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The genomic underpinnings of apoptosis in the silkworm, Bombyx mori.

Zhang JY, Pan MH, Sun ZY, Huang SJ, Yu ZS, Liu D, Zhao DH, Lu C - BMC Genomics (2010)

Bottom Line: However, the lack of genomic data for silkworms limits their usefulness in apoptosis studies, despite the advantages of silkworm as a representative of Lepidoptera and an effective model system.Herein we have identified apoptosis-related genes in the silkworm Bombyx mori and compared them to those from insects, mammals, and nematodes.These results lay the foundation for further apoptosis-related study in Bombyx mori.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China.

ABSTRACT

Background: Apoptosis is regulated in an orderly fashion by a series of genes, and has a crucial role in important physiological processes such as growth development, immunological response and so on. Recently, substantial studies have been undertaken on apoptosis in model animals including humans, fruit flies, and the nematode. However, the lack of genomic data for silkworms limits their usefulness in apoptosis studies, despite the advantages of silkworm as a representative of Lepidoptera and an effective model system. Herein we have identified apoptosis-related genes in the silkworm Bombyx mori and compared them to those from insects, mammals, and nematodes.

Results: From the newly assembled genome databases, a genome-wide analysis of apoptosis-related genes in Bombyx mori was performed using both nucleotide and protein Blast searches. Fifty-two apoptosis-related candidate genes were identified, including five caspase family members, two tumor necrosis factor (TNF) superfamily members, one Bcl-2 family member, four baculovirus IAP (inhibitor of apoptosis) repeat (BIR) domain family members and 1 RHG (Reaper, Hid, Grim, and Sickle; Drosophila cell death activators) family member. Moreover, we identified a new caspase family member, BmCaspase-New, two splice variants of BmDronc, and Bm3585, a mammalian TNF superfamily member homolog. Twenty-three of these apoptosis-related genes were cloned and sequenced using cDNA templates isolated from BmE-SWU1 cells. Sequence analyses revealed that these genes could have key roles in apoptosis.

Conclusions: Bombyx mori possesses potential apoptosis-related genes. We hypothesized that the classic intrinsic and extrinsic apoptotic pathways potentially are active in Bombyx mori. These results lay the foundation for further apoptosis-related study in Bombyx mori.

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Structures of the proteins in Bombyx mori predicted to contain BIR domains. A diagrammatic representation of the domain architecture of the Bir domain members of the silkworm and the two IAPs in Drosophila is shown here. The numbers are the start and end location of the domains in the protein sequences.
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Figure 4: Structures of the proteins in Bombyx mori predicted to contain BIR domains. A diagrammatic representation of the domain architecture of the Bir domain members of the silkworm and the two IAPs in Drosophila is shown here. The numbers are the start and end location of the domains in the protein sequences.

Mentions: The BIR domain is a unique structure originally identified in IAP proteins from baculoviruses. At least one BIR motif is essential for the antiapoptotic activity of IAP family members, but not all BIR-containing proteins (BIRPs) are IAPs [56]. We identified four proteins containing BIR domains in Bombyx mori, including two IAPs, one Bruce and one survivin. Huang and colleagues [50] cloned the first IAP family member BmIAP from Bombyx mori BmN cells. BmIAP is a specific inhibitor of mammalian caspase-9, but does not directly inhibit the downstream effector proteases caspase-3 and caspase-7. BmIAP inhibits apoptosis induced by Bax but not Fas in vitro. However, the function of BmIAP in vivo is not yet known. The other IAP family member BmIAP2 is located on the same chromosome as BmIAP, is 561 aa long and possesses three BIR domains and one Zn2+-finger domain. Compared with DIAP1 and DIAP2, BmIAP1 and BmIAP2 have two and three BIR domains, respectively, also (Figure 4). The BmBruce and survivin proteins each have one BIR domain, with a sequence consistent with the online BIR sequence (http://www.expasy.org/cgi-bin/nicedoc.pl?PS50143), and are 4236 aa and 136 aa long, respectively (Figure 4). Besides their size difference, BmBruce also has an ubiquitin-proteasome binding motif, which is homologous to Drosophila Bruce protein [66].


