Arabidopsis thaliana type I and II chaperonins

Abstract

An examination of the Arabidopsis thaliana genome sequence led to the identification of 29 predicted genes with the potential to encode members of the chaperonin family of chaperones (CPN60 and CCT), their associated cochaperonins, and the cytoplasmic chaperonin cofactor prefoldin. These comprise the first complete set of plant chaperonin protein sequences and indicate that the CPN family is more diverse than previously described. In addition to surprising sequence diversity within CPN subclasses, the genomic data also suggest the existence of previously undescribed family members, including a 10-kDa chloroplast cochaperonin. Consideration of the sequence data described in this review prompts questions about the complexities of plant CPN systems and the evolutionary relationships and functions of the component proteins, most of which have not been studied experimentally.

Fig 1.

Phylogenetic relationships of plant mitochondrial and chloroplast α and β Cpn60 proteins. Sequences included in the tree were predicted mature peptides (transit peptides removed). Scale bar indicates 0.1 substitution per site. Bootstrap values for the α, β, and mitochondrial clusters were all greater than 80%, indicating that the clusters are robust. Mitochondrial Cpn60 sequences included in this tree are from A thaliana (GenBank accession numbers AAC04902, BAB03017, BAB02911), Cucurbita sp. (CAA50217, CAA50218), B napus (CAA81689), and Zea mays (AAA44350, AAA33451, AAA33452, CAA77645, CAA78100, CAA78101). Cpn60-α sequences are from Canavalia lineata (AAC68501), Chlamydomonas reinhardtii (AAA98642), Triticum aestivum (HHWTBA), B napus (CAA81736), Pisum sativum (AAA87731), and A thaliana (TIGR locus 68105.t01491, AAD21502). Cpn60-β sequences are from Solanum tuberosum (AAB39827), P sativum (AAA66365), B napus (AAA32980), O sativa (BAA92724), and A thaliana (BAB11583, BAB01754, AAD10647, C079829_21)

Fig 2.

CLUSTALw alignment of plant Cpn10 sequences. Localization of the mature peptide is predicted to be either mitochondrial (m) or chloroplastidic (c) based on an analysis of predicted transit peptide sequences. Mitochondrial Cpn10 sequences are from B napus (GenBank accession number AAB07452), A thaliana (AAA32767, AAC00609), and O sativa (AAB63591). Chloroplast Cpn10 sequences are from L esculentum (AW649119) and A thaliana (CAB75936, AAC27467). The predicted chloroplast transit peptides (cTP) are underlined. The predicted mitochondrial targeting peptides (mTP) are overlined

Fig 3.

Phylogenetic relationships of plant mitochondrial and putative chloroplast Cpn10 proteins and N- and C-terminal portions of plant Cpn21 proteins derived from predicted mature peptide sequences (transit peptides removed). The tree was generated with distance data calculated using the PAM matrix option of protdist, followed by neighbor joining. Scale bar indicates 0.1 substitution per site. Bootstrap values for the clusters (chloroplast Cpn10, mitochondrial Cpn10, N-terminus of Cpn21, and C-terminus of Cpn21) were all greater than 80%, indicating the robustness of the clusters. Mitochondrial Cpn10 sequences included in this tree are from O sativa (GenBank accession number AAB63591), B napus (AAB07452), and A thaliana (AC012189_2, AAC00609). Chloroplast Cpn10 sequences are from L esculentum (AW649119) and A thaliana (CAB75936, AAC27467). Cpn21 proteins sequences are from L esculentum (AAF60293), Spinacia oleracea (AAB59307), and A thaliana (AF268068_1)

Fig 4.

