Table 3. In vitro growth analysis of STM mutants in fibroblasts

Name	Genome location (nt)	Coding strand	Possible function	Orientation of Tn	Position of Tn	In vitro growth	Conservation in subfamilies*	In vitro growth in
Name	Genome location (nt)	Coding strand	Possible function	Orientation of Tn	Position of Tn	In vitro growth	Conservation in subfamilies*	α (HSV-1)^†	β (HCMV)^‡
M1	2023–3282	Rt	Serpin	R	2425	NE ^§	MHV-68
M2	4031–4627	L	Unknown	R	4110	NE ^§	MHV-68
M3	6060–7277	L	Unknown	R	6547	NE ^§	MHV-68
M4	8409–9785	Rt	Unknown	R	8641	NE ^§	MHV-68
ORF 4	9873–11036	Rt	Complement regulatory protein	R	9923	NE	γ₂
ORF 6	11215–14523	Rt	ssDNA binding protein	R	11241	E ^§	α, β, γ	E (UL29)	E (UL57)
ORF 7	14526–16481	Rt	Transport protein	R	14534	E	α, β, γ	E (UL28)	E (UL56)
ORF 8	16505–19051	Rt	Glycoprotein B, (virion)^¶	R	16540	E ^§	α, β, γ	E (UL27)	E (UL55)
ORF 9	19217–22297	Rt	DNA polymerase	R	19526	E	α, β, γ	E (UL30)	E (UL54)
ORF 10	22269–23522	Rt	Unknown	R	22307	NE ^§	β, γ		A (UL72)
ORF 11	23488–24651	Rt	Unknown	F	23685	NE	γ
K3	24733–25335	L	Modulator of immune response	F	25276	NE ^§	γ₂(KSHV)
M5	26178–26672	Rt	Unknown	F	26214	A	MHV-68
M6	26554–28308	Rt	Unknown	F	26874	NE	MHV-68
ORF 17	28326–29957	L	Capsid protein	F	29138	E	α, β, γ	E (UL26)	E (UL80)
ORF 18	29917–30768	Rt	Unknown	F	30090	E	β, γ		E (UL79)
ORF 19	30726–32273	L	Tegument protein	R	31840	E	α, β, γ	E (UL25)	E (UL77)
ORF 20	32119–32880	L	Fusion protein, HSV UL24-like, (virion)^¶	R	32804	NE	α, β, γ	NE (UL24)	E/A(UL76)½ ½
ORF 21	32879–34810	Rt	Thymidine kinase	F	34425	NE ^§	α, γ	NE (UL21)
ORF 22	34833–37022	R	Glycoprotein H, (virion)^¶	F	35149	E ^§	α, β, γ	E (UL22)	E (UL75)
ORF 23	37025–38167	L	Unknown	R	38004	NE	γ
ORF 24	38103–40253	L	HCMV UL87-like, (virion)^¶	R	40220	E	β, γ		E (UL87)
ORF 25	40263–44381	Rt	Major capsid protein, (virion)^¶	R	40486	E **	α, β, γ	E (UL19)	E (UL86)
ORF 26	44423–45319	Rt	Capsid protein, triplex-2, (virion)^¶	R	44445	E	α, β, γ	E (UL18)	E (UL85)
ORF 27	45329–46090	Rt	Unknown	F	45336	NE ^§	γ
ORF 29b	46395–47438	L	Packaging protein, (virion)^¶	F	47224	E ^§	α, β, γ	E (UL15)	E (UL89)
ORF 31	47710–48309	Rt	Unknown	R	47921	E ^§	β, γ		E (UL92)
ORF 32	48294–49625	Rt	Unknown	R	48867	E	β, γ		E (UL93)
ORF 33	49588–50568	Rt	Unknown	F	49658	E ^§	α, β, γ	NE (UL16)	E/A (UL94)½ ½
ORF 29a	50549–51466	L	Packaging protein, (virion)^¶	R	51298	E ^§	α, β, γ	E (UL15)	E (UL89)
ORF 34	51465–52460	Rt	Unknown	R	51612	E ^§	β, γ		E (UL95)
ORF 35	52423–52878	Rt	Unknown	F	52670	E	γ
ORF 36	52847–54157	Rt	Kinase	F	52925	A	α, β, γ	NE (UL13)	A (UL97)
ORF 37	54129–55586	Rt	Alkaline exonuclease	R	54223	NE **	α, β, γ	NE (UL12)	E (UL98)
ORF 38	55544–55768	Rt	Myristylated tegument protein	R	55674	NE	γ
ORF 39	55802–56950	L	Glycoprotein M	R	56650	E ^§	α, β, γ	NE (UL10)	E (UL100)
