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Evolution of selenoproteins in the metazoan.

Jiang L, Ni J, Liu Q - BMC Genomics (2012)

Bottom Line: Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal.During evolutionary history, only a few new selenoproteins have emerged and few were lost.Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Life Sciences, Shenzhen University, Shenzhen, 518060, Guangdong Province, PR, China.

ABSTRACT

Background: The selenocysteine (Sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. Although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely reported outside of insects and nematodes.

Result: A more integrated view of selenoprotein evolution was constructed using several representative species from different evolutionary eras. Using a SelGenAmic-based selenoprotein identification method, 178 selenoprotein genes were identified in 6 invertebrates: Amphimedon queenslandica, Trichoplax adhaerens, Nematostella vectensis, Lottia gigantean, Capitella teleta, and Branchiostoma floridae. Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal. This gene structure suggests the existence of two different strategies for extension of Sec numbers in SelP for the preservation and transportation of selenium. In addition, novel eukaryotic AphC-like selenoproteins were identified in sponges.

Conclusion: Comparison of various animal species suggests that even the most primitive animals possess a selenoproteome range and variety similar to humans. During evolutionary history, only a few new selenoproteins have emerged and few were lost. Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.

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3NSelP of Amphioxus.A. The gene structure of 3NSelP with all Sec-TGA codons and SECIS elements is indicated. R1, R2, and R3 represent the 3-repeat regions. Each of the repeated regions can be divided into several parts and labeled parts a, b, c, and d. B. Multiple alignment 3-repeat region of the 3NSelP Sec residues and part a, b, c, and d are shown. C. The secondary structures of the two SECIS elements of the 3NSelP gene are shown.
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Figure 4: 3NSelP of Amphioxus.A. The gene structure of 3NSelP with all Sec-TGA codons and SECIS elements is indicated. R1, R2, and R3 represent the 3-repeat regions. Each of the repeated regions can be divided into several parts and labeled parts a, b, c, and d. B. Multiple alignment 3-repeat region of the 3NSelP Sec residues and part a, b, c, and d are shown. C. The secondary structures of the two SECIS elements of the 3NSelP gene are shown.

Mentions: SelP is present in all known vertebrate selenoproteomes, but rarely in invertebrates. Only 5 SelP genes were found in this work, and 4 of them were present in amphioxus (Branchiostoma floridae). The other one was found in Lottia gigantea. Among these, a special SelP was found in amphioxus that contained 5 Sec residues. In this SelP, 3 Sec residues located in the N-terminal region contained 3 repeats of the Trx-like domain. Each was found to be homologous with the N-terminal region containing a Sec residue in vertebrate SelP. The other 2 Sec residues were found in the C-terminal of amphioxus 3NSelP as well as the Sec-rich tail found in vertebrate SelP. This special SelP was named 3NSelP, containing a representative 3 Trx-like domains of the N-terminal. Figure 4 shows that the coding region of 3NSelP consists of 8 exons and that the first 3 Sec residues are located on the 1st, 3rd, and 5th coding exons. More meticulous manual analysis shows that the 3 Trx-like domains are repeatedly located on the first 7 coding exons. As shown in Figure 4, these 3 repeat regions are indicated as R1, R2 and R3. For each repeat region, the 3 coding exons structures are the same as other vertebrate SelP gene structures previously reported[29]. The multiple alignment of these 3 repeat regions is shown in Figure 4B, demonstrating the strong similarity between these elements. Only short sequence segments in the C-terminal of R1 and R2 do not appear in R3; however, strong similarities are also observed in these 2 short segments. According to multiple alignments and the exon structure of each repeat region, the 3 coding exons of each repeated region were labeled parts a, b, and c. Additionally, the short region missing from R3 is labeled part d in Figure 4A and B. Multiple alignment of R1, R2, and R3 with other amino-terminal vertebrate sequences of SelPs ( Additional file1: Figure S2) shows that the segment consists of parts a, b, and c homologous with other members, though no similarity appears in part d. Based on these observations, part d was likely developed to conjoin R1, R2, and R3.


