Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum.

Szczegóły
Abstrakt

Tytuł:: Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum.
Autorzy:: Mbanefo EC; Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan.
Chuanxin Y
Kikuchi M
Shuaibu MN
Boamah D
Kirinoki M
Hayashi N
Chigusa Y
Osada Y
Hamano S
Hirayama K
Źródło:: BMC genomics [BMC Genomics] 2012 Jun 20; Vol. 13, pp. 260. Date of Electronic Publication: 2012 Jun 20.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: London : BioMed Central, [2000-
MeSH Terms:: Evolution, Molecular*
Genes, Helminth/*genetics
Multigene Family/*genetics
Open Reading Frames/*genetics
Protein Sorting Signals/*genetics
Schistosoma japonicum/*genetics
Alternative Splicing/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Southern ; Computer Simulation ; DNA, Complementary/genetics ; Gene Duplication/genetics ; Genes, Duplicate/genetics ; Genetic Loci/genetics ; Genome, Helminth/genetics ; Helminth Proteins/chemistry ; Helminth Proteins/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Restriction Mapping ; Sequence Alignment ; Species Specificity
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Molecular Sequence:: GENBANK AY570737; AY570742; FN328299; FN329677
Substance Nomenclature:: 0 (DNA, Complementary)
0 (Helminth Proteins)
0 (Protein Sorting Signals)
Entry Date(s):: Date Created: 20120622 Date Completed: 20121219 Latest Revision: 20240318
Update Code:: 20240318
PubMed Central ID:: PMC3434034
DOI:: 10.1186/1471-2164-13-260
PMID:: 22716200
: Czasopismo naukowe

Pełny tekst

Background: Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar core promoter regions and signal sequence, we adopted an integrated approach utilizing whole genome, transcriptome and proteome database BLAST queries, other bioinformatics tools, and molecular analyses.
Results: Our data, in combination with database analyses showed evidences of expression of these genes both at the mRNA and protein levels exclusively in all developmental stages of S. japonicum. The signal sequence motif was identified in 27 distinct S. japonicum UniGene entries with multiple mRNA transcripts, and in 34 genome contigs distributed within 18 scaffolds with evidence of genome-wide dispersion. No homolog of these genes or similar domain was found in deposited data from any other organism. We observed preponderance of flanking repetitive elements (REs), albeit partial copies, especially of the RTE-like and Perere class at either side of the duplication source locus. The role of REs as major mediators of DNA-level recombination leading to dispersive duplication is discussed with evidence from our analyses. We also identified a stepwise pathway towards functional selection in evolving genes by alternative splicing. Equally, the possible transcription models of some protein-coding representatives of the duplicons are presented with evidence of expression in vitro.
Conclusion: Our findings contribute to the accumulating evidence of the role of REs in the generation of evolutionary novelties in organisms' genomes.

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