Overall, Kif13 has a similar domain organisation to other members of this subfamily. This conserved sequence has been termed the BimC box motif [ 40 ]. Mutation of threonine to alanine in this motif has been shown to prevent their association with the mitotic spindle for both Xenopus and human Eg5 [ 41 , 42 ].
This domain is a putative protein-protein interaction module that is present in a wide variety of proteins involved in many biological processes [ 44 ]. SAM domains do not form homo-oligomers in solution [ 45 , 46 ], although homodimers of SAM domains of different proteins have been found in crystal structures [ 47 ].
Instead, SAM domains hetero-oligomerize either by interacting with SAM domains of other proteins [ 44 ] or with other protein modules like the Src homology 2 SH2 domains [ 48 ]. Following the SAM domain, Dd Kif6 contains long stretches of consecutive asparagine, serine, glutamine and glutamic acid residues. Kinesin motor domains share a close structural homology to myosin motor domains [ 49 ].
In myosins, the loop following the P-loop helix called loop-1 is responsible for nucleotide affinity that decreases with the length and flexibility of this loop [ 50 ]. L6 might have a similar function in kinesin. The motor domain additionally contains a very long L12, having five positively charged residues in its sequence.
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This is similar to the K-loop composition in Kif1 kinesins from mammals. The tail of Dd Kif12 contains some predicted coiled-coil regions but does not show similarity to any protein in the databases. Dd Kif8 of the Kif4 subfamily and Dd Kif10 of the Kip3 subfamily belong to subfamilies members of which have been found to be involved in either mitosis or organelle transport, or which participate in both processes depending on the stages of the cell cycle.
The motor domain of Dd Kif8 contains the longest loop L10 of all sequenced kinesins, having about 70 extra residues compared to normal L10's Fig. This loop is involved in neither nucleotide binding nor in the direct kinesin-microtubule interface, so its function was not yet analysed.
Further possible functions include interactions with other microtubule bound proteins. The C-terminus is built of seven WD repeats which contribute to a seven-bladed beta propeller [ 53 ]. WD40 domains are known to mediate protein-protein interactions [ 54 ] and the function of this domain in Dd Kif8 might be the binding of a specific protein cargo, either as part of a protein complex or as a receptor attached to an organelle. Following the motor domain, Dd Kif10 is predicted to have some coiled-coil structure, interrupted by a negatively charged region mainly consisting of asparagines and aspartic acids.
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In the middle of the protein, there are two EF-hand binding domains, the first one having only weak homology. EF-hand motifs almost always occur in pairs, packed together in a face-to-face manner [ 55 ]. Recent investigations also show that EF-hand domains are responsible for homo- and heterodimerisation [ 56 , 57 ]. Directly behind the second EF-hand motif, Dd Kif10 contains a stretch of almost 50 consecutive asparagine residues.
The motor domain of Dd Kif9 does not group with any of the other known kinesins and may therefore be the founder of a new class. Its motor domain is located in the centre of the molecule and contains one of the longest loop-5s L5 of all kinesins Fig. In myosins, the length and flexibility of the loop following the P-loop helix named loop-1 has a strong effect on nucleotide affinity [ 50 , 58 ].
Whether L5 has a similar influence on the affinity of kinesins to nucleotides was not yet analysed. The C-terminus is concluded with a transmembrane domain that might be the linker to membranous cargos. Due to the broad diversity of the kinesin family, different evolutionary lineages have evolved different subfamilies with specialised functions. The only major subfamilies for which Dictyostelium does not contribute are the Osm3 N-4 and Kif15 N kinesins. Kif9 could not be grouped to one of the already assigned subfamilies. Structurally, two of the kinesins Dd Kif6 and Dd Kif9 are of the middle motor domain type, one Dd Kif2 has the motor domain at the C-terminus and the remaining are N-terminal kinesins.
Additionally, Dictyostelium has two kinesins of the Kip3 and Kif4 subfamilies, members of which were shown to participate in either or both of the above mentioned processes in other organisms. Like most other species, Dictyostelium also has its unique kinesin Dd Kif9 that has an unknown function.