Evolution of selenoproteins in the metazoan.

Jiang L, Ni J, Liu Q - BMC Genomics (2012)

3NSelP of Amphioxus.A. The gene structure of 3NSelP with all Sec-TGA codons and SECIS elements is indicated. R1, R2, and R3 represent the 3-repeat regions. Each of the repeated regions can be divided into several parts and labeled parts a, b, c, and d. B. Multiple alignment 3-repeat region of the 3NSelP Sec residues and part a, b, c, and d are shown. C. The secondary structures of the two SECIS elements of the 3NSelP gene are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473315&req=5

Figure 4: 3NSelP of Amphioxus.A. The gene structure of 3NSelP with all Sec-TGA codons and SECIS elements is indicated. R1, R2, and R3 represent the 3-repeat regions. Each of the repeated regions can be divided into several parts and labeled parts a, b, c, and d. B. Multiple alignment 3-repeat region of the 3NSelP Sec residues and part a, b, c, and d are shown. C. The secondary structures of the two SECIS elements of the 3NSelP gene are shown.
Mentions: SelP is present in all known vertebrate selenoproteomes, but rarely in invertebrates. Only 5 SelP genes were found in this work, and 4 of them were present in amphioxus (Branchiostoma floridae). The other one was found in Lottia gigantea. Among these, a special SelP was found in amphioxus that contained 5 Sec residues. In this SelP, 3 Sec residues located in the N-terminal region contained 3 repeats of the Trx-like domain. Each was found to be homologous with the N-terminal region containing a Sec residue in vertebrate SelP. The other 2 Sec residues were found in the C-terminal of amphioxus 3NSelP as well as the Sec-rich tail found in vertebrate SelP. This special SelP was named 3NSelP, containing a representative 3 Trx-like domains of the N-terminal. Figure 4 shows that the coding region of 3NSelP consists of 8 exons and that the first 3 Sec residues are located on the 1st, 3rd, and 5th coding exons. More meticulous manual analysis shows that the 3 Trx-like domains are repeatedly located on the first 7 coding exons. As shown in Figure 4, these 3 repeat regions are indicated as R1, R2 and R3. For each repeat region, the 3 coding exons structures are the same as other vertebrate SelP gene structures previously reported[29]. The multiple alignment of these 3 repeat regions is shown in Figure 4B, demonstrating the strong similarity between these elements. Only short sequence segments in the C-terminal of R1 and R2 do not appear in R3; however, strong similarities are also observed in these 2 short segments. According to multiple alignments and the exon structure of each repeat region, the 3 coding exons of each repeated region were labeled parts a, b, and c. Additionally, the short region missing from R3 is labeled part d in Figure 4A and B. Multiple alignment of R1, R2, and R3 with other amino-terminal vertebrate sequences of SelPs ( Additional file1: Figure S2) shows that the segment consists of parts a, b, and c homologous with other members, though no similarity appears in part d. Based on these observations, part d was likely developed to conjoin R1, R2, and R3.

Bottom Line: Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal.During evolutionary history, only a few new selenoproteins have emerged and few were lost.Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Life Sciences, Shenzhen University, Shenzhen, 518060, Guangdong Province, PR, China.

ABSTRACT

Background: The selenocysteine (Sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. Although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely reported outside of insects and nematodes.

Result: A more integrated view of selenoprotein evolution was constructed using several representative species from different evolutionary eras. Using a SelGenAmic-based selenoprotein identification method, 178 selenoprotein genes were identified in 6 invertebrates: Amphimedon queenslandica, Trichoplax adhaerens, Nematostella vectensis, Lottia gigantean, Capitella teleta, and Branchiostoma floridae. Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal. This gene structure suggests the existence of two different strategies for extension of Sec numbers in SelP for the preservation and transportation of selenium. In addition, novel eukaryotic AphC-like selenoproteins were identified in sponges.

Conclusion: Comparison of various animal species suggests that even the most primitive animals possess a selenoproteome range and variety similar to humans. During evolutionary history, only a few new selenoproteins have emerged and few were lost. Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.

Show MeSH
Related in: MedlinePlus