Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms

Abstract

Background: HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms.

Results: Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in vertebrates. Diplomonadida was identified as the most basal organism in the eukaryote lineage.

Conclusion: The present study presents the first comparative genomic study and evolutionary analysis of the HSP90 family of genes across all kingdoms of organisms. HSP90 family members underwent multiple duplications and also subsequent losses during their evolution. This study established an overall framework of information for the family of genes, which may facilitate and stimulate the study of this gene family across all organisms.

Figure 1

Exon splicing patterns of representative genes of the HSP90 family, identified with the genomic study and drawn to scale relative to the number of nucleotides present in each region. The black-filled rectangles depict protein-coding sequences, gray-filled rectangles represent untranslated regions, and unfilled rectangles represent introns.

Figure 2

Alignment of representative amino acid sequences of the HSP90 family of proteins, showing their conserved/variable regions, functionally important residues, and functional domains. Amino acid residues completely conserved throughout the HSP90 family are shaded in red, and those conserved throughout each subfamily are in green. The regions that distinguish HTPG Groups A, B and C are shaded in yellow. Gaps are marked with"-", the last residue in each line is assigned a number and subfamily names are indicated at the end of each line. The conserved/variable regions are separated by "||" with the names above the alignment, and the cleavage sites located just before the underlined residues. "▼" stands for the functionally important residues experimentally identified: E47 (refers to HSP90AA1) for ATP hydrolysis; D93 for ATP binding [33]; G95, G132, G135, G137, and G183 for both GA and p23 binding; K112 for GA binding [72]; R400 and Q404 for ATPase activity; F369 for interdomain interaction [63]; S231 and S263 for phosphorylation by casein kinase II [74]. The conserved and functional domains are indicated by: "≈" for HSP90 protein family signature; "=" for HSP90 protein; "~" for histidine kinase-like ATPases; "∞" for four-helical cytokine; and "..." for Glutamic acid-rich region. The number of each sequence represents: 1. (HSA)HSP90AA1, 2. (GGA)HSP90AA1, 3. (HSA)HSP90AB1, 4. (GGA)HSP90AB1, 5. (HSA)HSP90B1, 6. (ATH)HSP90B1, 7. (ATH)HSP90C1, 8. (ATH)HSP90C2, 9. (HSA)TRAP1, 10. (DME)TRAP1, 11. (ECO)HTPG1, 12. (BFR)HTPG1.

Figure 3

Most parsimonious tree inferred from HTPG and TRAP proteins with representative HSP90A, HSP90B and HSP90C members, rooted with HSP90-like proteins existing in Archaea and Bacteria. Bootstrap percentages of 5000 replicates are shown above the branches where they exceed 50%. Branch lengths are proportional to the number of character changes.

Figure 4

Most parsimonious tree inferred from HSP90A+B+C proteins, rooted with bacteria HTPG proteins. Bootstrap percentages of 5000 replicates are shown above the branches where they exceed 50%. Branch lengths are proportional to number of character changes.

Figure 5

Schematic diagram representing the evolution of proeukaryotic (A) and eukaryotic (B) HSP90 family of genes. The filled bars indicate gene duplication events. A) We propose that HSP90-like genes in Bacteria and Archaea are basal to HTPG genes that only exist in Bacteria. HTPG genes underwent two gene duplication events that gave rise to three groups (Group A, B and C). B) Eukaryotic members were derived from HTPG Group A, and evolved into four subfamilies TRAP (mitochondrial), HSP90A (cytosolic), HSP90B (ER) and HSP90C (chloroplast) throughout three gene duplication events. One additional gene duplication event led to the division of HSP90A into HSP90AA and HSP90AB in vertebrates. The organismal groups in parenthesis indicate where these HSP90 gene copies are found.