the virion after processing were acidic, whereas the mature domain remaining in the virion was nearly charge-neutral. For four of these processed virion proteins, the portions remaining in the mature virion were mutually homologous. Spectrum counts were found to overestimate the relative quantity of minor polypeptide species in the virion. The resulting sensitivity for minor species made it possible to observe a small amount of general proteolysis that also affected the virions.


Assuntos
Bacteriófagos/metabolismo , Processamento de Proteína Pós-Traducional , Proteoma/análise , Pseudomonas/virologia , Proteínas Virais/análise , Vírion/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Bacteriófagos/genética , Proteínas do Capsídeo/química , Proteínas do Capsídeo/metabolismo , Eletroforese em Gel de Poliacrilamida , Dados de Sequência Molecular , Peso Molecular , Peptídeos/química , Peptídeos/metabolismo , Reprodutibilidade dos Testes , Tripsina/metabolismo , Proteínas Virais/química , Proteínas Virais/metabolismo
11.
Adv Exp Med Biol ; 726: 469-87, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22297527

RESUMO

Large, tailed dsDNA-containing bacteriophage genomes are packaged to a conserved and high density (∼500 mg/ml), generally in ∼2.5-nm, duplex-to-duplex, spaced, organized DNA shells within icosahedral capsids. Phages with these condensate properties, however, differ markedly in their inner capsid structures: (1) those with a naked condensed DNA, (2) those with many dispersed unstructured proteins embedded within the DNA, (3) those with a small number of localized proteins, and (4) those with a reduced or DNA-free internal protein structure of substantial volume. The DNA is translocated and condensed by a high-force ATPase motor into a procapsid already containing the proteins that are to be ejected together with the DNA into the infected host. The condensed genome structure of a single-phage type is unlikely to be precisely determined and can change without loss of function to fit an altered capsid size or internal structure. Although no such single-phage condensed genome structure is known exactly, it is known that a single general structure is unlikely to apply to all such phages.


Assuntos
Bacteriófagos/genética , DNA Viral/ultraestrutura , Genoma Viral , Capsídeo/fisiologia , Capsídeo/ultraestrutura , Modelos Moleculares , Conformação Proteica , Proteínas Virais/química , Montagem de Vírus
12.
Viruses ; 14(4)2022 03 28.
Artigo em Inglês | MEDLINE | ID: mdl-35458430

RESUMO

Viruses are biochemically complex structures and mainly consist of folded proteins that contain nucleic acids. Bacteriophage T4 is one of most prominent examples, having a tail structure that contracts during the infection process. Intracellular phage multiplication leads to separate self-directed assembly reactions of proheads, tails and tail fibers. The proheads are packaged with concatemeric DNA produced by tandem replication reactions of the parental DNA molecule. Once DNA packaging is completed, the head is joined with the tail and six long fibers are attached. The mature particles are then released from the cell via lysis, another tightly regulated process. These processes have been studied in molecular detail leading to a fascinating view of the protein-folding dynamics that direct the structural interplay of assembled complexes. Lindsay W. Black dedicated his career to identifying and defining the molecular events required to form the T4 virion. He leaves us with rich insights into the astonishingly precise molecular clockwork that co-ordinates all of the players in T4 assembly, both viral and cellular. Here, we summarize Lindsay's key research contributions that are certain to stimulate our future science for many years to come.


Assuntos
Bacteriófago T4 , Beleza , Bacteriófago T4/química , Capsídeo/metabolismo , Empacotamento do DNA , DNA Viral/genética
13.
Cureus ; 14(11): e32051, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-36600857

RESUMO

Dieulafoy's lesions are uncommon causes of upper gastrointestinal bleeding (UGIB) that pose a life-threatening risk if not diagnosed promptly and treated appropriately. These lesions are composed of enlarged submucosal blood vessels that bleed despite any gross abnormality. Early intervention with esophagogastroduodenoscopy (EGD) is necessary to avoid more invasive treatment with angiogram embolization or surgical removal. This paper aims to discuss a case regarding a patient with difficult-to-control recurrent bleeding from a Dieulafoy's lesion located in the gastric fundus of a previously healthy 60-year-old female. This case highlights the need for dual therapy and special considerations regarding antiplatelet medications and supplements when treating patients with Dieulafoy's lesions.

