Deciphering the phylogenetic history of neuroserpin orthologs across metazoans by analysis of synteny and rare genomic characters

The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.
The objective of this study was to elucidate the phylogenetic kinships of serpins involved in surveying the secretory pathway routes against uncontrolled proteolytic activity. Though phylogenetic classification of vertebrate serpins into six groups based on gene organisation is well established, the evolutionary roots beyond the fish/tetrapod split are unresolved. This study illustrates that the analysis of microsynteny and other rare characters can provide insight into the intricate family history of metazoan serpins. Rare genomic characters/changes (RGC) are used to decipher that orthologs of neuroserpin, a prominent representative of vertebrate group 3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans.
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Ancestry and evolution of a secretory pathway serpin

Kumar A, Ragg H. Ancestry and evolution of a secretory pathway serpin. BMC Evolutionary Biology. 2008;8(1): 250.Background:The serpin (serine protease inhibitor) superfamily constitutes a class of functionally highly diverse proteins usually encompassing several dozens of paralogs in mammals. Though phylogenetic classification of vertebrate serpins into six groups based on gene organisation is well established, the evolutionary roots beyond the fish/tetrapod split are unresolved. The aim of this study was to elucidate the phylogenetic relationships of serpins involved in surveying the secretory pathway routes against uncontrolled proteolytic activity. Results: Here, rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group 3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait, though subtle functional and compartmental specialisations have developed during their evolution. The results also suggest that massive changes in the exon-intron organisation of serpin genes have occurred along the lineage leading to vertebrate neuroserpin, in contrast with the immediately adjacent PDCD10 gene that is linked to its neighbour at least since divergence of echinoderms. The intron distribution pattern of closely adjacent and co-regulated genes thus may experience quite different fates during evolution of metazoans. Conclusion: This study demonstrates that the analysis of microsynteny and other rare characters can provide insight into the intricate family history of metazoan serpins. Serpins with the capacity to defend the main cellular export/import routes against uncontrolled endogenous and/or foreign proteolytic activity represent an ancient trait in eukaryotes that has been maintained continuously in metazoans though subtle changes affecting function and subcellular location have evolved. It is shown that the intron distribution pattern of neuroserpin gene orthologs has undergone substantial rearrangements during metazoan evolution

Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes

Ragg H, Kumar A, Köster K, et al. Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes. BMC Evolutionary Biology. 2009;9(1):208.Background: Intron gains reportedly are very rare during evolution of vertebrates, and the mechanisms underlying their creation are largely unknown. Previous investigations have shown that, during metazoan radiation, the exon-intron patterns of serpin superfamily genes were subject to massive changes, in contrast to many other genes. Results: Here we investigated intron dynamics in the serpin superfamily in lineages pre- and postdating the split of vertebrates. Multiple intron gains were detected in a group of ray-finned fishes, once the canonical groups of vertebrate serpins had been established. In two genes, cooccurrence of non-standard introns was observed, implying that intron gains in vertebrates may even happen concomitantly or in a rapidly consecutive manner. DNA breakage/repair processes associated with genome compaction are introduced as a novel factor potentially favoring intron gain, since all non-canonical introns were found in a lineage of ray-finned fishes that experienced genomic downsizing. Conclusion: Multiple intron acquisitions were identified in serpin genes of a lineage of ray-finned fishes, but not in any other vertebrates, suggesting that insertion rates for introns may be episodically increased. The co-occurrence of non-standard introns within the same gene discloses the possibility that introns may be gained simultaneously. The sequences flanking the intron insertion points correspond to the proto-splice site consensus sequence MAG↑N, previously proposed to serve as intron insertion site. The association of intron gains in the serpin superfamily with a group of fishes that underwent genome compaction may indicate that DNA breakage/repair processes might foster intron birth

The role of serpins in the surveillance of the secretory pathway

Ragg H. The role of serpins in the surveillance of the secretory pathway. CELL. MOL. LIFE SCI. 2007;64(21):2763-2770.Serpins (serine protease inhibitors) constitute a class of proteins with an unusually wide spectrum of different functions at extracellular sites and within the nucleocytoplasmic compartment that extends from protease inhibition to hormone transport and regulation of chromatin organization. Recent investigations reveal a growing number of serpins acting in secretory pathway organelles, indicating that they are not simply cargo destined for export, but fulfill distinct roles within the classical organelle-coupled trafficking system. These findings imply that some serpins are part of a quality control system that monitors the export and possibly import routes of eukaryotic cells. The molecular targets of these serpins are often unknown, opening new avenues for future research

How control of thrombin by serpins in vertebrates arose

Ragg H, Wang Y. How control of thrombin by serpins in vertebrates arose. In: Abstracts of the XXIII Congress of the International Society on Thrombosis and Haemostasis 57th Annual SSC Meeting, July 23-28 2011, Kyoto, Japan. Journal of Thrombosis and Haemostasis. Vol 9. Wiley; 2011: 723

Not more than 117 base pairs of 5'-flanking sequence are required for inducible expression of a human IFN-alpha gene.

Ragg H, Weissmann C. Not more than 117 base pairs of 5'-flanking sequence are required for inducible expression of a human IFN-alpha gene. Nature. 1983;303:439-442

Target identification for Spn4, a gene encoding serpin isoforms with alternative reactive site loops

Oley M, Ragg H. Target identification for Spn4, a gene encoding serpin isoforms with alternative reactive site loops. FEBS JOURNAL. 2005;272(Suppl. 1):174-174

Structure and expression of the gene coding for the human serpin hLS2

Ragg H, Preibisch G. Structure and expression of the gene coding for the human serpin hLS2. J. Biol. Chem. 1988;263:12129-12134

Multitasking serpin genes in the genus Drosophila and beyond: evolution and functional diversification

Börner S, Ragg H. Multitasking serpin genes in the genus Drosophila and beyond: evolution and functional diversification. Presented at the Serpins 2008, 5th International Symposium on Serpin Biology, Structure and Function, Leuwen, Belgium

Messenger RNA coding for phenylalanine ammonia-lyase: Characterization and partial purification from cell suspension cultures of Petroselinum hortense

Ragg H, Hahlbrock K. Messenger RNA coding for phenylalanine ammonia-lyase: Characterization and partial purification from cell suspension cultures of Petroselinum hortense. Eur. J. Biochem. 1980;103:323-330