Table 3.
Key features of the amino acid sequences of type 2-like cystatins for various nematodes, including Dictyocaulus filaria and Dictyocaulus viviparus studied herein
| Nematodes | Protein sequence code | Accession number | Key elements of type 2-like cystatins
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| SP | G | QXVXG | CC | PW | AEP | AEP codons | |||||
| Order Strongylida | |||||||||||
| Ancylostoma caninum | Ac -CPI/a | Nematode.net: Acan_isotig04796 (trans) | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCG | AAT | GCT |
| Ac-CPI/b | Nematode.net: Acan_isotig01924 (trans) | ✓ | ✓ | ✓ | ✓ | ✓ | SNL | AGT | AAT | CTG | |
| Ac-CPI/c | Nematode.net: Acan_isotig06817 (trans) | ✓ | ✓ | ✓ | ✓ | ✓ | SNG | TCC | AAC | GGC | |
| Angiostrongylus vasorum | Ava-CPI | HelmDB:Avas8850088 | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCG | AAC | GCA |
| Dictyocaulus filaria | Df-CPI | HelmDB:Dfil1654476 | ✓ | ✓ | ✓ | ✓ | SNE | TCG | AAT | GAA | |
| Dictyocaulus viviparus | Dv-CPI | Sup. material: Dviv14021295 | ✓ | ✓ | ✓ | ✓ | SNE | TCA | AAT | GAA | |
| Haemonchus contortus | Hc-CPI/a | Sup. material: Hcon01 | ✓ | ✓ | ✓ | ✓ | ✓ | AND | GCG | AAT | GAT |
| Hc-CPI/b | Sup. material: Hcon02 | ✓ | ✓ | ✓ | ✓ | ✓ | SNE | TCA | AAT | GAA | |
| Hc-CPI/c | Sup. material: Hcon03 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Heligmosomoides polygyrus | Hp-CPI | NCBI: AGA95986.1 | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCG | AAC | GCT |
| Necator americanus | Na-CPI/a | HelmDB:Name4169628 | ✓ | ✓ | ✓ | ✓ | SN− | AGC | AAT | GGT | |
| Na-CPI/b | HelmDB:Name3969602 | ✓ | ✓ | ✓ | ✓ | ✓ | VND | GTC | AAC | GAC | |
| Na-CPI/c | HelmDB:Name3969149 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCT | AAC | GAT | |
| Nippostrongylus brasiliensis | Nb-CPI | NCBI: BAB59011.1 | ✓ | ✓ | ✓ | ✓ | ✓ | SNE | TCC | AAT | GAG |
| Oesophagostomum dentatum | Od-CPI/a | HelmDB:Oden4876005 | ✓ | ✓ | ✓ | ✓ | SNA | TCT | AAT | GCT | |
| Od-CPI/b | HelmDB:Oden4682688 | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCA | AAT | GCT | |
| Od-CPI/c | HelmDB:Oden4799499 | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCC | AAT | GCA | |
| Trichostrongylus axei | Ta-CPI | Sup. material: Taxe6078832 | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCA | AAT | GCC |
| Trichostrongylus colubriformis | Tc-CPI | Sup. material: Tcol3751336 | ✓ | ✓ | ✓ | ✓ | ✓ | SNA | TCA | AAT | GCC |
| Order Rhabditida | |||||||||||
| Caenorhabditis elegans | Ce-CPI-1 | WormBase:WP:CE18035 | ✓ | ✓ | ✓ | ✓ | ✓ | −NN | AAG | AAT | AAT |
| Ce-CPI-2 | WormBase: WP:CE25962 | ✓ | ✓ | ✓ | ✓ | ✓ | SNN | TCC | AAC | AAC | |
| Heterorhabditis bacteriophora | Hb-CPI | WUSTL: contig1346 (trans) | ✓ | ✓ | ✓ | ✓ | ✓ | NNG | AAC | AAT | GGT |
| Strongyloides ratti | Sr-CPI | Sanger: SRAE_2361000 | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAT | GAT | |
| Order Diplogasterida | ▪ | ▪ | ▪ | ▪ | ▪ | ||||||
| Pristionchus pacificus | Pp-CPI | www.pristionchus.org: TRA00000190911 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCC | AAT | GAC |
| Order Ascaridida | ▪ | ▪ | ▪ | ▪ | ▪ | ||||||
| Ascaris suum | As-CPI/a | HelmDB:Asuu7980596 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCG | AAC | GAT |