14.
Viruses ; 13(10)2021 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-34696524

RESUMO

Phage G is recognized as having a remarkably large genome and capsid size among isolated, propagated phages. Negative stain electron microscopy of the host-phage G interaction reveals tail sheaths that are contracted towards the distal tip and decoupled from the head-neck region. This is different from the typical myophage tail contraction, where the sheath contracts upward, while being linked to the head-neck region. Our cryo-EM structures of the non-contracted and contracted tail sheath show that: (1) The protein fold of the sheath protein is very similar to its counterpart in smaller, contractile phages such as T4 and phi812; (2) Phage G's sheath structure in the non-contracted and contracted states are similar to phage T4's sheath structure. Similarity to other myophages is confirmed by a comparison-based study of the tail sheath's helical symmetry, the sheath protein's evolutionary timetree, and the organization of genes involved in tail morphogenesis. Atypical phase G tail contraction could be due to a missing anchor point at the upper end of the tail sheath that allows the decoupling of the sheath from the head-neck region. Explaining the atypical tail contraction requires further investigation of the phage G sheath anchor points.


Assuntos
Myoviridae/ultraestrutura , Proteínas da Cauda Viral/ultraestrutura , Bacteriófagos/metabolismo , Bacteriófagos/ultraestrutura , Capsídeo/metabolismo , Proteínas do Capsídeo/metabolismo , Microscopia Crioeletrônica/métodos , Myoviridae/genética , Proteínas da Cauda Viral/genética , Proteínas da Cauda Viral/metabolismo , Vírion/metabolismo , Vírion/ultraestrutura
15.
Viruses ; 12(9)2020 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-32825132

RESUMO

"Giant" phages have genomes of >200 kbp, confined in correspondingly large capsids whose assembly and maturation are still poorly understood. Nevertheless, the first assembly product is likely to be, as in other tailed phages, a procapsid that subsequently matures and packages the DNA. The associated transformations include the cleavage of many proteins by the phage-encoded protease, as well as the thinning and angularization of the capsid. We exploited an amber mutation in the viral protease gene of the Salmonella giant phage SPN3US, which leads to the accumulation of a population of capsids with distinctive properties. Cryo-electron micrographs reveal patterns of internal density different from those of the DNA-filled heads of virions, leading us to call them "mottled capsids". Reconstructions show an outer shell with T = 27 symmetry, an embellishment of the HK97 prototype composed of the major capsid protein, gp75, which is similar to some other giant viruses. The mottled capsid has a T = 1 inner icosahedral shell that is a complex network of loosely connected densities composed mainly of the ejection proteins gp53 and gp54. Segmentation of this inner shell indicated that a number of densities (~12 per asymmetric unit) adopt a "twisted hook" conformation. Large patches of a proteinaceous tetragonal lattice with a 67 Å repeat were also present in the cell lysate. The unexpected nature of these novel inner shell and lattice structures poses questions as to their functions in virion assembly.


Assuntos
Capsídeo/metabolismo , Vírus Gigantes/fisiologia , Fagos de Salmonella/fisiologia , Montagem de Vírus , Capsídeo/ultraestrutura , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/metabolismo , Microscopia Crioeletrônica , Empacotamento do DNA , Genoma Viral , Vírus Gigantes/genética , Vírus Gigantes/ultraestrutura , Salmonella/virologia , Fagos de Salmonella/genética , Fagos de Salmonella/ultraestrutura , Vírion/genética , Vírion/fisiologia , Vírion/ultraestrutura
16.
J Mol Biol ; 432(14): 4139-4153, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32454153

RESUMO

Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Šresolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.


Assuntos
Bacteriófagos/ultraestrutura , Proteínas do Capsídeo/genética , DNA Viral/ultraestrutura , Conformação de Ácido Nucleico , Bacteriófagos/genética , Microscopia Crioeletrônica , Empacotamento do DNA/genética , DNA Viral/genética , Humanos , Montagem de Vírus/genética
17.
Viruses ; 12(7)2020 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-32635654

RESUMO

The head of Salmonella virus SPN3US is composed of ~50 different proteins and is unusual because within its packaged genome there is a mass (>40 MDa) of ejection or E proteins that enter the Salmonella cell. The assembly mechanisms of this complex structure are poorly understood. Previous studies showed that eight proteins in the mature SPN3US head had been cleaved by the prohead protease. In this study, we present the characterization of SPN3US prohead protease mutants using transmission electron microscopy and mass spectrometry. In the absence of the prohead protease, SPN3US head formation was severely impeded and proheads accumulated on the Salmonella inner membrane. This impediment is indicative of proteolysis being necessary for the release and subsequent DNA packaging of proheads in the wild-type phage. Proteomic analyses of gp245- proheads that the normal proteolytic processing of head proteins had not occurred. Assays of a recombinant, truncated form of the protease found it was active, leading us to hypothesize that the C-terminal propeptide has a role in targeting the protease into the prohead core. Our findings provide new evidence regarding the essential role of proteolysis for correct head assembly in this remarkable parasite.


