Kinesin superfamily proteins (KIFs) in the mouse transcriptome

Abstract

In the post genomic era where virtually all the genes and the proteins are known, an important task is to provide a comprehensive analysis of the expression of important classes of genes, such as those that are required for intracellular transport. We report the comprehensive analysis of the Kinesin Superfamily, which is the first and only large protein family whose constituents have been completely identified and confirmed in silico and at the cDNA, mRNA level. In FANTOM2, we have found 90 clones from 33 Kinesin Superfamily Protein (KIF) gene loci. The clones were analyzed in reference to sequence state, library of origin, detection methods, and alternative splicing. More than half of the representative transcriptional units (TU) were full length. The FANTOM2 library also contains novel splice variants previously unreported. We have compared and evaluated various protein classification tools and protein search methods using this data set. This report provides a foundation for future research of the intracellular transport along microtubules and proves the significance of intracellular transport protein transcripts as part of the transcriptome.

Figure 1

Coverage of KIFs in FANTOM2. Of the 45KIF loci found in the genome, 33 representative transcripts were found in FANTOM2, of which, 17 (51.5%) had full-length clones. Seven (21.2%) loci had 3′ truncated clones, 6 (18.2%) had 5′ truncated clones, 1 (3.0%) had 5′ and 3′ truncation, and 2 (6.1%) had clones with other problems.

Figure 2

Consistency of KIF detection in neural tissue. (A) Previously, 38 KIF transcripts (84.4%) were detected in brain or other neural tissue. (B) In FANTOM2, 25(75.8%) derived from neural tissue or mixtures of neural and other tissue. Adding the Phase I clones, 33 (78.6%) out of 42 were identified in neural tissues.

Figure 3

Alignment of transcripts and genomic sequences. Transcribed sequences of KIF3B, KIF9, KIF17, and KIF24 were aligned with respective genomic sequences to reveal intron–exon structures.

Figure 4

Protein search tool comparison. Five methods of detecting KIFs were compared. Twenty-eight clones were detected by all five methods. Pfam and InterPro had low false positive and high false negative rates. Auto-annotation detected the most KIFs but also the most false positives. The false positives were greatly reduced from 18 to 8 by human annotation. Clones identified by respective number of search tools are indicated by the following colors: (yellow) all 5search tools, (green) 4 search tools; (red) 3 search tools; (white) 2 search tools; (blue) 1 seach tool; (black) false positive.

Figure 5

Phylogenic tree of all KIFs found in mouse and human, flies, nematodes, and yeast. KIFs affiliated with 13 out of 14 subfamilies were represented by at least one gene in FANTOM2. KIFs found in FANTOM2 are underlined in yellow-green. Transcripts found in Phase I are underlined in black.