Supplemental Material to:
A Giant GTPase, Very Large Inducible GTPase-1, Is Inducible by Interferons1
Thorsten Klamp,* Ulrich Boehm,2* Daniela Schenk,* Klaus Pfeffer,† and Jonathan C. Howard3*
*Institute for Genetics, University of Cologne, Cologne, Germany; and †Institute for Medical Microbiology, University of Düsseldorf, Düsseldorf, Germany
1 This work was supported by grants from the Deutsche Forschungsgemeinschaft (to J.C.H. (Sonderforschungsbereich 243) and K.P. (Pf259/2-4, Sonderforschungsbereich 455 and 576)).
2 Present address: Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109
3 Address correspondence and reprint requests to Dr. Jonathan C. Howard, Institute for Genetics, University of Cologne, Zülpicher Strasse 47, D-50674 Cologne, Germany.
E-mail address: .
Running title: A GIANT GTPase, VLIG-1, IS INDUCIBLE BY IFNs
Table I. BAC clones containing VLIG-1
The following bacterial artificial chromosome (BAC) clones were screened positive for VLIG-1:
129/SvJ (Genome Systems, St. Louis, MO)in pBeloBAC11 (Clone Address/Clone Number) / C57BL/6J (German Resource Center for Genome Research, Berlin, Germany)
BAC library RP23
7:J23/19621 / RP23-454A11
226:M24/19622 / RP23-123C7
81:F18/19623 / RP23-406H8
114:E8/19624 / RP23-209J2
148:M7/19625 / RP23-477O14
The RP23 library BACs containing VLIG-1 all map to band F1 of Chromosome 7 and overlap in a region between 95.65 Mb and 95.73 Mb.
Table II. VLIG-1 related EST clones of C57BL/6 origin
This table collates 222 expressed sequence tags (ESTs) of C57BL/6 origin recovered from the NCBI public databases using searches based on the full VLIG-1 cDNA sequence (GenBank accession AY167972). After removal of insecure end sequence, each EST was aligned with the full sequence of VLIG-1 and a series of contigs was established by which VLIG-1 ESTs could be discriminated from ESTs derived from VLIG-1 homologs. Genes corresponding to VLIG homologous ESTs were identified from the mouse ENSEMBL genome database, thus allowing the assignment of non-overlapping contigs to individual genes. Genes identified from the EST collection with high certainty are named VLIG-1, VLIG-B, VLIG-C, VLIG-D and VLIG-E (see also Fig. 1A of the main text for their map positions in the mouse genome).
The 222 C57BL/6 EST clones break down as follows:
VLIG-1 99 (+ 7 very similar but not identical)
VLIG-A 0 (ESTs of VLIG-A can be found in the Barstead mouse colon library from the FVB/N strain)
VLIG-B 9
VLIG-C 48 (+ 4 very similar but not identical)
VLIG-D 31
VLIG-E 19
“new VLIG” 5 (These EST clones do not correspond to any identified gene and might represent different new VLIG family members)
A total of 6 VLIG genes (VLIG-1, VLIG-A, VLIG-B, VLIG-C, VLIG-D and VLIG-E) has been unambiguously distinguished using EST and genomic information. ESTs probably corresponding to all of these genes except VLIG-A have been identified from C57BL/6 (see above) suggesting that they are all transcribed constitutively, albeit at different levels. VLIG-A ESTs are not present in the C57BL/6 collection but are present in Barstead mouse colon library from the FVB/N strain. Overall, 76% of all C57BL/6 VLIG ESTs were derived from hemopoietic and lymphoid tissues.
Two ESTs from the main C57BL/6 EST database (AA611146 and AI607218) and three further ESTs from the Riken series (AV373816, BB184268 and BB549480) are still unassigned, they may correspond to different segments of a further VLIG family member (“new VLIG”, see above).
Sequences and alignments of all EST and genomic VLIG sequences are available from the authors.
