The human genome encodes 10 alpha-crystallin-related small heat shock proteins: HspB1-10

Abstract

To obtain an inventory of all human genes that code for alpha-crystallin-related small heat shock proteins (sHsps), the databases available from the public International Human Genome Sequencing Consortium (IHGSC) and the private Celera human genome project were exhaustively searched. Using the human Hsp27 protein sequence as a query in the protein databases, which are derived from the predicted genes in the human genome, 10 sHsp-like proteins were retrieved, including Hsp27 itself. Repeating the search procedure with all 10 proteins and with a variety of more distantly related animal sHsps, no further human sHsps were detected, as was the case when searches were performed at deoxyribonucleic acid level. The 10 retrieved proteins comprised the 9 earlier recognized human sHsps (Hsp27/HspB1, HspB2, HspB3, alphaA-crystallin/HspB4, alphaB-crystallin/HspB5, Hsp20/HspB6, cvHsp/HspB7, H11/HspB8, and HspB9) and a sperm tail protein known since 1993 as outer dense fiber protein 1 (ODF1). Although this latter protein probably serves a structural role and has a high cysteine content (14%), it clearly contains an alpha-crystallin domain that is characteristic for sHsps. ODF1 can as such be designated as HspB10. The expression of all 10 human sHsp genes was confirmed by expressed sequence tag (EST) searches. For Hsp27/HspB1, 2 retropseudogenes were detected. The HspB1-10 genes are dispersed over 9 chromosomes, reflecting their ancient origin. Two of the genes (HspB3 and HspB9) are intronless, and the others have 1 or 2 introns at various positions. The transcripts of several sHsp genes, notably HspB7, display low levels of alternative splicing, as supported by EST evidence, which may result in minor amounts of isoforms at the protein level.

Fig 1.

Alignment of the 10 human small heat shock proteins (sHsps). Intron positions and predicted secondary structure elements are indicated by arrowheads above and arrows (for ß strands) below the alignment, respectively. The α-crystallin domain is approximately located between positions 118 and 203. Sequences correspond to the protein accession numbers in Table 1 (but see footnote i for HspB6). The alignment is made with ClustalW and manually edited in GeneDoc. Residues in black are conserved in 8 or more sHsps and those in gray in 5–7. The secondary structure was predicted from the 10 aligned sequences with PHD (Rost and Sander 1994); predicted ß strands are numbered according to the approximate location of the corresponding ß strands in the crystal structures of M jannaschii Hsp16.5 (Kim et al 1998) and wheat Hsp16.9 (van Montfort et al 2001). Numbers above the arrowheads correspond to the HspB1–10 numbering: thus, in the HspB1 and HspB8 genes, 2 introns are present at the same positions, 152 (phase 1) and 175 (phase 2); HspB2 has a single phase 1 intron, at position 66; HspB3 and HspB9 are intronless; HspB4, HspB5, and HspB6 have 2 phase 0 introns at identical positions, between 117 and 118 and between 158 and 159; HspB7 has 2 introns, at positions 91 (phase 1) and between 157 and 158 (phase 0); HspB10 has 1 phase 2 intron, at position 107

Fig 2.

Alignment of the open reading frames and flanking intron sequences of the HspB1/Hsp27 gene and its 2 processed pseudogenes. The alignment was made with ClustalW and edited with GeneDoc. The 2 introns in the HspB1 gene are in gray. Sequence differences are highlighted in black; the black nucleotides from positions 390 to 425 in pseudogene 2 demarcate its 5′ boundary. Start and stop codons are underlined (the potential start codon for pseudogene 2 is at positions 468–470). The GA and AG sequences in bold at positions 343–344 and 615–616 indicate the alternative splice sites in exon 1 and exon 3 that are predicted to give rise to HspB1-alt2 (see Table 1 and text)