The new kinesin phylogenetic tree is a re-evaluation of the kinesin microtubule motor protein family (Kim and Endow, 2000) (see also Miki et al., 2001; Lawrence et al., 2002), inspired by the recent completion of the genome sequences of humans and several model organisms. The kinesin motors hydrolyze ATP as they move along microtubules, transporting vesicles and organelles (Hirokawa, 1998) and performing essential roles in chromosome motility and spindle assembly and function (Inoué and Salmon, 1995; Endow, 1999; Sharp et al., 2000). The new kinesin tree includes 155 proteins from 11 species and focuses on the organisms Plasmodium falciparum, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens and Arabidopsis thaliana – a protist, a yeast, two invertebrates, a vertebrate and a higher plant. The focus on humans and selected model organisms provides a look at the evolutionary relationships of the kinesin proteins from several well-studied species. A notable feature of the new tree is the emergence of several new groups consisting only of Arabidopsis proteins, which suggests that the kinesin motors may have a broader range of functions in higher plants than in other organisms.

The tree was built by parsimony methods using PAUP v. 4.0b10 (Swofford, 2002) from a sequence alignment of kinesin motor domains made with CLUSTAL W (Thompson et al., 1994) and refined manually. Tree-building trials used heuristic search methods with random stepwise addition, `tree-bisection-reconnection' (TBR) branch swapping and maximum parsimony settings. The tree includes founder proteins from previously identified kinesin groups and is arbitrarily rooted using ScSmy1 as the outgroup protein. ScSmy1 is not known to be the ancestral kinesin, but has a highly divergent motor domain sequence compared with that of other kinesin proteins. The numbers adjacent to nodes are the percentages of 1810 bootstrap trials performed in PAUP using full heuristic methods in which the proteins to the right grouped together. Bootstrap values of ≥90% provide confidence that the proteins in the group are orthologs or paralogs of one another, whereas lower values indicate less certainty. The horizontal branch lengths correspond to the number of changes needed to explain the differences in protein sequences, as indicated by the scale bar at the bottom. The tree is one of two optimal trees found in 600 tree-building trials and has an overall length of 17,867.

Trees were also built in PAUP using a neighbor-joining algorithm. Distance methods are less stringent than parsimony methods, but have the advantage of being less demanding computationally for analysis of large data sets. The neighbor-joining trees showed the same groups as the maximum parsimony trees, but some groups did not include proteins previously classified as members of the group. For example, AtKCBP, a minus-end-directed kinesin motor with a C-terminal motor domain (Song et al., 1997), did not fall into the C-terminal motor group in the neighbor-joining trees but was included in the group in the maximum parsimony trees. We therefore show a maximum parsimony tree, rather than a neighbor-joining tree, as representative of the evolutionary relationships of the kinesin proteins in the alignment.

Five groups in the tree, the KRP85/95, ChrKin/KIF4, BimC, C-terminal motor and CENP-E kinesins, had bootstrap values of <90% by parsimony analysis. The bootstrap values by neighbor-joining analysis of two of these groups, KRP85/95 and ChrKin/KIF4, were 100% and 95%, respectively, which supports their classification as groups. The bootstrap value of the BimC group was only 85% and 86% by parsimony and distance analysis, respectively. Analysis of the new proteins in the group showed high sequence identity (>50%) between their motor domains and that of AnBimC, the founding member of the group (Table 1), which supports their classification as members of the group. A new P. falciparum kinesin, PfMAL3P6.13, has only 37.0% sequence identity to AnBimC in its motor domain, but is shown as a member of the group on the basis of the branching pattern. Its assignment to the BimC group will ultimately rely on functional properties and structural features of the protein, when this information is available. The C-terminal motor group, which contains all the known minus-end-directed kinesin motors, in contrast to the plus-end-directed kinesins outside the group, may lack a high bootstrap value because of divergence within the group. The proteins in this group have in common a C-terminal motor domain and a conserved neck region (Table 1). Two Arabidopsis proteins in the group, AtT12M4.14 and AtF15A18.10, have N-terminal instead of C-terminal motor domains, which is either a new feature of some proteins in the group or due to misassembly of the deposited sequences. The assignment of the two proteins to the C-terminal motor group is supported by high sequence identity to AtKatD and a conserved neck in AtF15A18.10 (Table 1).