EST clone ID
/ % identity / Alignment length / Mis-matches / Gap openings / Start position / End position /Origin
/ VLIG memberAA086707 / 98.97 / 388 / 3 / 1 / 7344 / 7731 / CD4+ T-cells / VLIG-1
AA098105 / 100.00 / 105 / 0 / 0 / 1572 / 1676 / CD4+ T-cells / VLIG-1
AA138503 / 100.00 / 227 / 0 / 0 / 8547 / 8773 / spleen / VLIG-1
AA144268 / 100.00 / 143 / 0 / 0 / 8633 / 8775 / spleen / VLIG-1
AA144391 / 99.43 / 522 / 0 / 3 / 8042 / 8563 / spleen / VLIG-1
AA154933 / 99.54 / 432 / 2 / 0 / 7345 / 7776 / spleen / VLIG-1
AA162117 / 99.74 / 378 / 1 / 0 / 7656 / 8033 / spleen / VLIG-1
AA175269 / 99.80 / 494 / 1 / 0 / 1979 / 2472 / spleen / VLIG-1
AA175630 / 100.00 / 334 / 0 / 0 / 8407 / 8740 / spleen / VLIG-1
AA177940 / 99.76 / 410 / 0 / 1 / 7773 / 8182 / spleen / VLIG-1
AA178657 / 98.55 / 415 / 5 / 1 / 8381 / 8794 / spleen / VLIG-1
AA183700 / 99.80 / 499 / 1 / 0 / 7525 / 8023 / spleen / VLIG-1
AA183873 / 99.71 / 349 / 1 / 0 / 7525 / 7873 / spleen / VLIG-1
AA184264 / 100.00 / 458 / 0 / 0 / 8187 / 8644 / spleen / VLIG-1
AA273598 / 100.00 / 222 / 0 / 0 / 8092 / 8313 / spleen / VLIG-1
AA273679 / 100.00 / 495 / 0 / 0 / 7808 / 8302 / spleen / VLIG-1
AA273726 / 99.77 / 444 / 1 / 0 / 8331 / 8774 / spleen / VLIG-1
AA419826 / 100.00 / 522 / 0 / 0 / 8352 / 8873 / heart / VLIG-1
AA444665 / 99.76 / 423 / 1 / 0 / 8099 / 8521 / mammary gland / VLIG-1
AA718714 / 99.53 / 424 / 2 / 0 / 8378 / 8801 / mammary gland / VLIG-1
AA794517 / 100.00
100.00 / 297
59 / 0
0 / 0
0 / 8578
8888 / 8874
8946 / skin / VLIG-1
AA833316 / 99.65 / 570 / 2 / 0 / 7382 / 7951 / uterus / VLIG-1
AA867503 / 100.00 / 353 / 0 / 0 / 3194 / 3546 / macrophages / VLIG-1
AA980077 / 99.81 / 538 / 1 / 0 / 1253 / 1790 / mammary gland / VLIG-1
AI098949 / 99.35 / 155 / 1 / 0 / 12 / 166 / liver / VLIG-1
AI152922 / 98.24 / 512 / 2 / 1 / 6027 / 6538 / uterus / sim. VLIG-1
AI153750 / 99.70 / 337 / 0 / 1 / 7903 / 8239 / mammary gland / VLIG-1
AI450858 / 98.09 / 367 / 2 / 3 / 2481 / 2842 / spleen / VLIG-1
AI510154 / 99.37 / 316 / 2 / 0 / 3194 / 3509 / macrophages / VLIG-1
AI639820 / 99.53 / 424 / 1 / 1 / 1980 / 2402 / spleen / VLIG-1
AW989511 / 99.53 / 424 / 2 / 0 / 8138 / 8561 / mammary gland / VLIG-1
BB113565 / 95.90 / 268 / 11 / 0 / 8333 / 8600 / urinary bladder / sim. VLIG-1
BB119067 / 94.25
96.61
100.00 / 174
59
21 / 10
2
0 / 0
0
