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Table III
Introns and their protein products (IEP) encoded by staphylococcal Twort-like phagesa
Intron name
(phage)b
Intron
length
(nucleotide)
Name of
interrupted
gene
Known or
Name of
predicted function
IEP
of interrupted
gene
Length of
IEP
(amino
acid)
Known or
predicted
function
of IEPc
Lys-I1
(K)
876
32&30
(lysK)
Lysin
I-KsaI
166
HNH
endonuclease
Pol-I1
(K)
798
86&88
(polA)
DNA
polymerase
I-KsaII
170
Two zinc
fingers
Pol-I2
(K)
1082
88&90
(polA)
DNA
polymerase
I-KsaIII
269
HNH
endonuclease
Phages containing homologous intron at
conserved DNA position
(name of interrupted gene; length of conserved
region if different; % identity if less than 100)d
G1 (60&42)
ISP(201&203)
Sb-1(53&55)
A5W (lysK)
Staph1N (lysK)
A3R (lysK)
Fi200W (lysK)
676Z (lysK)
P4W (lysK)
MSA6 (lysK)
G1 (33&19&37)
ISP (59&61&63)
Sb-1 (129&129b&129c)
A5W (polA)
Staph1N(polA)
A3R (polA)
Fi200W (polA)
676Z (polA)
P4W (polA)
MSA6 (polA)
G1 (33&19&37)
ISP (59&61&63)
Sb-1 (129&129b&129c)
A5W (polA)
Staph1N (polA; 798; 100)
A3R (polA)
nrd-I1
(Twort)
429
45&33
(nrdI)
nrd-I2
(Twort)
1087
33&118
(nrdE)
tub-I1
(Twort)
tub-I2
(Twort)
tub-I3
(Twort)
ter-I1
(Twort)
ter-I2
(Twort)
ter-I3
(MSA6)
rec-I1
(MSA6)
325
1337
106&NC
(tmpA)
106&NC
(tmpA)
106&NC
(tmpA)
151&59
(ter)
59&36
(ter)
ter
1494
tmpA-I1
(676Ż)
tmpA-I2
(676Ż)
Ribonucleotide
reductase
regulatory subunit
Ribonucleotide
I-TwoI
reductase large
subunit
Tail tube
—
Fi200W (polA; 1081; >99)
676Z (polA)
P4W (polA; 1081; >99)
MSA6 (polA)
—
NA
NA
243
HNH
endonuclease
—
NA
NA
—
Tail tube
—
NA
NA
—
Tail tube
—
NA
NA
—
Large terminase
gp31
316
Unknown
—
Large terminase
gp119
320
Unknown
MSA6 (ter,221; 91)e
Large terminase
I-MsaI
323
Unknown
Twort (ter; 221; 91)e
rec
Recombinase
I-MsaII
322
putative
endonuclease
812 (NC [homologue of A5W rec];1376; 92)
305
tmpA
Tail tube
—
NA
NA
256
tmpA
Tail tube
—
NA
NA
Fi200W (tmpA)
P4W (tmpA)
A3R (tmpA)
Fi200W (tmpA)
P4W (tmpA)
A3R (tmpA)
282
252
1514
1312
aCharacteristic of introns and IEP-encoding genes in phages K, G1, Twort, and A5W is given according to Stewart et al. (2009a), Kasparek et al.,
(2007) and Ulatowska et al. (in preparation). Characteristic of introns and IEP-encoding genes in other phages is based on homologies of relevant
regions in DNA of these phages to known intron and IEP encoding sequences. The lengths of the MSA6 ter-I3 and rec-I1 introns, as well as 676Z
˙ tmpA-I1 and tmpA-I2 introns were predicted based on homologies of predicted translation products of intron-encoding and -flanking regions
to ter, rec and tmpA gene products of other staphylococcal Twort-like phages, respectively. Coordinates of these introns are as in the relevant
GenBank files (see Table I).
bThe name of phage, in which a given intron was originally described, is in parentheses.
cNot applicable.
dHomologies of certain phage MSA6, 676Z˙ , P4W, Fi200, and A3R introns to introns of phage 812 are based on the comparison of DNA
sequences of these phages with the fragments of 812 sequence that are deposited in GenBank (Acc. No. EF136586 and EF136582; Kasparek et al.,
2007).
eHomology concerns 5' regions of Twort ter-I2 and MSA6-ter-I1 introns.