Analysis and Results of Core Motifs and Conserved Peptides
In further examination of the P. reichenowi and P. falciparum DBLα domain homology
blocks, we revealed multiple regions of high sequence homology, classified here in two
groups: core motifs and conserved peptides. The core motifs are defined as regions of 100%
sequence identity that are found in at least one P. reichenowi gene matching two or more
from P. falciparum (unique pairs of matches are considered conserved peptides, details
below) and correspond to one of the five known degenerate motifs [1] that characterize the
DBLα domains. These domains, listed starting from the N-terminus side are HB4, HB3, HB5,
HB2, and HB1 [1]. We recovered 18 sequences corresponding to the conserved motifs,
between 10 and 29 residues, in 36 different P. reichenowi var genes and shared with 85 of
those from 3D7 and HB3. The HB2 motifs are the most frequently represented in this group,
corresponding to 11 of the 18 different motifs, and were found in 26 P. reichenowi and 63 P.
falciparum paralogs total, with a mid-sized motif (19 residues) found in 16 out of 49 standard
(non-csa) P.reichenowi PFEMP1 sequences. The HB3 motifs are found in two different
forms, in 12 P. reichenowi and 54 P. falciparum domains, and HB5 in four forms in 9 P.
reichenowi genes and 19 from the P. falciparum sets. The HB4 had only one identical form
matching two P. falciparum (one each in 3D7 and HB3). Notably, HB1 motifs were not
present in these results. Although one match was found for this motif, it is not counted
among these results in this group as it was only found in a unique pair, and it was between
the P. reichenowi and HB3 var1csa genes, a locus which is already known to have a
relatively recombination rate and high degree of conservation, quite distinct from the standard
PfEMP1s (these results are summarized in Table S7).
The var genes are classified as upsaA, upsB, or upsC based on conserved upstream
sequences. A combination of all the results of the P. falciparum matches from all the motifs
shows a total of 555 hits, with individual genes represented between 1 and 14 times. Of
these 555 hits, 13 were from uspA genes, 368 were from upsB, and 164 from upsC.
Because there are a total of 18 upsA, 55 upsB, and 21 upsC genes in the analysis, this
indicates that upsB and upsC genes show greater levels of conservation, with upsA genes
more divergent [2].
In addition to these core motifs, we also found 53 regions that define conserved
peptides, determined by pairwise matches of high identity/similarity between P. reichenowi
and P. falciparum DBLα domains. These peptides range between 24 and 140 residues in
length, and between 70% and 100% identity (identical amino acids) and 80% to 100%
similarity (amino acids with the same or similar functional characteristics). The conserved
regions are drawn from 48 non-redundant matches, with the five additional peptides each
drawn from a smaller portion of a conserved peptide with even higher identity. While many P.
reichenowi loci revealed none of this highly conserved sequence, some loci were represented
in multiple matches, the most frequent being Preich_4 with 6 non-redundant regions plus one
additional sub-region of high P. reichenowi/P. falciparum homology, Preich_11 with four
peptides and one additional sub-region of high identity, and Preich_7.2, and Preich_84, both
with four matches
1.
2.
Rask TS, Hansen DA, Theander TG, Gorm Pedersen A, Lavstsen T: Plasmodium
falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes: Divide
and Conquer. PLoS Comput Biol 2010, 6(9):e1000933.
Lavstsen T, Salanti A, Jensen ATR, Theander TG, Copenhagen D: Sub-grouping of
Plasmodium falciparum 3D7 var genes based on sequence analysis of coding
and non-coding regions. Malaria Journal 2003, 2:27.
Sequence
VFEVWLGNQQEAFKKQK
FDYVPQYLRWF
FDYVPQYLRWFEEW
FDYVPQYLRWFEEWAE
DYVPQYLRWFEEWAEDFCR
FDYVPQYLRWFEEWAEDFC
FDYVPQYLRWFEEWAEDFCR
PTYFDYVPQYLRWFEEWAEDFCR
VPTYFDYVPQYLRWFEEWAEDFCRK
DQVPTYFDYVPQYLRWFEEWAEDFCRK
PTYFDYVPQYLRWFEEWAEDFCRKKKK
PTYFDYVPQYLRWFEEWAEDFCRLRKHKL
LARSFADIGDIVRG
CTVLARSFADIGDIVRGRDLY
APYRRRHICDYNLHHINENN
WWTANRETVW
KLREDWWTANR
LREDWWTANRETVW
KLREDWWTANRETVW
Table S7: Summary of core motifs
Matches Motif
2
87
78
75
69
70
67
63
40
12
23
8
66
5
3
16
20
15
8
HB1
HB2
HB2
HB2
HB2
HB2
HB2
HB2
HB2
HB2
HB2
HB2
HB3
HB3
HB4
HB5
HB5
HB5
HB5
Length No.