0 / 8701
8888
8982 / 8874
8946
9002 / urinary bladder / VLIG-1
BB133401 / 98.80 / 500 / 3 / 3 / 3748 / 4244 / bone / VLIG-1
BB207257 / 87.29
91.53
100.00 / 118
59
24 / 15
5
0 / 0
0
0 / 8757
8888
8982 / 8874
8946
9005 / thymus / VLIG-1
BB215400 / 92.37
98.31
100.00 / 131
59
21 / 10
1
0 / 0
0
0 / 8744
8888
8982 / 8874
8946
9002 / aorta and vein / VLIG-1
BB222319 / 91.30
98.31 / 184
59 / 16
1 / 0
0 / 8691
8888 / 8874
8946 / aorta and vein / VLIG-1
BB328085 / 94.58 / 240 / 13 / 0 / 8359 / 8598 / aipose / sim. VLIG-1
BB548315 / 95.75 / 259 / 11 / 0 / 8340 / 8598 / oviduct / sim. VLIG-1
BB582727 / 95.93 / 221 / 9 / 0 / 6470 / 6690 / cecum / sim. VLIG-1
BB607726 / 96.48 / 284 / 10 / 0 / 5581 / 5864 / cecum / sim. VLIG-1
BB629307 / 97.00 / 566 / 12 / 5 / 1 / 561 / bone / VLIG-1
BB636647 / 100.00 / 104 / 0 / 0 / 1 / 104 / aorta and vein / VLIG-1
BB653757 / 99.08 / 652 / 6 / 0 / 6545 / 7196 / liver tumor / VLIG-1
BE133953 / 100.00
100.00
100.00 / 337
59
24 / 0
0
0 / 0
0
0 / 8538
8888
8982 / 8874
8946
9005 / mammary gland / VLIG-1
BE197403 / 99.78 / 458 / 0 / 1 / 7893 / 8350 / mammary gland / VLIG-1
BE200148 / 99.75 / 407 / 1 / 0 / 8376 / 8782 / mammary gland / VLIG-1
BE286411 / 97.64 / 550 / 11 / 2 / 7283 / 7830 / mammary gland / VLIG-1
BE291987 / 99.80 / 495 / 0 / 1 / 5465 / 5958 / infiltrating ductal carcinoma / VLIG-1
BE335962 / 100.00 / 352 / 0 / 0 / 8407 / 8758 / spleen / VLIG-1
BE632294 / 100.00 / 478 / 0 / 0 / 7605 / 8082 / spleen / VLIG-1
BE632705 / 100.00 / 513 / 0 / 0 / 7386 / 7898 / spleen / VLIG-1
BE632853 / 99.53 / 427 / 0 / 1 / 6394 / 6820 / spleen / VLIG-1
BE633854 / 100.00 / 438 / 0 / 0 / 8014 / 8451 / spleen / VLIG-1
BE634495 / 100.00 / 514 / 0 / 0 / 8268 / 8781 / spleen / VLIG-1
BE634861 / 99.82 / 570 / 0 / 1 / 8213 / 8782 / spleen / VLIG-1
BE634937 / 100.00 / 535 / 0 / 0 / 8238 / 8772 / spleen / VLIG-1
BE687270 / 99.52 / 421 / 2 / 0 / 8152 / 8572 / spleen / VLIG-1
BE687325 / 100.00 / 456 / 0 / 0 / 6279 / 6734 / spleen / VLIG-1
BE692412 / 100.00 / 461 / 0 / 0 / 8140 / 8600 / spleen / VLIG-1
BE850056 / 99.25 / 399 / 3 / 0 / 7489 / 7887 / spleen / VLIG-1
BF453143 / 100.00 / 288 / 0 / 0 / 8587 / 8874 / spleen / VLIG-1
BF453400 / 99.59 / 488 / 2 / 0 / 7582 / 8069 / spleen / VLIG-1
BF660853 / 99.52 / 413 / 2 / 0 / 8025 / 8437 / spleen / VLIG-1