Phylogenetic relationships of eukaryotic cytoplasmic chaperonin (CCT) subunits. The subunit clusters are indicated by labels on the major branches (α, β, γ, δ, ε, η, θ, and ζ). The tree was generated with distance data calculated using the PAM matrix option of protdist, followed by neighbor joining. Scale bar indicates 0.1 substitution per site. Bootstrap values for the 8 subunit clusters were all greater than 90%, indicating the robustness of these clusters. CCT-α subunit proteins included in the tree are from Trichomonas vaginalis (GenBank accession number AAG18494), Giardia intestinalis (AAG18500), A thaliana (BAA01955), C elegans (AAB05072), S cerevisiae (NP_010498), Homo sapiens (P17987), and Mus musculus (228954). CCT-β subunit proteins are from G intestinalis (AAG18501), C elegans (AAA93233), S cerevisiae (S48232), H sapiens (P78371), M musculus (CAA83428), and A thaliana (TIGR locus 68077.t00006). CCT-γ subunit proteins are from Guillardia theta (CAB40401), S cerevisiae (NP_01250), C elegans (AAF35963), A thaliana (AAC26244), H sapiens (NP_005989), and M musculus (CAA83431). CCT-δ subunit proteins are from M musculus (BAA81875), H sapiens (AAC96010), A thaliana (BAB02032), S cerevisiae (CAA98716), C elegans (AAA92842), and T vaginalis (AAG18497). CCT-ε subunit proteins are from Avena sativa (CAA53396, CAA53397), A thaliana (AAB61513), C sativus (1587206), M musculus (CAA83430), S cerevisiae (S57083), C elegans (AAA92843), and G intestinalis (AAG18504). CCT-η subunit proteins are from S cerevisiae (CAA98716), A thaliana (C016795_12), C elegans (AAC19229), M musculus (CAA83274), and H sapiens (AAC96011). CCT-θ subunits are from Candida albicans (P47828), G intestinalis (AAG18505), A thaliana (AC011698_6), H sapiens (XP_009716), C elegans (AAF60806), S cerevisiae (P47079), and M musculus (CAA85521, BAA81879). TriC-ζ subunit proteins are from S cerevisiae (P39079), C elegans (P46550), G intestinalis (AAG18506), T vaginalis (AAG18498), A thaliana (AAF32460, CAC01806), H sapiens (P40227), and M musculus (CAA83432, BAA81891)

Fig 5.

Phylogenetic relationships of eukaryotic PFD subunits Pfd1–6. The tree was generated with distance data calculated using the PAM matrix option of protdist, followed by neighbor joining. Scale bar indicates 0.1 substitution per site. Pfd1 sequences included in the tree are from S cerevisiae (Genbank accession number P46988), A thaliana (AAD15526*), C elegans (Q17827), H sapiens (O60925), S pombe (O14334), and Neurospora crassa (T50987). Pfd2 sequences are from A thaliana (BAB01463), S pombe (Q9UTC9), S cerevisiae (P40005), Drosophila melanogaster (Q9VTE5), Mus musculus (O70591), Homo sapiens (AAF17218), C elegans (Q9N5M2), and Leishmania major (CAB71282). Pfd3 sequences are from S cerevisiae (P48363), S pombe (Q10143), A thaliana (BAB10764), L major (CAB98114), D melanogaster (Q9VTE5), H sapiens (CAA76761), and C elegans (O18054). Pfd4 sequences are from D melanogaster (Q9VRL3), H sapiens (CAB98782), C elegans (Q17435), A thaliana (AAF99774), A fatua (Q9M4C4), S cerevisiae (P53900), and S pombe (Q9UTD4). Pfd5 sequences are from S pombe (Q94307), S cerevisiae (Q04493), A thaliana (BAB11184), H sapiens (Q99471), M musculus (NP_064415), D melanogaster (Q9VCZ8), L major (AAF01572), and C elegans (Q21993). Pfd6 sequences are from S pombe (O14450), S cerevisiae (P52553), C elegans (P52554), D melanogaster (Q9VW56), A thaliana (AAG52059*), H sapiens (O15212), and M musculus (Q03958). A thaliana sequences marked with asterisks are modified by the authors to include exons adjacent to those annotated by TIGR Arabidopsis thaliana Annotation Database (see text for details)