Table 1.

Analysis of previously unclassified kinesin proteins for assignment to groups

Group Proteins compared to Protein Motor position* Motor sequence ID (%) Predicted coiled-coil position Notes Neck analysis
At1
 
AtF3K23.6
 
AtF24M12.190
 
N
 
66.9
 
380-425
 

 

 

 

 
AtK1L20.9
 
N
 
67.1
 
383-434
 

 

 

 

 
AtT19F6.160
 
N
 
66.6
 
329-360
 

 

 

 

 
AtMDH9.19
 

 
52.9
 
None
 

 

 

 

 
AtF19H22.50
 
N
 
76.6
 
336-365
 

 

 

 

 
AtF7K15.60
 
N
 
55.0
 
385-434
 

 

 

 

 
AtF15H18.12
 
N
 
44.9
 
418-464
 
1 aa missing from alignment
 

 

 

 
AtF3K23.6
 
N
 
100
 
364-393
 

 

 
At2
 
AtF3K23.14
 
AtF19H22.150
 
N
 
73.8
 
489-580
 

 

 

 

 
AtT21B14.15e
 
N
 
74.2
 
385-426
 

 

 

 

 
AtF15M7.20
 
N
 
72.0
 
394-432
 

 

 

 

 
AtF8K7.17
 
N
 
76.7
 
394-474
 

 

 

 

 
AtF3K23.14
 
N
 
100
 
422-513
 

 

 
Unnamed At group
 
AtF28P10.150
 
AtF22M8.8
 
N
 
65.7
 
423-452
 

 

 

 

 
AtF5011.15
 
N
 
69.7
 
466-495
 

 

 

 

 
AtF28P10.150
 
N
 
100
 
473-524
 

 

 
Unnamed At group
 
AtPAKRP1
 
AtMAL21.18
 
N
 
44.1
 
421-453
 

 

 

 

 
AtMDB19.17
 
N
 
89.6
 
439-468
 
Phragmoplast-associated
 

 

 

 
AtPAKRP1
 
N
 
100
 
1044-1073
 
Phragmoplast-associated
 

 
Unnamed At group
 
AtT15B3.190
 
AtMGD8.20
 
N
 
64.9
 
494-527
 

 

 

 

 
AtK13E13.17
 
N
 
64.1
 
771-805
 

 

 

 

 
AtT15B3.190
 
N
 
100
 
578-609
 

 

 
Unnamed At group
 
AtT1E22.130
 
AtMRO11.5
 
N
 
34.5
 
None
 
Grouped by bootstrap
 

 

 

 
AtT1E22.130
 

 
100
 
None
 

 

 
BimC
 
AnBimC
 
PfMAL3P6.13
 
N
 
37.0
 
None
 

 

 

 

 
HsKIF8
 

 
(53.5)
 

 
Partial sequence
 

 

 

 
AtKRP125a
 
N
 
50.1
 
(438-467) P=0.41
 

 

 

 

 
AtKRP125b
 
N
 
50.8
 
406-477
 
GenBank identifies as cytokinesis motor
 

 

 

 
AtKRP125c
 
N
 
53.3
 
438-518
 
GenBank identifies as spindle motor
 

 

 

 
AtF16L2.60
 
N
 
50.1
 
433-523
 

 

 
CENP-E
 
HsCENP-E
 
DmCana
 
N
 
40.4
 
487-536
 
Kinetochore motor (Yucel et al 2000)
 

 

 

 
DmCmeta
 
N
 
48.1
 
333-374
 
Kinetochore motor (Yucel et al 2000)
 

 

 

 
AtF14P13.22
 
N
 
49.3
 
364-410
 
GenBank identifies as putative kinesin-like centromere protein
 

 

 

 
AtZCF125
 
N
 
51.0
 
359-414
 

 