Matches: P.
reichenowi
17
11
14
16
19
19
20
23
25
27
27
29
14
21
20
10
11
14
15
1
24
19
18
16
16
14
11
7
3
2
2
12
1
1
8
5
8
4
No.
Matches: P.
falciparum
1
63
59
57
53
54
53
52
33
9
21
6
54
4
2
8
15
7
4
P. falciparum
HB3var16
HB3var16
HB3var16
HB3var17
HB3var18
HB3var18
HB3var21
HB3var22
HB3var24
HB3var25
HB3var27
HB3var27
HB3var2
HB3var2
HB3var34
HB3var34*
HB3var34**
HB3var36
HB3var36
HB3var36*
HB3var6
HB3var7
HB3var8
HB3var8_2
MAL7P1.187
MAL7P1.56
MAL7P1.56*
PF07_0050
PF07_0050
PF07_0050*
PF070051
PF080103
PF080103*
PF080103
PF080140
PF100406
PF110521
PF140773_truncated
PF140773_truncated
PFB1055c
PFB1055c
P.
reichenowi
Preich_24
Preich_126
Preich_102
Preich_7.2
Preich_9
Preich_7.2
Preich_7.2
Preich_84
Preich_40
Preich_17
Preich_4
Preich_61
Preich_5.2
Preich_8.2
Preich_5
Preich_5*
Preich_5**
Preich_26
Preich_4
Preich_4*
Preich_8.2
Preich_1
Preich_46
Preich_46
Preich_7
Preich_4
Preich_4*
Preich_11
Preich_7.2
Preich_11*
Preich_4
Preich_133
Preich_4.2*
Preich_4.2
Preich_11
Preich_61
Preich_11
Preich_5
Preich_61
Preich_25
Preich_84
Identical
Aas
48
61
51
101
63
105
103
72
42
33
37
35
44
47
76
47
27
37
102
81
30
26
79
24
31
45
36
70
39
22
37
115
32
65
23
28
23
29
53
49
31
Length
60
84
73
138
82
139
136
95
48
40
39
35
50
59
83
55
27
47
142
101
36
29
100
29
36
63
40
99
46
29
46
145
35
87
29
34
30
37
67
59
37
Percent
Identity
80
73
70
73
77
76
76
76
88
83
95
100
88
80
81
85
100
79
72
80
83
90
79
83
86
71
90
71
85
76
80
79
91
75
79
82
77
78
79
83
84
Percent
Similar AAs Similarity
56
93
75
89
62
85
114
83
74
90
116
83
118
87
79
83
47
98
36
90
39
100
x
x
48
96
55
93
73
88
51
93
x
x
42
89
121
85
92
91
36
100
26
90
85
85
27
93
33
92
51
81
38
95
82
83
43
93
26
90
40
87
126
87
35
100
77
89
26
90
30
88
29
97
35
95
58
87
53
90
34
92
PFC0005w
PFC0005w
PFC0005w
PFC0005w
PFC1120c
PFD1245c
PFE1640w_truncated
PFL0005w
PFL1955w
PFL1970w
PFL2665c
PFL2665c
Preich_32
Preich_46
Preich_11
Preich_84
Preich_84
Preich_9
Preich_8.2
Preich_5
Preich_40
Preich_78
Preich_129
Preich_4
57
72
21
37
43
47
48
28
38
67
97
21
73
101
30
41
58
56
58
37
43
92
139
24
78
71
70
90
74
84
83
76
88
73
70
88
61
81
26
41
50
52
52
34
41
74
117
24
84
80
87
100
86
93
90
92
95
80
84
100
Table S8: Summary of conserved peptide matches. Stars (*) indicate sub sections of higher
homology