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1.
BMC Bioinformatics ; 19(1): 326, 2018 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-30219026

RESUMO

BACKGROUND: Spanins are phage lysis proteins required to disrupt the outer membrane. Phages employ either two-component spanins or unimolecular spanins in this final step of Gram-negative host lysis. Two-component spanins like Rz-Rz1 from phage lambda consist of an integral inner membrane protein: i-spanin, and an outer membrane lipoprotein: o-spanin, that form a complex spanning the periplasm. Two-component spanins exist in three different genetic architectures; embedded, overlapped and separated. In contrast, the unimolecular spanins, like gp11 from phage T1, have an N-terminal lipoylation signal sequence and a C-terminal transmembrane domain to account for the topology requirements. Our proposed model for spanin function, for both spanin types, follows a common theme of the outer membrane getting fused with the inner membrane, effecting the release of progeny virions. RESULTS: Here we present a SpaninDataBase which consists of 528 two-component spanins and 58 unimolecular spanins identified in this analysis. Primary analysis revealed significant differences in the secondary structure predictions for the periplasmic domains of the two-component and unimolecular spanin types, as well as within the three different genetic architectures of the two-component spanins. Using a threshold of 40% sequence identity over 40% sequence length, we were able to group the spanins into 143 i-spanin, 125 o-spanin and 13 u-spanin families. More than 40% of these families from each type were singletons, underlining the extreme diversity of this class of lysis proteins. Multiple sequence alignments of periplasmic domains demonstrated conserved secondary structure patterns and domain organization within family members. Furthermore, analysis of families with members from different architecture allowed us to interpret the evolutionary dynamics of spanin gene arrangement. Also, the potential universal role of intermolecular disulfide bonds in two-component spanin function was substantiated through bioinformatic and genetic approaches. Additionally, a novel lipobox motif, AWAC, was identified and experimentally verified. CONCLUSIONS: The findings from this bioinformatic approach gave us instructive insights into spanin function, evolution, domain organization and provide a platform for future spanin annotation, as well as biochemical and genetic experiments. They also establish that spanins, like viral membrane fusion proteins, adopt different strategies to achieve fusion of the inner and outer membranes.


Assuntos
Bacteriófago lambda/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Bacteriófago lambda/genética , Conformação Proteica , Domínios Proteicos , Homologia de Sequência , Proteínas Virais/química
2.
Genome Announc ; 5(31)2017 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-28774966

RESUMO

Citrobacter freundii is responsible for various opportunistic nosocomial infections. Phage therapies against C. freundii may prove useful in human medicine for treatment of infections caused by the ubiquitous bacteria. Here, we announce the complete genome sequence of the C. freundii Felix O1-like myophage Mijalis and present its features.

3.
PLoS Comput Biol ; 13(5): e1005425, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-28542180

RESUMO

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., the list of variable sites). The subsequent exploratory stage is much more ad hoc and requires the development of custom scripts and pipelines, making it problematic for biomedical researchers. Here, we describe a hybrid platform combining common analysis pathways with the ability to explore data interactively. It aims to fully encompass and simplify the "raw data-to-publication" pathway and make it reproducible.


Assuntos
Pesquisa Biomédica/métodos , Pesquisa Biomédica/organização & administração , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , Pesquisadores , Software , Humanos
4.
F1000Res ; 62017.
Artigo em Inglês | MEDLINE | ID: mdl-29333231

RESUMO

Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.

5.
Nucleic Acids Res ; 44(W1): W3-W10, 2016 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-27137889

RESUMO

High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.


Assuntos
Biologia Computacional/estatística & dados numéricos , Conjuntos de Dados como Assunto/estatística & dados numéricos , Interface Usuário-Computador , Pesquisa Biomédica , Biologia Computacional/métodos , Bases de Dados Genéticas , Humanos , Internet , Reprodutibilidade dos Testes
6.
Genome Announc ; 3(6)2015 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-26607888

RESUMO

Podophage Percy infects Caulobacter crescentus, a Gram-negative bacterium that divides asymmetrically and is a commonly used model organism to study the cell cycle, asymmetric cell division, and cell differentiation. Here, we announce the sequence and annotated complete genome of the phiKMV-like podophage Percy and note its prominent features.