 
Chromokinesin/KIF4
 
HsKIF4
 
HsNYREN62
 
N
 
50.7
 
467-509
 
Group supported by neighbor-joining bootstrap value of 95% and high % sequence ID to HsKIF4  
 

 

 
AtMSL3.5
 
N
 
49.5
 
581-615
 
 
 

 

 
AtMCA23.16
 
N
 
47.2
 
539-573
 
 
 

 

 
AtF11C1.80
 
N
 
50.4
 
411-443
 
 
 
Unnamed Hs group
 
HsKIAA1236
 
HsKIAA1236
 

 
100
 
None
 

 

 

 

 
HsLOC343489
 

 
54.4
 
None
 
May not be full-length sequence
 

 
KHC
 
DmKHC
 
AtMAA21.110
 
N
 
40.6
 
374-418
 
Bootstrap values do not support placement in KHC group
 

 
Kip3
 
ScKip3
 
PfMAL3P7.1
 
N
 
41.9
 
594-629
 
Bootstrap values do not support placement in Kip3 group  
 

 

 
HsKIF18
 
N
 
47.7
 
None
 
 
 

 

 
AtF25I16.11
 
N
 
44.7
 
502-540
 
 
 

 

 
DmK1p67A
 
N
 
43.6
 
362-398
 
 
 

 

 
DmKIF19A
 
N
 
39.0
 
550-598
 
 
 

 

 
HsFLJ37300
 
N
 
45.4
 
420-451
 
DmKIF19A listed in alignment as DmK1p19A  
 

 

 
PfMAL1P2.n
 
N
 
46.6
 
1412-1442
 
 
 
KRP85/95
 
CeOsm3
 
HsKIAA1405
 
N
 
58.3
 
368-411
 
Group supported by neighbor-joining bootstrap value of 100% and high % sequence ID to CeOsm3  
 

 

 
DmKIF3C
 
N
 
50.9
 
(351-380) P=0.44
 
 
 
MCAK/KIF2
 
HsMCAK
 
HsK1p17q22
 
Central
 
67.7
 
None P<0.4
 

 

 

 

 
DmK1p59D
 
Central
 
61.7
 
None
 

 

 

 

 
AtMGL6.9
 
Central
 
52.1
 
705-741
 

 

 

 

 
AtMSL1.9
 
Central
 
53.3
 
596-627
 

 

 

 

 
PfL2165w
 
(Central)
 
45.3
 
None
 
Motor towards N terminus
 

 
MKLP1
 
DmPAV
 
HsK1pMPP1
 
N
 
33.2
 
568-607
 
Bootstrap values and % sequence ID to DmPav do not support placement in MKLP1 group
 

 

 

 
HsRabK6
 
N
 
27.0
 
680-718
 
 
 

 

 
AtT20H2.17
 
(N)
 
13.5
 
(839-868) P=0.49
 
 
 
Unc104/KIF1
 
CeUnc104
 
HsKIF1B
 
N
 
70.6
 
504-533
 

 

 

 

 
HsGAKIN
 
N
 
58.5
 
612-644
 

 

 

 

 
HsRBKIN1
 
N
 
57.5
 
391-420
 

 

 

 

 
HsKIF16B
 
N
 
49.7
 
None P<0.4
 
Sequence only ∼65 aa longer than motor domain, may not be full length
 

 
C-Terminal motor
 
AtKATD
 
AtT12M4.14
 
N
 
67.3
 
750-788
 
Coiled-coil after motor domain Groups with AtKatD by bootstrap
 
+ + +G+ KICNIKSNECITGS
 

 

 
AtF15H18.10
 
C
 
62.1
 
433-523
 

 
++L N ++L+GN NQKLFNELQELKGN
 

 

 
AtF25P22.28
 
C
 
63.8
 
352-444
 

 
++L N ++L+GN NRKLFNELQELKGN
 

 

 
AtF24D7.17
 
C
 
62.1
 
285-384
 

 
+ L+N V+L+GN NRRLYNEVQELKGN
 

 

 
AtK1013.11
 
C
 
61.5
 
276-331
 

 
+ L+N V+L+GN NRRLYNEVQELKGN
 

 

