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Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses.

Simonis N, Rual JF, Lemmens I, Boxus M, Hirozane-Kishikawa T, Gatot JS, Dricot A, Hao T, Vertommen D, Legros S, Daakour S, Klitgord N, Martin M, Willaert JF, Dequiedt F, Navratil V, Cusick ME, Burny A, Van Lint C, Hill DE, Tavernier J, Kettmann R, Vidal M, Twizere JC - Retrovirology (2012)

Bottom Line: Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively.Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway.This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave,, Boston, MA 02215, USA.

ABSTRACT

Background: Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression.

Results: We employ a scalable methodology for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two-hybrid screening and systematic retest, as well as two independent validations through an additional protein interaction detection method and a functional transactivation assay. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins. Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway.

Conclusions: This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

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Pipeline of the HT-Y2H experiment. (A) Retroviral ORFeome screened against Human ORFeome 3.1 in both configurations (DB-hORF AD-rvORF and DB-rvORF AD-hORF). Interactions found in the primary screen were subjected to homologous individual retest, where any human interactor of HTLV 1-2 protein was also retested for interaction with all homologous HTLV l and 2 proteins. An example of homologous group with Tax and Rex is shown. To guarantee high specificity, only interactions identified with at least two out of three reporter phenotypes were considered positive. (B) Venn diagram of the number of human proteins targeted by each virus.
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Figure 1: Pipeline of the HT-Y2H experiment. (A) Retroviral ORFeome screened against Human ORFeome 3.1 in both configurations (DB-hORF AD-rvORF and DB-rvORF AD-hORF). Interactions found in the primary screen were subjected to homologous individual retest, where any human interactor of HTLV 1-2 protein was also retested for interaction with all homologous HTLV l and 2 proteins. An example of homologous group with Tax and Rex is shown. To guarantee high specificity, only interactions identified with at least two out of three reporter phenotypes were considered positive. (B) Venn diagram of the number of human proteins targeted by each virus.

Mentions: HTLV structural and regulatory proteins have significant sequence or functional similarity (for example HTLV-1 Tax and HTLV-2 Tax share 77% of sequence similarity, and both are transcriptional activators of viral expression). These homologous viral proteins might share one or more interacting partners amongst the human proteins, interactions that were not identified in initial screens because (i) highly overlapping or similar viral ORFs may be misidentified with BLAST, and (ii) interactions can be missed in a single screen [12,13,18]. We retested all homologous HTLV proteins for interaction with each human protein found in our initial screen with at least one homologous viral protein. For instance, all human proteins identified as HTLV-1 Tax interactors were also retested against HTLV-1 and HTLV-2 Tax and Rex proteins (Additional file 1: Table S1). This strategy combines the advantages of pooling [14] with individual testing, to reduce the cost and workload of the initial screen while keeping the ability to differentiate similar proteins, overcome sensitivity and specificity issues and permits comparison of negative results. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins (Figure 1 and Additional file 1: Table S2). Among the 166 PPIs identified 87 and 79 interactions involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Twenty-eight out of the one hundred and twenty-two human proteins were found to interact with both viruses (Figure 1B).


Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses.

Simonis N, Rual JF, Lemmens I, Boxus M, Hirozane-Kishikawa T, Gatot JS, Dricot A, Hao T, Vertommen D, Legros S, Daakour S, Klitgord N, Martin M, Willaert JF, Dequiedt F, Navratil V, Cusick ME, Burny A, Van Lint C, Hill DE, Tavernier J, Kettmann R, Vidal M, Twizere JC - Retrovirology (2012)

Pipeline of the HT-Y2H experiment. (A) Retroviral ORFeome screened against Human ORFeome 3.1 in both configurations (DB-hORF AD-rvORF and DB-rvORF AD-hORF). Interactions found in the primary screen were subjected to homologous individual retest, where any human interactor of HTLV 1-2 protein was also retested for interaction with all homologous HTLV l and 2 proteins. An example of homologous group with Tax and Rex is shown. To guarantee high specificity, only interactions identified with at least two out of three reporter phenotypes were considered positive. (B) Venn diagram of the number of human proteins targeted by each virus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351729&req=5

Figure 1: Pipeline of the HT-Y2H experiment. (A) Retroviral ORFeome screened against Human ORFeome 3.1 in both configurations (DB-hORF AD-rvORF and DB-rvORF AD-hORF). Interactions found in the primary screen were subjected to homologous individual retest, where any human interactor of HTLV 1-2 protein was also retested for interaction with all homologous HTLV l and 2 proteins. An example of homologous group with Tax and Rex is shown. To guarantee high specificity, only interactions identified with at least two out of three reporter phenotypes were considered positive. (B) Venn diagram of the number of human proteins targeted by each virus.
Mentions: HTLV structural and regulatory proteins have significant sequence or functional similarity (for example HTLV-1 Tax and HTLV-2 Tax share 77% of sequence similarity, and both are transcriptional activators of viral expression). These homologous viral proteins might share one or more interacting partners amongst the human proteins, interactions that were not identified in initial screens because (i) highly overlapping or similar viral ORFs may be misidentified with BLAST, and (ii) interactions can be missed in a single screen [12,13,18]. We retested all homologous HTLV proteins for interaction with each human protein found in our initial screen with at least one homologous viral protein. For instance, all human proteins identified as HTLV-1 Tax interactors were also retested against HTLV-1 and HTLV-2 Tax and Rex proteins (Additional file 1: Table S1). This strategy combines the advantages of pooling [14] with individual testing, to reduce the cost and workload of the initial screen while keeping the ability to differentiate similar proteins, overcome sensitivity and specificity issues and permits comparison of negative results. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins (Figure 1 and Additional file 1: Table S2). Among the 166 PPIs identified 87 and 79 interactions involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Twenty-eight out of the one hundred and twenty-two human proteins were found to interact with both viruses (Figure 1B).

Bottom Line: Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively.Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway.This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave,, Boston, MA 02215, USA.

ABSTRACT

Background: Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression.

Results: We employ a scalable methodology for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two-hybrid screening and systematic retest, as well as two independent validations through an additional protein interaction detection method and a functional transactivation assay. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins. Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway.

Conclusions: This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

Show MeSH
Related in: MedlinePlus