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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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Phylogenetic tree of the TNF superfamily. This phylogenetic tree of the TNF superfamily was produced by neighbor-joining of multiple sequence alignment of TNF superfamily sequences from insect and the homologous sequences of the TNFSF from higher animals [including Homo sapiens, Rattus norvegicus, Monodelphis domestica, Oncorhynchus mykiss, Salmo salar and Xenopus (Silurana) tropicalis]. Because the silkworm TNFSF homologs were produced by alignment with TNFSF5 and TNFSF13, the TNFSF sequences used in this phylogenetic tree were the TNFSF5 and TNFSF13 in different species. The TNFSF members predicted in Bombyx mori are marked with large red dots. The protein names use an abbreviation of species and gene names. The full species names are listed in the black frame on the right.
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Figure 5: Phylogenetic tree of the TNF superfamily. This phylogenetic tree of the TNF superfamily was produced by neighbor-joining of multiple sequence alignment of TNF superfamily sequences from insect and the homologous sequences of the TNFSF from higher animals [including Homo sapiens, Rattus norvegicus, Monodelphis domestica, Oncorhynchus mykiss, Salmo salar and Xenopus (Silurana) tropicalis]. Because the silkworm TNFSF homologs were produced by alignment with TNFSF5 and TNFSF13, the TNFSF sequences used in this phylogenetic tree were the TNFSF5 and TNFSF13 in different species. The TNFSF members predicted in Bombyx mori are marked with large red dots. The protein names use an abbreviation of species and gene names. The full species names are listed in the black frame on the right.

Mentions: TNF family ligands and their corresponding receptors (TNFR) have pivotal roles in many important physiological processes, such as host defense, inflammation, apoptosis, autoimmunity and immune system organogenesis. The TNF-related ligands are type II (intracellular N-terminus) transmembrane proteins containing a TNF homology domain (THD) at the extracellular C terminus. Protein sequences of 18 TNFSF ligands in mammals[70] and the TNF ligand Eiger in Drosophila[62] used as queries were aligned with the silkworm predicted protein database by BlastP. Two TNFSF members, Bm3585 and Bm3614, were identified. They are located on chromosome 5 (Table 1). Bm3585 and Bm3614 possess the typical THD as predicted (http://blast.ncbi.nlm.nih.gov/; Table 1), and demonstrated that potential TNF ligands are present in Bombyx mori. The phylogenetic tree of TNFSF between silkworm and other species show that Bm3614 and the insect Eiger homolog are in one cluster, while Bm3585 and TNFSF5 are classified close together, but the two TNF ligand homologs are evolutionarily distant (Figure 5), all of which indicate that a gene deletion or duplication event might had happened.


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)

Phylogenetic tree of the TNF superfamily. This phylogenetic tree of the TNF superfamily was produced by neighbor-joining of multiple sequence alignment of TNF superfamily sequences from insect and the homologous sequences of the TNFSF from higher animals [including Homo sapiens, Rattus norvegicus, Monodelphis domestica, Oncorhynchus mykiss, Salmo salar and Xenopus (Silurana) tropicalis]. Because the silkworm TNFSF homologs were produced by alignment with TNFSF5 and TNFSF13, the TNFSF sequences used in this phylogenetic tree were the TNFSF5 and TNFSF13 in different species. The TNFSF members predicted in Bombyx mori are marked with large red dots. The protein names use an abbreviation of species and gene names. The full species names are listed in the black frame on the right.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Phylogenetic tree of the TNF superfamily. This phylogenetic tree of the TNF superfamily was produced by neighbor-joining of multiple sequence alignment of TNF superfamily sequences from insect and the homologous sequences of the TNFSF from higher animals [including Homo sapiens, Rattus norvegicus, Monodelphis domestica, Oncorhynchus mykiss, Salmo salar and Xenopus (Silurana) tropicalis]. Because the silkworm TNFSF homologs were produced by alignment with TNFSF5 and TNFSF13, the TNFSF sequences used in this phylogenetic tree were the TNFSF5 and TNFSF13 in different species. The TNFSF members predicted in Bombyx mori are marked with large red dots. The protein names use an abbreviation of species and gene names. The full species names are listed in the black frame on the right.
Mentions: TNF family ligands and their corresponding receptors (TNFR) have pivotal roles in many important physiological processes, such as host defense, inflammation, apoptosis, autoimmunity and immune system organogenesis. The TNF-related ligands are type II (intracellular N-terminus) transmembrane proteins containing a TNF homology domain (THD) at the extracellular C terminus. Protein sequences of 18 TNFSF ligands in mammals[70] and the TNF ligand Eiger in Drosophila[62] used as queries were aligned with the silkworm predicted protein database by BlastP. Two TNFSF members, Bm3585 and Bm3614, were identified. They are located on chromosome 5 (Table 1). Bm3585 and Bm3614 possess the typical THD as predicted (http://blast.ncbi.nlm.nih.gov/; Table 1), and demonstrated that potential TNF ligands are present in Bombyx mori. The phylogenetic tree of TNFSF between silkworm and other species show that Bm3614 and the insect Eiger homolog are in one cluster, while Bm3585 and TNFSF5 are classified close together, but the two TNF ligand homologs are evolutionarily distant (Figure 5), all of which indicate that a gene deletion or duplication event might had happened.

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