 
AtF14P13.9
 
Central
 
55.8
 
None
 
Neck present Groups with AtKatD by bootstrap
 
++L+N VDL+GN NRKLYNMVQDLKGN
 

 

 
HsKIFC2
 
C
 
37.8
 
270-320
 
C-terminal motor
 
++L+GN PAGCPGRLPELKGN
 

 

 
AtT9I22.5
 
C
 
39.9
 
388-430
 
C-terminal motor Neck present
 
RKEL+N + ++GN RKELYNHIQETKGN
 

 

 
AtF15A18.10
 
N
 
51.9
 
375-410
 
Coiled-coil after motor domain Neck present
 
RK L+NV++L+GN RKRLYNEVIELKGN
 

 

 
AtT9N14.6
 
C
 
52.0
 
341-373
 

 
RKEL+N+++L+GN RKELYNKILELKGN
 

 

 
AtF15F15.20
 
C
 
42.2
 
35-78
 
C-terminal motor Neck present
 
RK++ N ++D+G+ RKQVLNKIIDTKGS
 

 

 
AtF12B17.180
 
C
 
36.4
 
57-92
 
C-terminal motor Neck present
 
+K L N +++GN KKRLFNDLLTAKGN
 

 

 
AtMNA5.20
 
C
 
33.8
 
52-85
 
C-terminal motor Neck present
 
+K L N +++GN KKRLFNDLLTTKGN
 
   AtC17L7.110   C   44.5   383-413   C-terminal motor Neck present   RK+LHNT+++L+GN RKKLHNTILELKGN  
Group Proteins compared to Protein Motor position* Motor sequence ID (%) Predicted coiled-coil position Notes Neck analysis
At1
 
AtF3K23.6
 
AtF24M12.190
 
N
 
66.9
 
380-425
 

 

 

 

 
AtK1L20.9
 
N
 
67.1
 
383-434
 

 

 

 

 
AtT19F6.160
 
N
 
66.6
 
329-360
 

 

 

 

 
AtMDH9.19
 

 
52.9
 
None
 

 

 

 

 
AtF19H22.50
 
N
 
76.6
 
336-365
 

 

 

 

 
AtF7K15.60
 
N
 
55.0
 
385-434
 

 

 

 

 
AtF15H18.12
 
N
 
44.9
 
418-464
 
1 aa missing from alignment
 

 

 

 
AtF3K23.6
 
N
 
100
 
364-393
 

 

 
At2
 
AtF3K23.14
 
AtF19H22.150
 
N
 
73.8
 
489-580
 

 

 

 

 
AtT21B14.15e
 
N
 
74.2
 
385-426
 

 

 

 

 
AtF15M7.20
 
N
 
72.0
 
394-432
 

 

 

 

 
AtF8K7.17
 
N
 
76.7
 
394-474
 

 

 

 

 
AtF3K23.14
 
N
 
100
 
422-513
 

 

 
Unnamed At group
 
AtF28P10.150
 
AtF22M8.8
 
N
 
65.7
 
423-452
 

 

 

 

 
AtF5011.15
 
N
 
69.7
 
466-495
 

 

 

 

 
AtF28P10.150
 
N
 
100
 
473-524
 

 

 
Unnamed At group
 
AtPAKRP1
 
AtMAL21.18
 
N
 
44.1
 
421-453
 

 

 

 

 
AtMDB19.17
 
N
 
89.6
 
439-468
 
Phragmoplast-associated
 

 

 

 
AtPAKRP1
 
N
 
100
 
1044-1073
 
Phragmoplast-associated
 

 
Unnamed At group
 
AtT15B3.190
 
AtMGD8.20
 
N
 
64.9
 
494-527
 

 

 

 

 
AtK13E13.17
 
N
 
64.1
 
771-805
 

 

 

 

 
AtT15B3.190
 
N
 
100
 
578-609
 

 

 
Unnamed At group
 
AtT1E22.130
 
AtMRO11.5
 
N
 
34.5
 
None
 
Grouped by bootstrap
 

 

 

 
AtT1E22.130
 

 
100
 
None
 

 