Osm3 kinesins comprise a subfamily of mainly heterotrimeric motors built of two kinesin chains and a tightly associated subunit. They are involved in "intraflagellar transport" [ 1 ] and other specialised tasks such as the movement of vesicular cargo in neurons or pigmented melanosomes in melanophore cells. Kif15 kinesins are involved in mitosis by transiently positioning spindle poles, specifically during prometaphase [ 59 ] or by maintaining spindle bipolarity [ 60 ]. The Dictyostelium genome contains four kinesins belonging to subfamilies involved in organelle transport.
Their biochemical properties and cellular functions have been discussed elsewhere [ 61 ]. Dd Kif13 is phylogenetically one of the most divergent BimC kinesins but has a similar domain organisation and contains the BimC motif. Therefore, it is expected to form a bipolar tetramer and is likely to fulfil the same function as other BimC kinesins. Dd Kif2 and Dd Kif13 are therefore the Dictyostelium kinesins responsible for the organisation of the spindle microtubules.
Members of this subfamily bind to kinetochores during mitosis [ 62 ] and are responsible for the alignment of the chromosomes [ 63 ]. Dd Kif4 is phylogenetically more similar to the mammalian homologues, with a similar length and domain organisation, having only coiled-coil regions in its tail.noroi-jusatsu.info/wp-content/2020-05-22/747-comment-pirater-liphone.php
As the nuclear envelope does not break down during mitosis of Dictyostelium cells, the nuclear localisation signal that lack mammalian homologues is obviously important for its destination. Dd Kif4 therefore likely operates in kinetochore binding and chromosome separation. Dd Kif11 is by far the shortest of the Dictyostelium kinesins. None of these plant kinesins has been functionally analysed, so it has yet to be determined whether they have a similar function to their mammalian homologues.
Dd Kif11 also has a PDZ domain-binding motif. These motifs are implicated in transport, localization and assembly of supramolecular signalling complexes [ 39 ]. It is therefore unlikely that Dd Kif4 and Dd Kif11 have entirely overlapping functions. This is consistent with their observed function in vivo where their inhibition interferes with the poleward movement of chromosomes during anaphase A [ 22 ], a process being associated with the shortening of the microtubules that connect the chromosomes to the poles.
The self-association of SAM domains has been known for some time to play a regulatory role in proteins involved in the regulation of developmental processes among diverse eukaryotes [ 44 ]. For example, in Dictyostelium cells, the levels of DPYK1, a SAM-containing protein-tyrosine kinase, increase as the cells initiate their signal-mediated developmental cycle [ 64 ].
The SAM domain of Dd Kif6 might therefore be the reason for its observed developmental regulation [ 30 ].
Based on their amino acid sequence, MKLP1 kinesins are characterised by their extremely long L6, the loop following the P-loop helix. The specific function of this loop has not yet been analysed in detail but from the close structural similarity of the kinesin motor domain to the motor domain of myosins [ 49 ], this loop might be involved in determining nucleotide affinity.
Mammals have three kinesins of this subfamily of different length and domain organisation. CHO1 Kif23 , the most extensively analysed MKLP1 kinesin, is involved in mitosis and has been shown to mediate antiparallel microtubule sliding [ 65 ], most probable by cross-linking antiparallel microtubules by its second, nucleotide insensitive microtubule binding site [ 66 ]. Rab6-Kif Kif20A also functions in cell division during cleavage furrow formation and cytokinesis [ 67 ] but additionally localises to the Golgi apparatus and plays a role in the dynamics of this organelle [ 68 ].
In addition to their tasks during mitosis, some MKLP1 kinesins might thus perform other functions during interphase and this might also be true for Dd Kif Dd Kif10 belongs to the Kip3 subfamily of kinesin motors. The only member of this subfamily that has been analysed yet is Kip3 from S. Dd Kif10 might therefore fulfil several different functions during interphase and mitosis.
Another Dictyostelium kinesin potentially performing multiple functions is Dd Kif8, belonging to the Kif4 subfamily. Kif4 from mammals has been shown to function in the anterograde transport of certain organelles in juvenile neurons and other cells [ 69 ]. Furthermore, it colocalized at the mitotic spindle during mitosis, where it is associated with chromosomes [ 70 ]. Dd Kif8 was found to be constitutively expressed [ 30 ].