Assuntos
Proteínas do Capsídeo/metabolismo , Capsídeo/metabolismo , Fagos de Salmonella/metabolismo , Montagem de Vírus , Capsídeo/ultraestrutura , Genoma Viral/genética , Espectrometria de Massas , Microscopia Eletrônica de Transmissão , Salmonella/virologia , Fagos de Salmonella/genética , Fagos de Salmonella/ultraestrutura , Análise de Sequência de DNA , Internalização do Vírus
18.
Biol Blood Marrow Transplant ; 15(5): 643-8, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19361758

RESUMO

Early recognition of gastrointestinal graft-versus-host disease (GI GVHD) after allogeneic hematopoietic stem cell transplantation (alloHSCT) is vital to initiation of therapy. However, the most common location, the small bowel (SB), is difficult to access with upper and lower endoscopy (UGE/LGE). Wireless capsule endoscopy (WCE) is a noninvasive technology allowing complete SB evaluation. The capsule location can also be tracked to identify motility derangements. From August 2006 to July 2007, 11 alloHSCT patients with GI symptoms underwent WCE, and visual grading was performed. UGE and LGE with biopsies were done when clinically indicated. All patients had evidence of probable acute GVHD (aGVHD) on WCE. WCE revealed lesions of greater severity than those seen by UGE or LGE in most patients. WCE demonstrated that 45% of patients had delayed gastric transit time. WCE is an excellent, noninvasive method for assessing GI GVHD, with the ability to more accurately assess the severity of GVHD, evaluate clinical symptoms, and follow response to treatment.


Assuntos
Endoscopia por Cápsula/métodos , Diagnóstico por Imagem/instrumentação , Gastroenteropatias/diagnóstico , Doença Enxerto-Hospedeiro/diagnóstico , Intestino Delgado , Adolescente , Adulto , Idoso , Endoscopia por Cápsula/normas , Feminino , Transplante de Células-Tronco Hematopoéticas/efeitos adversos , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Índice de Gravidade de Doença , Transplante Homólogo , Adulto Jovem
19.
Methods Mol Biol ; 501: 55-66, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-19066810

RESUMO

Viruses are detected via either biological properties such as plaque formation or physical properties. The physical properties include appearance during microscopy and DNA sequence derived from community sequencing. The assumption is that these procedures will succeed for most, if not all, viruses. However, we have found that some bacteriophages are in a category of viruses that are not detected by any of these classical procedures. Given that the data already indicate viruses to be the "largest reservoir of unknown genetic diversity on earth," the implied expansion of this reservoir confirms the belief that the genome project has hardly begun. The first step is to fill gaps in our knowledge of the biological diversity of viruses, an enterprise that will also help to determine the ways in which (a) viruses have participated in evolution and ecology and (b) viruses can be made to participate in disease control and bioremediation. We present here the details of procedures that can be used to cultivate previously undetectable viruses that are either comparatively large or aggregation-prone.


Assuntos
Bacteriófagos/isolamento & purificação , Biodiversidade , Bacteriófagos/genética , Variação Genética , Genoma Viral
20.
J Family Med Prim Care ; 8(12): 4015-4020, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31879652

RESUMO

BACKGROUND AND AIMS: Medical vandalism has become a major matter of concern in today's world. The number of violent mob attacks on doctors and other medical personnel is on the rise. This trend is having a negative impact on the proper functioning of healthcare system thus affecting the quality of care and treatment. The aim of this study is to assess the awareness and opinions of the stakeholders in healthcare facilities about vandalism in today's medical practice. METHODS: A cross-sectional survey study was conducted in Acharya Vinoba Bhave Rural Hospital among 360 participants, comprising of nurses, patient's relatives, security personnel and non-medical staff in the Emergency Care Units and wards. A detailed questionnaire was prepared and used to assess the opinion of the subjects covering various aspects of medical vandalism such as prevalence of vandalism, experiences of vandalism at work, various factors causing medical vandalism, initiatives taken by the respondents to curb vandalism and awareness about various laws implemented by the government that help prevent vandalism. RESULTS: Majority of the participants were of the opinion that medical vandalism was prevalent in India. Overcrowding of patients, inadequate skilled healthcare providers and occurrence of sudden death in casualty are among the major factors that trigger vandalism. This issue has been on the rise in both government and private setups, and nurses seem to be the major victims of such cruelness. 80% of the subjects admitted that verbal abuse was more common than physical abuse. CONCLUSION: Although violence against all healthcare professionals has been recorded since historical times, the current scenario of the country is disturbing. Immediate measures need to be taken to curb vandalism. Various laws need to be implemented to strictly punish those who create violence. Likewise, institutions must ensure the availability of adequate staff and facilities to reduce events that make the bystanders aggressive.

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