 
BimC
 
AnBimC
 
PfMAL3P6.13
 
N
 
37.0
 
None
 

 

 

 

 
HsKIF8
 

 
(53.5)
 

 
Partial sequence
 

 

 

 
AtKRP125a
 
N
 
50.1
 
(438-467) P=0.41
 

 

 

 

 
AtKRP125b
 
N
 
50.8
 
406-477
 
GenBank identifies as cytokinesis motor
 

 

 

 
AtKRP125c
 
N
 
53.3
 
438-518
 
GenBank identifies as spindle motor
 

 

 

 
AtF16L2.60
 
N
 
50.1
 
433-523
 

 

 
CENP-E
 
HsCENP-E
 
DmCana
 
N
 
40.4
 
487-536
 
Kinetochore motor (Yucel et al 2000)
 

 

 

 
DmCmeta
 
N
 
48.1
 
333-374
 
Kinetochore motor (Yucel et al 2000)
 

 

 

 
AtF14P13.22
 
N
 
49.3
 
364-410
 
GenBank identifies as putative kinesin-like centromere protein
 

 

 

 
AtZCF125
 
N
 
51.0
 
359-414
 

 

 
Chromokinesin/KIF4
 
HsKIF4
 
HsNYREN62
 
N
 
50.7
 
467-509
 
Group supported by neighbor-joining bootstrap value of 95% and high % sequence ID to HsKIF4  
 

 

 
AtMSL3.5
 
N
 
49.5
 
581-615
 
 
 

 

 
AtMCA23.16
 
N
 
47.2
 
539-573
 
 
 

 

 
AtF11C1.80
 
N
 
50.4
 
411-443
 
 
 
Unnamed Hs group
 
HsKIAA1236
 
HsKIAA1236
 

 
100
 
None
 

 

 

 

 
HsLOC343489
 

 
54.4
 
None
 
May not be full-length sequence
 

 
KHC
 
DmKHC
 
AtMAA21.110
 
N
 
40.6
 
374-418
 
Bootstrap values do not support placement in KHC group
 

 
Kip3
 
ScKip3
 
PfMAL3P7.1
 
N
 
41.9
 
594-629
 
Bootstrap values do not support placement in Kip3 group  
 

 

 
HsKIF18
 
N
 
47.7
 
None
 
 
 

 

 
AtF25I16.11
 
N
 
44.7
 
502-540
 
 
 

 

 
DmK1p67A
 
N
 
43.6
 
362-398
 
 
 

 

 
DmKIF19A
 
N
 
39.0
 
550-598
 
 
 

 

 
HsFLJ37300
 
N
 
45.4
 
420-451
 
DmKIF19A listed in alignment as DmK1p19A  
 

 

 
PfMAL1P2.n
 
N
 
46.6
 
1412-1442
 
 
 
KRP85/95
 
CeOsm3
 
HsKIAA1405
 
N
 
58.3
 
368-411
 
Group supported by neighbor-joining bootstrap value of 100% and high % sequence ID to CeOsm3  
 

 

 
DmKIF3C
 
N
 
50.9
 
(351-380) P=0.44
 
 
 
MCAK/KIF2
 
HsMCAK
 
HsK1p17q22
 
Central
 
67.7
 
None P<0.4
 

 

 

 

 
DmK1p59D
 
Central
 
61.7
 
None
 

 

 

 

 
AtMGL6.9
 
Central
 
52.1
 
705-741
 

 

 

 

 
AtMSL1.9
 
Central
 
53.3
 
596-627
 

 

 

 

 
PfL2165w
 
(Central)
 
45.3
 
None
 
Motor towards N terminus
 

 
MKLP1
 
DmPAV
 
HsK1pMPP1
 
N
 
33.2
 
568-607
 
Bootstrap values and % sequence ID to DmPav do not support placement in MKLP1 group
 

 

 

 
HsRabK6
 
N
 
27.0
 
680-718
 
 
 

 

 
AtT20H2.17
 
(N)
 
13.5
 
(839-868) P=0.49
 
 
 
Unc104/KIF1
 
CeUnc104
 
HsKIF1B
 
N
 
70.6
 
504-533
 

 