BF661277 / 100.00 / 379 / 0 / 0 / 8404 / 8782 / spleen / VLIG-1
BF661278 / 99.75 / 401 / 1 / 0 / 8201 / 8601 / spleen / VLIG-1
BF661438 / 99.48
100.00 / 385
42 / 2
0 / 0
0 / 8490
8888 / 8874
8929 / spleen / VLIG-1
BF661718 / 100.00
100.00
100.00 / 298
59
21 / 0
0
0 / 0
0
0 / 8577
8888
8982 / 8874
8946
9002 / spleen / VLIG-1
BF661928 / 100.00 / 453 / 0 / 0 / 8151 / 8603 / spleen / VLIG-1
BF662016 / 98.82 / 338 / 4 / 0 / 8439 / 8776 / spleen / VLIG-1
BG090660 / 100.00 / 373 / 0 / 0 / 8059 / 8431 / spleen / VLIG-1
BG090949 / 99.66 / 298 / 1 / 0 / 6874 / 7171 / spleen / VLIG-1
BG091185 / 99.52 / 415 / 1 / 1 / 8334 / 8747 / spleen / VLIG-1
BG092829 / 100.00 / 604 / 0 / 0 / 8193 / 8796 / spleen / VLIG-1
BG092938 / 99.32
100.00
100.00 / 293
59
24 / 2
0
0 / 0
0
0 / 8582
8888
8982 / 8874
8946
9005 / spleen / VLIG-1
BG094732 / 97.21 / 430 / 1 / 10 / 8450 / 8868 / spleen / sim. VLIG-1
BG095308 / 100.00 / 424 / 0 / 0 / 8301 / 8724 / spleen / VLIG-1
BG095578 / 100.00
100.00 / 228
34 / 0
0 / 0
0 / 8647
8888 / 8874
8921 / spleen / VLIG-1
BG228183 / 99.70
100.00
100.00 / 337
59
24 / 1
0
0 / 0
0
0 / 8538
8888
8982 / 8874
8946
9005 / spleen / VLIG-1
BM120854 / 100.00 / 551 / 0 / 0 / 8225 / 8775 / kidney / VLIG-1
BM243571 / 100.00 / 618 / 0 / 0 / 8155 / 8772 / hemopoietic stem cell / VLIG-1
BQ563058 / 100.00 / 538 / 0 / 0 / 8235 / 8772 / unknown / VLIG-1
BQ563059 / 99.85 / 661 / 1 / 0 / 6092 / 6752 / unknown / VLIG-1
BY129867 / 99.39 / 326 / 0 / 1 / 1 / 326 / brain / VLIG-1
BY155594 / 96.86 / 414 / 4 / 9 / 7799 / 8205 / macrophages / VLIG-1
BY159356 / 98.60 / 358 / 4 / 1 / 7799 / 8155 / macrophages / VLIG-1
BY170890 / 98.13 / 375 / 6 / 1 / 7799 / 8172 / macrophages / VLIG-1
BY173169 / 98.90 / 362 / 3 / 1 / 7799 / 8159 / macrophages / VLIG-1
BY199517 / 99.50
100.00 / 201
156 / 1
0 / 0
0 / 296
1 / 496
156 / dendritic cells / VLIG-1
BY200869 / 98.99
95.10 / 296
102 / 2
5 / 1
0 / 297
1 / 591
102 / dendritic cells / VLIG-1
BY201672 / 97.89
98.04
100.00 / 142
102
27 / 1
2
0 / 2
0
0 / 297
1
457 / 436
102
483 / dendritic cells / VLIG-1
BY504453 / 98.16 / 381 / 4 / 3 / 8394 / 8771 / macrophages / VLIG-1
BY515071 / 96.68 / 391 / 11 / 2 / 8378 / 8768 / macrophages / VLIG-1
BY516353 / 99.75 / 404 / 1 / 0 / 8372 / 8775 / macrophages / VLIG-1
BY516378 / 99.04 / 418 / 3 / 1 / 8359 / 8775 / macrophages / VLIG-1
