[34] GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes

Walhout, Albertha J.M.; Temple, Gary F.; Brasch, Michael A.; Hartley, James L.; Lorson, Monique A.; Heuvel, Sander van den; Vidal, Marc

doi:10.1016/s0076-6879(00)28419-x

Cited by 593 publications

(459 citation statements)

References 25 publications

Supporting

Mentioning

455

Contrasting

Unclassified

Order By: Relevance

“…We are using the Gateway ® recombinational cloning system (Invitrogen, (23,24)) in order to clone viral ORFs and to construct viral ORFeomes (see our LIMS, viralORFeome at http:/ /www.viralorfeome.com (16)). Using these viral ORFs entry clones, we can recombine them by an LR reaction into pGBKT7-gw.…”

Section: Grow Each Yeast Bait Colony Overnight In 2 ML Sd-w Under Agimentioning

confidence: 99%

Virus–Human Cell Interactomes

Tafforeau¹,

Rabourdin–Combe²,

Lotteau³

2011

Methods in Molecular Biology

View full text Add to dashboard Cite

Using global approaches and high-throughput technologies in virology brings a new vision of the infections physiology and allows the identification of cellular factors, mandatory for viral life cycle, that could be targeted by original therapeutic agents. It opens perspectives for the treatment of viral infections by acting on cellular pathways that the virus must use for its own replication. Combining these new molecules with classical antiviral drugs and immunomodulators diversifies and enlarges the antiviral arsenal and contributes to fight drug resistance.Our laboratory and others are constructing virus-human interactomes to propose a comprehensive analysis of viral infection at the cellular level. Studying these infection maps, where the viral infection can be visualized as perturbation of the human protein-protein interaction network, and identifying the biological functions that are impaired by these perturbations may lead to discovery of new therapeutic targets. These virus-human interaction maps are constructed in a stringent yeast two-hybrid system by screening human cDNA libraries with viral proteins as bait and integrating interactions mined from literature and public databases. Key words:Yeast two-hybrid screen, Mating, Yeast two-hybrid array, Protein-protein interactionThe rapidly growing knowledge of protein-protein interaction networks (interactomes) for model organisms and human provides a network-based model to understand molecular and cellular biology. Recently, virus-host relationships also began to be studied at the proteome level by identifying interactions between viral and host-cell proteins (1-5), as reviewed in ref. 6. These virus-host interactomes compose a repertoire of interactions between viral and human proteins that can be analyzed in a network approach. By this mean, viral infections can be viewed as the expression of new constraints imposed by the virus on the cellular interactome.

show abstract

Section: Grow Each Yeast Bait Colony Overnight In 2 ML Sd-w Under Agimentioning

confidence: 99%

Virus–Human Cell Interactomes

Tafforeau¹,

Rabourdin–Combe²,

Lotteau³

2011

Methods in Molecular Biology

View full text Add to dashboard Cite

show abstract

“…Several recombination-based methods are now widely used that allow the facile shuttling of the cloned ORFs into various types of expression systems [22]. The use of such methods is unnecessary, however, if the choice of expression is clear or if the compromises involved in the use of a single system are acceptable.…”

Section: Content: Producing the Proteinsmentioning

confidence: 99%

Microarrays to characterize protein interactions on a whole‐proteome scale

Schweitzer¹,

Predki²,

Snyder

2003

Proteomics

148

View full text Add to dashboard Cite

Protein microarrays contain a defined set of proteins spotted and analyzed at high density, and can be generally classified into two categories; protein profiling arrays and functional protein arrays. Functional protein arrays can be made up of any type of protein, and therefore have a diverse set of useful applications. Advantages of these arrays include low reagent consumption, rapid interpretation of results, and the ability to easily control experimental conditions. The ultimate form of a functional protein array consists of all of the proteins encoded by the genome of an organism; such an array would be the whole proteome equivalent of the whole genome DNA arrays that are now available. While proteome microarrays may not have reached the stage of maturity of DNA microarrays, recent developments have shown that many of the barriers holding back the technology can be overcome. Arrays of this type have already been used to rapidly screen large numbers of proteins simultaneously for biochemical activities, protein-protein interactions, protein-lipid interactions, protein-nucleic acid interactions, and protein-small molecule interactions. Eventually, functional protein arrays will be used to facilitate various steps in the drug discovery and early development processes that are currently bottlenecks in the drug development continuum.

show abstract

“…Structural genomics research has made major contribution to number of structure and the coverage of fold space in the protein structure database (PDB) [6]. Structural genomics research has also lead to methods, commercial instrumentation, labware, and reagents for high throughput cloning, expression, and crystallization of proteins [12][13][14][15][16]. New software tools for structure prediction [17,19], design of experiments, laboratory information management, novel structure based informatics [20][21][22], such as function prediction from structure, have also been developed [23][24][25].…”

Section: Introductionmentioning

confidence: 99%

“…Notable examples of methods innovation that enable structural genomics but also impact laboratory scale research are: gateway cloning [13], autoinduction [26], nanoscale crystallization [15,27], and automated structure determination [28][29][30][31][32]. Gateway cloning facilitates the rapid construction of a variety of expression plasmids from a single entry clone and provides a basis for establishing a more useful clone collection [13].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Practical applications of structural genomics technologies for mutagen research

Zemła

Segelke

2011

Mutation Research/Genetic Toxicology and Environmental Mutagene

View full text Add to dashboard Cite

Here we present a perspective on a range of practical uses of structural genomics for mutagen research. Structural genomics is an overloaded term and requires some definition to bound the discussion; we give a brief description of public and private structural genomics endeavors, along with some of their objectives, their activities, their capabilities, and their limitations. We discuss how structural genomics might impact mutagen research in three different scenarios: at a structural genomics center, at a lab with modest resources that also conducts structural biology research, and at a lab that conducting mutagen research absent experimental structural biology. Applications span functional annotation of single genes, to constructing gene networks and pathways, to an integrated systems biology approach. Structural genomics centers can take advantage of systems biology models to target high value targets for structure determination and in turn extend systems models to better understand systems biology diseases or phenomenon. Individual investigator run structural biology laboratories can collaborate with structural genomics centers, but can also take advantage of technical advances and tools developed by structural genomics centers and can employ a structural genomics approach to advancing biological understanding. Individual investigator run non-structural biology laboratories can also collaborate with structural genomics center, possibly influencing targeting decisions, but can also use structure based annotation tools enabled by the growing coverage of protein fold space provided by structural genomics. Better functional annotation can inform pathway and systems biology models.

show abstract

[34] GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes

Cited by 593 publications

References 25 publications

Virus–Human Cell Interactomes

Virus–Human Cell Interactomes

Microarrays to characterize protein interactions on a whole‐proteome scale

Practical applications of structural genomics technologies for mutagen research

Contact Info

Product

Resources

About