 

 

 
HsGAKIN
 
N
 
58.5
 
612-644
 

 

 

 

 
HsRBKIN1
 
N
 
57.5
 
391-420
 

 

 

 

 
HsKIF16B
 
N
 
49.7
 
None P<0.4
 
Sequence only ∼65 aa longer than motor domain, may not be full length
 

 
C-Terminal motor
 
AtKATD
 
AtT12M4.14
 
N
 
67.3
 
750-788
 
Coiled-coil after motor domain Groups with AtKatD by bootstrap
 
+ + +G+ KICNIKSNECITGS
 

 

 
AtF15H18.10
 
C
 
62.1
 
433-523
 

 
++L N ++L+GN NQKLFNELQELKGN
 

 

 
AtF25P22.28
 
C
 
63.8
 
352-444
 

 
++L N ++L+GN NRKLFNELQELKGN
 

 

 
AtF24D7.17
 
C
 
62.1
 
285-384
 

 
+ L+N V+L+GN NRRLYNEVQELKGN
 

 

 
AtK1013.11
 
C
 
61.5
 
276-331
 

 
+ L+N V+L+GN NRRLYNEVQELKGN
 

 

 
AtF14P13.9
 
Central
 
55.8
 
None
 
Neck present Groups with AtKatD by bootstrap
 
++L+N VDL+GN NRKLYNMVQDLKGN
 

 

 
HsKIFC2
 
C
 
37.8
 
270-320
 
C-terminal motor
 
++L+GN PAGCPGRLPELKGN
 

 

 
AtT9I22.5
 
C
 
39.9
 
388-430
 
C-terminal motor Neck present
 
RKEL+N + ++GN RKELYNHIQETKGN
 

 

 
AtF15A18.10
 
N
 
51.9
 
375-410
 
Coiled-coil after motor domain Neck present
 
RK L+NV++L+GN RKRLYNEVIELKGN
 

 

 
AtT9N14.6
 
C
 
52.0
 
341-373
 

 
RKEL+N+++L+GN RKELYNKILELKGN
 

 

 
AtF15F15.20
 
C
 
42.2
 
35-78
 
C-terminal motor Neck present
 
RK++ N ++D+G+ RKQVLNKIIDTKGS
 

 

 
AtF12B17.180
 
C
 
36.4
 
57-92
 
C-terminal motor Neck present
 
+K L N +++GN KKRLFNDLLTAKGN
 

 

 
AtMNA5.20
 
C
 
33.8
 
52-85
 
C-terminal motor Neck present
 
+K L N +++GN KKRLFNDLLTTKGN
 
   AtC17L7.110   C   44.5   383-413   C-terminal motor Neck present   RK+LHNT+++L+GN RKKLHNTILELKGN  
*

Position of motor domain in protein and/or relative to predicted coiled-coil

Coiled-coil predicted by PAIRCOIL (P≥50%). Coiled-coil position is that closest to the end of the motor domain for N-terminal motors and the beginning of the motor domain for C-terminal motors

Sequence similarity to DmNcd neck, the region adjacent to the beginning of the conserved motor domain (RKELHNTVMDLRGN; top); sequence at bottom from corresponding region of protein under analysis

The new CENP-E group has the kinetochore motor HsCENP-E as its founding member. Two A. thaliana proteins, AtZCF125 and AtF14P13.22, are supported by a 95% bootstrap value as members of the CENP-E group by the neighboring-joining but not the maximum parsimony analysis. The Drosophila proteins DmCmeta and DmCana are thought to be related to HsCENP-E, on the basis of sequence identity and functional analysis (Yucel et al., 2000), but assignment of these two proteins to the CENP-E group is not currently supported by either neighbor-joining or maximum parsimony analysis, possibly owing to the lack of intermediate taxa. Classification of the Drosophila proteins as members of the group is based on functional similarity and sequence identity (in the case of DmCmeta) to CENP-E (Table 1).