BY516469 / 99.76 / 415 / 1 / 0 / 8361 / 8775 / macrophages / VLIG-1
BY518318 / 96.31 / 271 / 9 / 1 / 6792 / 7062 / thymus / VLIG-1
BY544114 / 98.79 / 412 / 3 / 2 / 2678 / 3088 / dendritic cells / VLIG-1
BY545920 / 98.60 / 429 / 6 / 0 / 2657 / 3085 / dendritic cells / VLIG-1
BY577205 / 95.80
94.79
94.92 / 119
96
59 / 4
5
3 / 1
0
0 / 8757
8631
8888 / 8874
8726
8946 / whole embryo / VLIG-1
BY579139 / 98.45
100.00
100.00 / 258
56
24 / 4
0
0 / 0
0
0 / 8617
8891
8982 / 8874
8946
9005 / whole embryo / VLIG-1
BY727534 / 99.70 / 656 / 2 / 0 / 4094 / 4749 / adipose / VLIG-1
BY744674 / 98.78 / 655 / 3 / 5 / 7799 / 8453 / macrophages / VLIG-1
BY761115 / 99.81
100.00 / 531
59 / 0
0 / 1
0 / 8344
8888 / 8874
8946 / liver tumor / VLIG-1
CA575820 / 99.15 / 353 / 2 / 1 / 6092 / 6443 / hemopoietic stem cell / VLIG-1
CA576693 / 100.00 / 567 / 0 / 0 / 6092 / 6658 / hemopoietic stem cell / VLIG-1
AA178585 / 97.77
84.32 / 179
236 / 4
35 / 0
2 / 6259
5945 / 6437
6179 / spleen / VLIG-B
AI592325 / 97.77
87.43 / 179
167 / 4
20 / 0
1 / 6259
6014 / 6437
6179 / spleen / VLIG-B
BB220598 / 82.67 / 427 / 62 / 5 / 8395 / 8813 / aorta and vein / VLIG-B
BB637247 / 86.58 / 544 / 70 / 3 / 5591 / 6132 / aorta and vein / VLIG-B
BE632843 / 84.29
84.81 / 210
158 / 25
18 / 4
2 / 8395
8167 / 8600
8320 / spleen / VLIG-B
BE687308 / 96.58
85.00
92.11 / 234
160
38 / 8
18
3 / 0
2
0 / 6268
8165
8395 / 6501
8320
8432 / spleen / VLIG-B
BG229372 / 86.23
94.74 / 167
76 / 22
4 / 1
0 / 6014
6259 / 6179
6334 / spleen / VLIG-B
BY199399 / 87.10
98.94 / 248
94 / 32
1 / 0
0 / 3579
7 / 3826
100 / dendritic cells / VLIG-B
BY544023 / 86.15 / 130 / 18 / 0 / 8684 / 8813 / dendritic cells / VLIG-B
AA155018 / 88.93 / 271 / 28 / 2 / 8590 / 8860 / spleen / VLIG-C
AA163327 / 89.96 / 249 / 25 / 0 / 7326 / 7574 / spleen / VLIG-C
AA164015 / 91.34 / 404 / 32 / 1 / 1144 / 1547 / spleen / VLIG-C
AA174668 / 94.53 / 384 / 21 / 0 / 6308 / 6691 / spleen / VLIG-C
AA174843 / 98.56 / 139 / 2 / 0 / 6374 / 6512 / spleen / VLIG-C
AA175777 / 88.44 / 294 / 26 / 2 / 8468 / 8753 / spleen / VLIG-C
AA177731 / 86.93 / 436 / 43 / 5 / 8100 / 8527 / spleen / VLIG-C
AA189193 / 91.25 / 377 / 33 / 0 / 1590 / 1966 / lymph node / VLIG-C
AA200749 / 88.14 / 194 / 17 / 5 / 6515 / 6706 / spleen / sim. VLIG-C
AA212297 / 89.73 / 185 / 15 / 2 / 8400 / 8580 / thymus / VLIG-C