ORF 40	57046–58875	Rt	Helicase-primase	F	57084	E	γ
ORF 42	58876–59634	L	Unknown	F	59400	E	α, β, γ	E (UL7)	A (UL103)
ORF 43	59634–61334	L	Capsid protein	R	61179	E ^§	α, β, γ	E (UL6)	E (UL104)
ORF 44	61303–63630	Rt	Helicase-primase	R	61360	E ^§	α, β, γ	E (UL5)	E (UL105)
ORF 45	63655–64272	L	IRF-7 binding protein homologue, (virion)^¶	F	63821	E ^§	γ
ORF 46	64275–65021	L	Uracil DNA glycosylase	R	64712	NE	α, β, γ	NE (UL2)	A (UL114)
ORF 48	65584–66582	L	(virion)^¶	R	66462	E	γ
ORF 49	66741–67643	L	Transcriptional activator	F	67320	A ^§	γ
ORF 50	67907–69373	Rt	Transcriptional activator	F	68075	E ^§	γ
M7	69466–70914	Rt	gp150, (virion)^¶	F	69767	NE ^§	MHV-68
ORF 52	70960–71364	L	Unknown, (virion)^¶	F	71349	E	γ
ORF 53	71447–71701	L	Unknown	R	71645	E	β, γ		E (UL73)
ORF 54	71806–72702	Rt	dUTPase	F	71898	NE	α, γ	NE (UL50)
ORF 55	72744–73313	L	Unknown	R	72951	E	β, γ		E/A (UL71)½ ½
ORF 56	73289–75793	Rt	Helicase-primase	F	73320	E ^§	α, β, γ	E (UL52)	E (UL70)
M8	76015–76485	Rt	Unknown	F	76127	E	MHV-68
ORF 57	76662–77159	Rt	Posttranscriptional regulator	R	76975	E	α, β, γ	E (UL54)	A (UL69)
ORF 58	77214–78254	L	Unknown	R	78084	NE	γ
ORF 59	78258–79439	L	Processivity factor	F	78836	NE	γ
ORF 60	79565–80479	L	Ribonucleotide reductase (small)	F	80360	A ^§	α, γ	NE (UL40)
ORF 61	80517–82865	L	Ribonucleotide reductase (large)	F	82619	NE **	α, β, γ	NE (UL39)	NE (UL45)
ORF 62	82871–84010	L	Assembly, DNA maturation, triplex-1, capsid protein, (virion)^¶	F	83900	E	γ
ORF 63	83751–86564	Rt	Tegument protein	R	84079	E	γ
ORF 64	86567–93937	Rt	Tegument protein	F	87421	E ^§	α, β, γ	E (UL36)	E/A (UL48)½ ½
M9 (ORF 65)	93962–94519	L	Small capsid protein, (virion)^¶	R	94297	E **	γ
ORF 66	94515–95741	L	Unknown	F	95491	E ^§	β, γ		E (UL49)
ORF 67	95738–96415	L	Tegument protein	R	96361	E	β, γ		E (UL50)
ORF 68	96673–98052	Rt	Glycoprotein	R	96741	E	α, β, γ	E (UL32)	E (UL52)
ORF 69	98061–98936	Rt	Unknown	R	98140	E	α, β, γ	E (UL31)	E (UL53)
ORF 72	102426–103181	L	vCyclin D	R	102797	NE ^§	γ₂
M11	103418–103930	Rt	vBcl-2	R	103663	NE	γ
ORF 73	103927–104868	L	KSHV LANA homologue	F	104381	A **	γ₂
ORF 74	105057–106067	Rt	vGPCR (IL-8 receptor homologue)	R	105079	NE ^§	β, γ₂		NE (UL33)
ORF 75c	106070–109999	L	Tegument protein/ FGARAT, (virion)^¶	R	109961	E	γ
ORF 75b	110077–113901	L	Tegument protein/FGARAT	R	112615	NE ^§	γ
ORF 75a	114032–117904	L	Tegument protein/FGARAT	R	116851	NE	γ
M12	117992–118681	Rt	Unknown	F	118092	A **	MHV-68

Rt, right; L, left; R, ; reverse; F, forward; FGARAT, N -formylglycinamide ribotide amidotransferase; LANA, latency-associated nuclear antigen; HCMV, human cytomegalovirus; KSHV, Kaposi’s sarcoma-associated herpesvirus; IRF-7, IFN regulatory factor 7; vGPCR, KSHV-encoded G protein-coupledreceptor; dUTPase, deoxyuridine-triphosphatase; NE, nonessential; E, essential; A, attenuated.

