Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Nov 18:9:266.
doi: 10.1186/1471-2148-9-266.

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

Dusan Kordis  1 , Vito Turk
Affiliations

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

Dusan Kordis et al. BMC Evol Biol. .

Abstract

Background: The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea.

Results: We have identified in silico the full complement of the cystatin superfamily in more than 2100 prokaryotic and eukaryotic genomes. The analysis of numerous eukaryotic genomes has provided strong evidence for the emergence of this superfamily in the ancestor of eukaryotes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. While stefins remain encoded by a single or a small number of genes throughout the eukaryotes, the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications. In the cystatin superfamily we discovered twenty vertebrate-specific and three angiosperm-specific orthologous families, indicating that functional diversification has occurred only in multicellular eukaryotes. In vertebrate orthologous families, the prevailing trends were loss of the ancestral inhibitory activity and acquisition of novel functions in innate immunity. Bacterial cystatins and stefins may be emergency inhibitors that enable survival of bacteria in the host, defending them from the host's proteolytic activity.

Conclusion: This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future structural and evolutionary studies of the cystatin superfamily as well as of other protease inhibitors and proteases.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Vertebrate multidomain representatives of the cystatin superfamily: kininogens, fetuins A and B and HRGs. The rooted neighbor-joining tree shows the evolutionary relationships between the vertebrate-specific kininogen, fetuin and HRG orthologous families. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 50% are indicated. Sequences were obtained from the GenBank, genus names and accession numbers are included.
Figure 2
Figure 2
Vertebrate-specific latexin and TIG1 orthologous families. The rooted neighbor-joining tree shows the evolutionary relationships between the vertebrate-specific latexin and TIG1 orthologous families. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 50% are indicated. Sequences were obtained from the GenBank and ENSEMBL, genus names and accession numbers are included.
Figure 3
Figure 3
Vertebrate-specific cathelicidin orthologous family. The rooted neighbor-joining tree shows the evolutionary relationships inside the vertebrate-specific cathelicidin orthologous family. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 30% are indicated. Sequences were obtained from the GenBank and ENSEMBL, genus names and accession numbers are included.
Figure 4
Figure 4
Vertebrate-specific Spp24 orthologous family. The rooted neighbor-joining tree shows the evolutionary relationships inside the vertebrate-specific Spp24 orthologous family. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 50% are indicated. Sequences were obtained from the GenBank and ENSEMBL, genus names and accession numbers are included.
Figure 5
Figure 5
Evolutionary relationships between the major vertebrate-specific orthologous families of the cystatin superfamily. The rooted neighbor-joining tree shows the evolutionary relationships between the major vertebrate-specific orthologous families cystatins C, M and F, kininogens, fetuins A and B, HRGs, spp24s, cathelicidins, latexins and TIG1s. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 50% are indicated. The following sequences were used in the reconstruction of the evolutionary relationships among diverse vertebrate orthologous families: cystatins E/M: Bos taurus (AAT46121), Homo sapiens (NP_001314) and Monodelphis domestica (XP_001379474); cystatins C: Homo sapiens (CAA36497), Acipenser transmontanus (DR975381) and Gekko japonicus (EB169380); cystatins F: Gallus gallus (XP_415013), Xenopus tropicalis (AAH88052) and Monodelphis domestica (XP_001382090); kininogens: Xenopus laevis (AAH83002), Gallus gallus (XP_422766) and Homo sapiens (NP_000884); fetuins A:Xenopus tropicalis (NP_001011278), Gallus gallus (XP_422764) and Homo sapiens (BAA22652); fetuins B: Homo sapiens (AAH69820), Monodelphis domestica (XP_001373317) and Gallus gallus (XP_422765); HRGs: Gallus gallus (XP_001233925), Homo sapiens (EAW78183) and platypus (ENSOANP00000001023); spp24s: Gallus gallus (CAD21839), Homo sapiens (NP_008875) and Oncorhynchus mykiss (CAE45341); cathelicidins: Ambystoma tigrinum (CN057800), Bos taurus (NP_777250) and Gallus gallus (AAZ65842); TIG1s: Xenopus laevis (AAH73285), Homo sapiens (EAW78675) and Gallus gallus (NP_989865) and latexins: Xenopus laevis (NP_001088750), Gallus gallus (XP_001233654) and Homo sapiens (AAH05346). Hydra magnipapillata stefin (CV151842) has been used as an outgroup. Six Eutheria-specific CRES orthologous families and rodent-specific CRP1 family have not been included into the analysis, since they originated from the cystatin C.
Figure 6
Figure 6
Evolutionary relationships between the six Eutheria-specific orthologous families of the CRES subgroup of cystatins. The rooted neighbor-joining tree shows the evolutionary relationships between the Eutheria-specific cystatin 12, cystatin 9, cystatin 11, cystatin 13, cystatin 8 and cystatin 1L orthologous families. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 50% are indicated. Sequences were obtained from the GenBank and ENSEMBL, genus names and accession numbers are included.
Figure 7
Figure 7
Evolutionary relationships between the Amniota-specific stefin A and B orthologous families. The rooted neighbor-joining tree shows the evolutionary relationships between the vertebrate-specific stefin A and B orthologous families. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 30% are indicated. Sequences were obtained from the GenBank, genus names and accession numbers are included.
Figure 8
Figure 8
Evolutionary relationships between the representatives of the cystatin superfamily in the land plants (Embryophyta). The rooted neighbor-joining tree shows the evolutionary relationships between the three orthologous families in the land plants. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 30% are indicated. Sequences were obtained from the GenBank, genus names and accession numbers are included.
Figure 9
Figure 9
Bacterial representatives of the cystatin superfamily. The rooted neighbor-joining tree shows the evolutionary relationships between the bacterial cystatins and stefins. NJ tree represents the bootstrap consensus following 1000 replicates, nodes with confidence values greater than 30% are indicated. Sequences were obtained from the GenBank, species names and accession numbers are included.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Barrett AJ, Rawlings ND, Davies ME, Machleidt W, Salvesen G, Turk V. In: Proteinase Inhibitors. Barrett AJ, Salvesen G, editor. Amsterdam: Elsevier; 1986. Cysteine proteinase inhibitors of the cystatin superfamily; pp. 519–569.
    1. Alvarez-Fernandez M, Barrett AJ, Gerhartz B, Dando PM, Ni J, Abrahamson M. Inhibition of mammalian legumain by some cystatins is due to a novel second reactive site. J Biol Chem. 1999;274:19195–19203. doi: 10.1074/jbc.274.27.19195. - DOI - PubMed
    1. Abrahamson M, Alvarez-Fernandez M, Nathanson CM. Cystatins. Biochem Soc Symp. 2003;70:179–199. - PubMed
    1. Turk V, Stoka V, Turk D. Cystatins: biochemical and structural properties, and medical relevance. Front Biosci. 2008;13:5406–5420. doi: 10.2741/3089. - DOI - PubMed
    1. Barrett AJ, Fritz H, Grubb A, Isemura S, Järvinen M, Katunuma N, Machleidt W, Müller-Esterl W, Sasaki M, Turk V. Nomenclature and classification of the proteins homologous with the cysteine-proteinase inhibitor chicken cystatin. Biochem J. 1986;236:312. - PMC - PubMed

Publication types

LinkOut - more resources