Genes coding for intermediate filament proteins: common features and unexpected differences in the genomes of humans and the teleost fish Fugu rubripes

Abstract

We screened the genomic sequences of the teleost fish Fugu rubripes for genes that encode cytoplasmic intermediate filament (IF) proteins. Here, we compare the number of genes per subfamily (I to IV) as well as the gene mapping in the human and fish genomes. There are several unexpected differences. F. rubripes has a sizeable excess of keratin type I genes over keratin type II genes. Four of the six keratin type II genes map close to four keratin type I genes. Thus, a single keratin II gene cluster (as in mammals) seems excluded. Although a continuous genome sequence is not yet available for F. rubripes, it is difficult to see how all 19 keratin type I genes can be collected as in the human genome into a single cluster without the presence of type II genes and various unrelated genes. F. rubripes has more type III and type IV genes than humans. Some of the type IV genes acquired additional novel intron positions. One gene even harbors (in addition to the two type IV introns) three novel introns and three introns usually present only in mammalian and F. rubripes type I-III genes. This mixture of type IV and type I-III intron positions poses a problem for the traditional view that the first type IV gene arose in evolution by a mRNA-mediated translocation event. In the 42 F. rubripes genes analysed here, there are several differences in intron patterns compared with mammalian genes. Most correspond to additional introns in the fish genes. A search for genes encoding nuclear lamins reveals the four established fish lamins (A, B1, B2 and LIII) as well as an unexpected second lamin A.