7.
Genome Announc ; 3(5)2015 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-26430046

RESUMO

Bacteriophage Merlin is a T4-like myophage which infects Citrobacter freundii, a member of the Enterobacteriaceae family. C. freundii is an opportunistic pathogen that is a common cause of nosocomial infections. This report announces the complete genome of myophage Merlin and describes its features.

8.
Genome Announc ; 3(5)2015 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-26430045

RESUMO

Caulobacter crescentus is a water-dwelling bacterium known to have a dimorphic life cycle. Here, we announce the complete genome of Seuss, a C. crescentus icosahedral siphophage, and describe key features. Seuss is unique among phages deposited in GenBank, with genes encoding novel hypothetical proteins composing 45% of its genome.

9.
Genome Announc ; 3(5)2015 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-26430049

RESUMO

Klebsiella pneumoniae is a leading cause of nosocomial infections in the United States. Due to the emergence of multidrug-resistant strains, phages targeting K. pneumoniae may be a useful alternative against this pathogen. Here, we announce the complete genome of K. pneumoniae pseudo-T-even myophage Matisse and describe its features.

10.
Genome Announc ; 3(5)2015 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-26430050

RESUMO

Klebsiella pneumoniae is a Gram-negative pathogen frequently associated with antibiotic-resistant nosocomial infections. Bacteriophage therapy against K. pneumoniae may be possible to combat these infections. The following describes the complete genome sequence and key features of the pseudo-T-even K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae myophage Miro.

11.
Genome Announc ; 3(5)2015 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-26430047

RESUMO

Citrobacter freundii is a Gram-negative opportunistic pathogen that causes dangerous infections such as neonatal meningitis. C. freundii also harbors antibiotic resistance, making phages infecting this host valuable tools. Here, we announce the complete genome of the C. freundii FelixO1-like myophage Michonne and describe its notable features.

12.
Genome Announc ; 3(5)2015 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-26430048

RESUMO

Murica is an rv5-like myophage that infects enterotoxigenic Escherichia coli. Pathogenic E. coli strains are responsible for many intestinal diseases, and phages that infect these bacteria may prove useful in preventing severe health issues. The following is a report of the complete genome sequence of Murica and its important features.

13.
Genome Announc ; 3(5)2015 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-26450722

RESUMO

Silence is a newly isolated siphophage that infects Bacillus megaterium, a soil bacterium that is used readily in research and commercial applications. A study of B. megaterium phage Silence will enhance our knowledge of the diversity of Bacillus phages. Here, we describe the complete genome sequence and annotated features of Silence.

14.
Genome Announc ; 3(5)2015 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-26450723

RESUMO

Caulobacter crescentus is a Gram-negative dimorphic model organism used to study cell differentiation. Siphophage Sansa is a newly isolated siphophage with an icosahedral capsid that infects C. crescentus. Sansa shares no sequence similarity to other phages deposited in GenBank. Here, we describe its genome sequence and general features.

15.
Genome Announc ; 3(5)2015 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-26472844

RESUMO

Citrobacter freundii is a Gram-negative opportunistic pathogen that is associated with urinary tract infections. Bacteriophages infecting C. freundii can be used as an effective treatment to fight these infections. Here, we announce the complete genome sequence of the C. freundii Felix O1-like myophage Mordin and describe its features.

16.
Genome Announc ; 3(5)2015 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-26337888

RESUMO

Bacillus megaterium is a large spore-forming bacterium found widely in the environment. Phages infecting B. megaterium can be used as genetic tools to expand the array of uses of B. megaterium in research and industry. Here, we present the complete genome of Pavlov, a podophage infecting B. megaterium.

17.
Genome Announc ; 3(5)2015 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-26337889

RESUMO

Klebsiella pneumoniae is a Gram-negative bacterium in the family Enterobacteriaceae. It is associated with numerous nosocomial infections, including respiratory and urinary tract infections in humans. The following reports the complete genome sequence of K. pneumoniae carbapenemase-producing K. pneumoniae T1-like siphophage Sushi and describes its major features.

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