The new tree includes 60 A. thaliana proteins, 21 of which fall into the C-terminal motor group. Arabidopsis is thought to lack axonemal and cytoplasmic dyneins (Lawrence et al., 2001) and minus-end-directed kinesins may perform functions carried out by dyneins in other organisms. Two new A. thaliana groups, referred to here as At1 and At2, as well as several smaller groups, emerged on the new tree with bootstrap values of 95-100%. At1 and At2 contain 8 and 5 proteins, respectively. The proteins in these groups have N-terminal motor domains with a high sequence identity to an early branching member of the group (Table 1).

Kinesins that group together are thought to perform similar functions, although this idea may change as more kinesin functions become known. The groups are color coded according to function (red represents chromosome/spindle motility and green represents vesicle/organelle transport). The MCAK/KIF2 group (orange) includes proteins thought to perform both functions. The At1 and At2 protein functions are not yet known; the groups are therefore not colored. The color coding of groups in the tree implies that previously unclassified proteins have roles similar to those of proteins with determined functions, but analysis of cellular functions was not undertaken.

Further methods used in our tree building, including manual refinement of the alignment and analysis of partial motor sequences, are detailed elsewhere (Goodson et al., 1994; Moore and Endow, 1996). The tree does not include all known kinesin proteins and is not meant to be exhaustive, but includes all the presently known kinesins (as of July 2003) with reliable sequences found in database searches for the model organisms P. falciparum, S. cerevisiae, C. elegans, D. melanogaster, H. sapiens and A. thaliana, whose genomes have now been completely sequenced. We could not control for misassembled sequences deposited into the public databases or entries from contaminating DNA in the sequenced genomes. Some of the proteins that were analyzed showed divergence of conserved sequence motifs (see Table 2). Alternative names for proteins and protein groups have been published previously (Miki et al., 2001; Vale and Fletterick, 1997) and can also be found at the Kinesin Home Page [www.proweb.org/kinesin (E. A. Greene, S. Henikoff and S. A. Endow, 1996)], which has links to protein and DNA databases together with additional information about the kinesin proteins.

Table 2.

Analysis of divergence in conserved motifs

Protein P-loop GQTGSGKTY Switch I SSRSH Switch II DLAGSE Mt-binding HIPYR Notes
AtF12B17.180    FNVTH     
AtMAA21.110   MQTGAGKTY   -----     
AtMDH9.19      -DIAQ   
AtMNA.20    STVTH     
AtMRO11.5   GARNSGKTH   PTRSH   DMAGYE    
AtT20H2.17   GPSGSGKTH     GIAET   
DmK1p19A   SDRAPPTAS     YVNYR   
HsKIAA1236   GHMSLGKSY    DLGSCE    
HsKIF7      -----   Sequence only available from P-loop to DLAGSE Deleted from alignment - moved into different groups with different tree runs  
HsKIF8      -----   Sequence only available from P-loop to DLAGSE  
HsK1p6q27   ---------      
HsLOC343489   GHAKLGKSY    DLGSCV    SSRSH motif upstream, does not align  
PfMAL3P6.13   NNLKINKEP      
Pf07_010   NKENTNKDN     NISYR   Deleted from alignment  
Protein P-loop GQTGSGKTY Switch I SSRSH Switch II DLAGSE Mt-binding HIPYR Notes
AtF12B17.180    FNVTH     
AtMAA21.110   MQTGAGKTY   -----     
AtMDH9.19      -DIAQ   
AtMNA.20    STVTH     
AtMRO11.5   GARNSGKTH   PTRSH   DMAGYE    
AtT20H2.17   GPSGSGKTH     GIAET   
DmK1p19A   SDRAPPTAS     YVNYR   
HsKIAA1236   GHMSLGKSY    DLGSCE    
HsKIF7      -----   Sequence only available from P-loop to DLAGSE Deleted from alignment - moved into different groups with different tree runs  
HsKIF8      -----   Sequence only available from P-loop to DLAGSE  
HsK1p6q27   ---------      
HsLOC343489   GHAKLGKSY    DLGSCV    SSRSH motif upstream, does not align  
PfMAL3P6.13   NNLKINKEP      
Pf07_010   NKENTNKDN     NISYR   Deleted from alignment  

Motifs not noted above were present in the proteins. Some putative kinesins, such as DmCostal2, PfMAL1P2.n and HsKIF12, were not included in alignment because they lack some or all of the above motifs. Proteins with short sequence lengths (<50% of the DmKHC motor length) were also not included (e.g. HsKIF16A and HsKIF18B).