*Based on data available at www.biochem.ucl.ac.uk/bsm/virus_database/ (1).

^{†Based on the summary in ref. 2.
^{‡Based on the results from refs. 3 and 4.
^{§Consistent with the results from previous publications (5-19).
^{¶Based on the results in ref. 20.
^{½
½
Indicates different phenotypes of the same ORF: E (3)/ A (4).
**Inconsistent with the results from previous publications (19).

1. Alba, M. M., Das, R., Orengo, C. A. & Kellam, P. (2001) Genome Res. 11, 43-54.

2.Roizman, B. & Knipe, D. M. (2001) in Fields Virology, eds. Knipe, D. M. & Howley, P. M. (Lippincott Williams & Wilkins, Philadelphia), Vol. 2, pp. 2399-2460.

3. Dunn, W., Chou, C., Li, H., Hai, R., Patterson, D., Stolc, V., Zhu, H. & Liu, F. (2003) Proc. Natl. Acad. Sci. USA 100, 14223-14228.

4.Yu, D., Silva, M. C. & Shenk, T. (2003) Proc. Natl. Acad. Sci. USA 100, 12396-12401.

5. Clambey, E. T., Virgin, H. W., 4th, & Speck, S. H. (2000) J. Virol. 74, 1973-1984.

6. Fowler, P., Marques, S., Simas, J. P. & Efstathiou, S. (2003) J. Gen. Virol. 84, 3405-3416.

7. Jacoby, M. A., Virgin, H. W., 4th, & Speck, S. H. (2002) J. Virol. 76, 1790-1801.

8. Macrae, A. I., Usherwood, E. J., Husain, S. M., Flano, E., Kim, I. J., Woodland, D. L., Nash, A. A., Blackman, M. A., Sample, J. T. & Stewart, J. P. (2003) J. Virol. 77, 9700-9709.

9. Stevenson, P. G., May, J. S., Smith, X. G., Marques, S., Adler, H., Koszinowski, U. H., Simas, J. P. & Efstathiou, S. (2002) Nat. Immunol. 3, 733-740.

10. Coleman, H. M., de Lima, B., Morton, V. & Stevenson, P. G. (2003) J. Virol. 77, 2410-2417.

11. de Lima, B. D., May, J. S. & Stevenson, P. G. (2004) J. Virol. 78, 5103-5112.

12. Simas, J. P., Bowden, R. J., Paige, V. & Efstathiou, S. (1998) J. Gen. Virol. 79, 149-153.

13. Moorman, N. J., Virgin, H. W., 4th, & Speck, S. H. (2003) Virology 307, 179-190.

14. Moorman, N. J., Willer, D. O. & Speck, S. H. (2003) J. Virol. 77, 10295-10303.

15.Bridgeman, A., Stevenson, P. G., Simas, J. P. & Efstathiou, S. (2001) J. Exp. Med. 194, 301-312.

16. van Dyk, L. F., Virgin, H. W., 4th, & Speck, S. H. (2000) J. Virol. 74, 7451-7461.

17. Gangappa, S., van Dyk, L. F., Jewett, T. J., Speck, S. H. & Virgin, H. W., 4th (2002) J. Exp. Med. 195, 931-940.

18. Pavlova, I. V., Virgin, H. W., 4th, & Speck, S. H. (2003) J. Virol. 77, 5731-5739.

19. Moorman, N. J., Lin, C. Y. & Speck, S. H. (2004) J. Virol. 78, 10282-10290.

20. Bortz, E., Whitelegge, J. P., Jia, Q., Zhou, Z. H., Stewart, J. P., Wu, T. T. & Sun, R. (2003) J. Virol. 77, 13425-13432.}}}}}