Its tail contains seven WD40 repeats, which are also found in mammalian Kif21 kinesins and other kinesins of this subfamily. In subsequent studies the full set of members of the kinesin superfamily were identified and classified from Saccharomyces cerevisiae [ 71 ], Saccharomyces pombe , Drosophila melanogaster [ 72 ], mouse and human [ 10 ], Arabidopsis thaliana [ 73 ] and Caenorhabditis elegans [ 74 ]. The Arabidopsis genome contains by far the most kinesin genes 61 Kif's; Table 2. Some of the kinesin subfamilies only include members from specific kingdoms.
The N, N, M-2, and C-4 classes are plant specific, the N subfamily exclusively harbours yeast members and only mammals contribute to a special class of C-terminal kinesins C-2 as well as to the N kinesins. The N-9 and N subfamilies are, as yet, reserved for members of the metazoan subkingdom. This is similar to results of the analysis of the myosin superfamily, which also showed that some classes are restricted to specific kingdoms. Taking into account that the yet to be classified kinesins will appear as members of new classes, the mammalian genomes comprise by far the highest diversity, harbouring kinesins of 19 subfamilies.
Compared to the other completed genomes, Dictyostelium has a similar percentage of kinesin genes. The thirteen kinesins group into nine characterised subfamilies and one new class. This subfamily diversity is comparable to that observed for the Drosophila and C. While Dictyostelium mostly contributes only one member to the subfamilies, more complex organisms show additional diversity, often having several members per subfamily.
Some of the kinesins are implicated in intracellular traffic and a few have unpredictable functions. Additionally, for Dd Kif4 the mRNA sequence is available, differing from the genomic sequence by a gap of about bp that is, however, dubious. All reads containing at least parts of the domains were sampled and assembled together with adjacent sequence reads.
To obtain contigs containing the full length genes, reads were added to the contigs until the gene prediction software geneid predicted the same gene structure for the kinesin domain containing genes independently from the contig length. Furthermore, all six reading frames of contigs larger than 1 kb resulting from a phrap based assembly of all sequences were scanned for the presence of these domains. One kinesin domain-containing gene kif 11 could only be detected by the single read examination, indicating that the phrap based assembly failed to produce larger contigs in this particular genomic region.
Taking advantage of uneven distributions of reads derived from different chromosome specific libraries, the predicted kinesin domain containing genes were assigned to specific chromosomes. Most of the predicted genes could at least partly be covered by EST sequences indicating expression of the genes. Only for kif 5 and kif 9 was no EST available.
This may be due to the fact that most of the ESTs were derived from cells entering the sexual or developmental cycle. The sequences obtained were compared with recent compilations of kinesin sequences [ 3 , 10 , 73 ] and missing sequences were manually added. Altogether kinesin sequences from 50 species were obtained see supplemental material and aligned together with the thirteen Dictyostelium kinesins using ClustalW [ 76 ] software. The alignment showed that especially the sequences of kinesins from L. The crude alignment was extensively manually improved according to the conserved secondary structural elements of the motor domain, which were obtained from a superposition of all crystal structures Kollmar, unpublished data.
An unrooted phylogenetic tree was generated using the Bootstrap 1, replicates method implemented in ClustalW standard settings and drawn by using TreeView [ 77 ]. The tree did not change considerably when a correction for multiple substitutions was applied, nor did it change when 10, replicates were used.
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BMC Genomics. Siddiqui SS: Metazoan motor models: kinesin superfamily in C. Few would have predicted 20 years ago that myosins constitute a superfamily with at least two-dozen classes and that these molecular motors are involved in a multitude of intracellular activities including cell division, cell movement, intracellular transport and signal transduction. Application of state-of-the-art cellular and molecular biological, structural biological, genetic, biochemical and biophysical techniques has provided and continues to provide critical information regarding the structure—function relationship; and the cellular roles of various myosins in organisms as diverse as protozoa, yeast, plants and higher animals.
The association of myosins with diseases including neurological disorders, immu- deficiencies, cardiomyopathies, hearing and vision loss testify to the importance of understanding the biochemical properties and cellular roles of myosins. The 16 chapters in this volume summarize the tremendous progress made in studying members of the myosin superfamily in recent years and offer critical insight into what future research will yield.
I would like to express my sincere gratitude to the authors of this volume.
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It was a pleasure to work with each of you and I thank you for the considerable efforts in making this international endeavor possible. I also thank John Trinick from the University of Leeds, UK, for the elegant montage of images of single molecules of myosins on the cover, which beautifully shows the structures of some of these amazing molecules.