-, missing amino acid.

This work was supported by grants from the NIH and HFSP to S.A.E.

Species abbreviations: An, Aspergillus nidulans (Emericella nidulans); At, Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cf, Cylindrotheca fusiformis (diatom); Dm, Drosophila melanogaster; Hs, Homo sapiens; Lm, Leishmania major; Mm, Mus musculus; Pf, Plasmodium falciparum; Sc, Saccharomyces cerevisiae; and Spo, Schizosaccharomyces pombe.

Websites used in searches for kinesin proteins: GenBank, www.ncbi.nlm.nih.gov/Genbank/; P. falciparum, www.sanger.ac.uk; D. melanogaster, www.fruitfly.org and flybase.bio.indiana.edu; H. sapiens, www.genome.gov; A. thaliana, www.arabidopsis.org

Endow, S. A. (
1999
). Microtubule motors in spindle and chromosome motility.
Eur. J. Biochem.
262
,
12
-18.
Goodson, H. V., Kang, S. J. and Endow, S. A. (
1994
). Molecular phylogeny of the kinesin family of microtubule motor proteins.
J. Cell Sci.
107
,
1875
-1884.
Hirokawa, N. (
1998
). Kinesin and dynein superfamily proteins and the mechanism of organelle transport.
Science
279
,
519
-526.
Inoué, S. and Salmon, E. D. (
1995
). Force generation by microtubule assembly/disassembly in mitosis and related movements.
Mol. Biol. Cell
6
,
1619
-1640.
Kim, A. J. and Endow, S. A. (
2000
). A kinesin family tree.
J. Cell Sci.
113
,
3681
-3682.
Lawrence, C. J., Morris, N. R., Meagher, R. B. and Dawe, R. K. (
2001
). Dyneins have run their course in plant lineage.
Traffic
2
,
362
-363.
Lawrence, C. J., Malmberg, R. L., Muszynski, M. G. and Dawe, R. K. (
2002
). Maximum likelihood methods reveal conservation of function among closely related kinesin families.
J. Mol. Evol.
54
,
42
-53.
Miki, H., Setou, M., Kaneshiro, K. and Hirokawa, N. (
2001
). All kinesin superfamily protein, KIF, genes in mouse and human.
Proc. Natl Acad. Sci. USA
98
,
7004
-7011.
Moore, J. D. and Endow, S. A. (
1996
). Kinesin proteins: a phylum of motors for microtubule-based motility.
BioEssays
18
,
207
-219.
Sharp, D. J., Rogers, G. C. and Scholey, J. M. (
2000
). Microtubule motors in mitosis.
Nature
407
,
41
-47.
Song, H., Golovkin, M., Reddy, A. S. N. and Endow, S. A. (
1997
). In vitro motility of AtKCBP, a calmodulin-binding kinesin protein of Arabidopsis.
Proc. Natl Acad. Sci. USA
94
,
322
-327.
Swofford, D. L. (
2002
).
PAUP*, Phylogenetic Analysis Using Parsimony (*and other Methods)
. Sunderland, MA: Sinauer Associates.
Thompson, J. D., Higgins, D. G. and Gibson, T. J. (
1994
). CLUSTAL W: improving the sensitivity of progessive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acid. Res.
22
,
4673
-4680.
Vale, R. D. and Fletterick, R. J. (
1997
). The design plan for the kinesin motors.
Annu. Rev. Cell Dev. Biol.
13
,
745
-777.
Yucel, J. K., Marszalek, J. D., McIntosh, J. R., Goldstein, L. S. B., Cleveland, D. W. and Philp, A. V. (
2000
). CENP-meta, an essential kinetochore kinesin required for the maintenance of metaphase chromosome alignment in Drosophila.
J. Cell Biol.
150
,
1
-12.