| As-CPI/b | HelmDB:Asuu7717467 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCG | AAC | GAT | |
| As-CPI/c | WormBase: Scaffold798 (trans) | ✓ | ✓ | ✓ | ✓ | SND | TCG | AAC | GAT | ||
| Order Spirurida | ▪ | ▪ | ▪ | ▪ | ▪ | ||||||
| Acanthocheilonema viteae | Avi-CPI | NCBI: AAA87228 | ✓ | ✓ | ✓ | ✓ | SNV | TCA | AAC | GTG | |
| Brugia malayi | Bm-CPI-1 | NCBI:AAC47623 | ✓ | ✓ | ✓ | ✓ | TRY | ACT | AGA | TAT | |
| Bm-CPI-2 | NCBI:XP_001895475 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Bm-CPI-3 | NCBI:AAB69857 | ✓ | ✓ | LR− | TTG | AGA | GGT | ||||
| Dirofilaria immitis | Di-CPI-2/a | Nematodes.org:Ndi.2.2.2.t08234-RA | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT |
| Di-CPI2/b | Nematodes.org:Ndi.2.2.2.t08235-RA | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Litomosoides sigmodontis | Ls-CPI | NCBI:AAF35896 | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Loa loa | Ll-CPI-1 | NCBI: XP_003136654 | ✓ | ✓ | ✓ | ✓ | ✓ | TRS | ACT | AGG | AGC |
| Ll-CPI-2/a | NCBI: XP_003147913 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Ll-CPI-2/b | NCBI: XP_003145409 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Onchocerca volvulus | Ov-CPI-1 | NCBI:AAD51087 | ✓ | ✓ | ✓ | ✓ | ✓ | MK Y |
ATG | AAA | TAT |
| Ov-CPI-2 | UniProt:P22085 | ✓ | ✓ | ✓ | ✓ | ✓ | SND | TCA | AAC | GAT | |
| Wuchereria bancrofti | Wb-CPI-1 | NCBI: EJW82673 | ✓ | ✓ | ✓ | ✓ | ✓ | TNY | ACT | AAC | TAC |
| Order Trichocephalida | ▪ | ▪ | ▪ | ▪ | ▪ | ||||||
| Trichinella spiralis | Tsp-PI/a | WUSTL: Contig1.89 (trans) | ✓ | ✓ | ✓ | ✓ | SKE | TCC | AAA | GAA | |
| Tsp-PI/b | WUSTL: Contig1.103 (trans) | ✓ | ✓ | ✓ | ✓ | ✓ | SNS | AGC | AAT | AGC | |
| Trichuris suis | Tsu-PI/a | HelmDB:Tsui7356239 | ✓ | ✓ | ✓ | ✓ | ✓ | TDS | ACC | GAC | AGT |
| Tsu-PI/b | HelmDB:Tsui7387460 | ✓ | ✓ | ✓ | ✓ | SND | TCC | AAC | GAT | ||
| Order Tylenchida | ▪ | ▪ | ▪ | ▪ | ▪ | ||||||
| Meloidogyne hapla | Mh-CPI | WormBase: MhA1_Contig41.frz3.gene10 | ✓ | ✓ | ✓ | ✓ | ✓ | SNS | TCT | AAT | TCT |
Key structural or functional elements in the type-2-like cystatins, identified based on the conserved motifs present in chicken cystatin C (Bode et al., 1988). For type 2-like cystatins, the presence (tick) of a signal peptide domain (SP); residues involved in papain-like peptidase binding, including the N-terminus glycine (G); the primary inhibitor domain (QXVXG), the central cysteine disulfide bond (CC); the C-terminus domain (PW); and a conserved motif known to be involved in the binding of the asparaginyl endopeptidase (AEP). Accession numbers of cystatin-like proteins are given where available. If proteins were conceptually translated from nucleotide sequence data (trans), accession numbers of nucleotide sequences are listed. Accession numbers are linked to public databases, including HelmDB (HelmDB: www.helmdb.org), National Center for Biotechnology Information (NCBI:www.ncbi.nlm.nih.gov/), Nematode & Neglected Genomics at the Blaxter Laboratory, Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, UK (Nematodes.org: www.nematodes.org/); the Genome Institute at Washington University, USA (WUSTL; nematode.net); WormBase (www.wormbase.org); and the Pristionchus pacificus genome website at Max-Planck-Institut für Entwicklungsbiologie, Germany (www.pristionchus.org).