The genomic underpinnings of apoptosis in the silkworm, Bombyx mori.

Zhang JY, Pan MH, Sun ZY, Huang SJ, Yu ZS, Liu D, Zhao DH, Lu C - BMC Genomics (2010)

Structures of the proteins in Bombyx mori predicted to contain BIR domains. A diagrammatic representation of the domain architecture of the Bir domain members of the silkworm and the two IAPs in Drosophila is shown here. The numbers are the start and end location of the domains in the protein sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091752&req=5

Figure 4: Structures of the proteins in Bombyx mori predicted to contain BIR domains. A diagrammatic representation of the domain architecture of the Bir domain members of the silkworm and the two IAPs in Drosophila is shown here. The numbers are the start and end location of the domains in the protein sequences.
Mentions: The BIR domain is a unique structure originally identified in IAP proteins from baculoviruses. At least one BIR motif is essential for the antiapoptotic activity of IAP family members, but not all BIR-containing proteins (BIRPs) are IAPs [56]. We identified four proteins containing BIR domains in Bombyx mori, including two IAPs, one Bruce and one survivin. Huang and colleagues [50] cloned the first IAP family member BmIAP from Bombyx mori BmN cells. BmIAP is a specific inhibitor of mammalian caspase-9, but does not directly inhibit the downstream effector proteases caspase-3 and caspase-7. BmIAP inhibits apoptosis induced by Bax but not Fas in vitro. However, the function of BmIAP in vivo is not yet known. The other IAP family member BmIAP2 is located on the same chromosome as BmIAP, is 561 aa long and possesses three BIR domains and one Zn2+-finger domain. Compared with DIAP1 and DIAP2, BmIAP1 and BmIAP2 have two and three BIR domains, respectively, also (Figure 4). The BmBruce and survivin proteins each have one BIR domain, with a sequence consistent with the online BIR sequence (http://www.expasy.org/cgi-bin/nicedoc.pl?PS50143), and are 4236 aa and 136 aa long, respectively (Figure 4). Besides their size difference, BmBruce also has an ubiquitin-proteasome binding motif, which is homologous to Drosophila Bruce protein [66].

Bottom Line: However, the lack of genomic data for silkworms limits their usefulness in apoptosis studies, despite the advantages of silkworm as a representative of Lepidoptera and an effective model system.Herein we have identified apoptosis-related genes in the silkworm Bombyx mori and compared them to those from insects, mammals, and nematodes.These results lay the foundation for further apoptosis-related study in Bombyx mori.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China.

ABSTRACT

Background: Apoptosis is regulated in an orderly fashion by a series of genes, and has a crucial role in important physiological processes such as growth development, immunological response and so on. Recently, substantial studies have been undertaken on apoptosis in model animals including humans, fruit flies, and the nematode. However, the lack of genomic data for silkworms limits their usefulness in apoptosis studies, despite the advantages of silkworm as a representative of Lepidoptera and an effective model system. Herein we have identified apoptosis-related genes in the silkworm Bombyx mori and compared them to those from insects, mammals, and nematodes.

Results: From the newly assembled genome databases, a genome-wide analysis of apoptosis-related genes in Bombyx mori was performed using both nucleotide and protein Blast searches. Fifty-two apoptosis-related candidate genes were identified, including five caspase family members, two tumor necrosis factor (TNF) superfamily members, one Bcl-2 family member, four baculovirus IAP (inhibitor of apoptosis) repeat (BIR) domain family members and 1 RHG (Reaper, Hid, Grim, and Sickle; Drosophila cell death activators) family member. Moreover, we identified a new caspase family member, BmCaspase-New, two splice variants of BmDronc, and Bm3585, a mammalian TNF superfamily member homolog. Twenty-three of these apoptosis-related genes were cloned and sequenced using cDNA templates isolated from BmE-SWU1 cells. Sequence analyses revealed that these genes could have key roles in apoptosis.

Conclusions: Bombyx mori possesses potential apoptosis-related genes. We hypothesized that the classic intrinsic and extrinsic apoptotic pathways potentially are active in Bombyx mori. These results lay the foundation for further apoptosis-related study in Bombyx mori.

Show MeSH
Related in: MedlinePlus