Table 2. Gene essentiality mapping of Phage P1 genome.
|
locus_tag |
gene |
function[52] |
EOP_average |
SD |
This work |
Literature |
|---|---|---|---|---|---|---|
| P1_gp002 | cra | cre associated function | 6.6E-01 | 1.3E-01 | NE | NE[117,118] |
| P1_gp003 | cre | cyclization recombinase | 1.2E+00 | 8.1E-01 | NE | NE[117,118] |
| P1_gp004 | c8 | establishment of lysogeny | 1.5E+00 | 3.9E-01 | NE | |
| P1_gp005 | ref | recombination enhancement | 1.3E+00 | 3.5E-01 | NE | NE[118] |
| P1_gp006 | mat | maturation control | 2.8E-01 | 3.5E-03 | NE | E[119] |
| P1_gp007 | res | restriction component | 1.2E+00 | 3.5E-02 | NE | NE[120] |
| P1_gp008 | mod | modification component | 1.0E+00 | 3.2E-01 | NE | NE[120] |
| P1_gp009 | lxc | modulator of C1 action; | 7.0E-01 | 4.2E-01 | NE | NE[121] |
| P1_gp010 | ulx | enhances incorporation of darB | 6.4E-01 | 1.6E-01 | NE | NE[122] |
| P1_gp011 | darB | antirestriction | 5.8E-01 | 2.5E-01 | NE | NE[122] |
| P1_gp012 | prt | portal | <3.4E-6 | E | E[52] | |
| P1_gp013 | pro | head processing | <3.4E-6 | E | E[52] | |
| P1_gp115 | lydE | putative antiholin | 9.8E-01 | 8.8E-01 | NE | |
| P1_gp014 | lydD | putative holin | 1.1E+00 | 1.0E-01 | NE | |
| P1_gp015 | lyz | lysozyme | 5.0E-02 | 3.5E-03 | E | E[123] |
| P1_gp016 | ssb | single stranded DNA binding protein | 5.7E-01 | 2.0E-02 | NE | |
| P1_gp017 | isaA | IS1 insertion-associated gene | 8.6E-01 | 4.7E-01 | NE | |
| P1_gp018 | insB | IS1 transposition protein | 5.1E-01 | 1.6E-01 | NE | |
| P1_gp019 | insA | IS1 transposition protein | 1.0E+00 | 2.2E-01 | NE | |
| P1_gp020 | isaB | IS1 insertion-associated gene | 1.4E+00 | 2.2E-01 | NE | |
| P1_gp021 | hxr | possible repressor; homolog of Xre | 1.6E+00 | 1.2E+00 | NE | NE[122] |
| P1_gp022 | ddrB | antirestriction | 8.5E-01 | 1.3E-01 | NE | NE[122] |
| P1_gp116 | iddB | internal to ddrB | 5.4E-01 | 2.6E-01 | NE | NE[122] |
| P1_gp023 | ddrA | antirestriction | 9.8E-01 | 3.1E-01 | NE | NE[122] |
| P1_gp024 | darA | antirestriction | 6.5E-01 | 2.9E-01 | NE | NE[122] |
| P1_gp025 | hdf | antirestriction | 1.2E+00 | 8.4E-01 | NE | NE[122] |
| P1_gp026 | lydB | lysis determinant; prevents premature lysis |
2.3E-02 | 2.6E-02 | E | NE[123,124] |
| P1_gp027 | lydA | holin | 1.2E-01 | 2.4E-03 | NE | NE[123,124] |
| P1_gp028 | lydC | holin | 1.1E+00 | 1.2E-01 | NE | |
| P1_gp029 | cin | site-specific recombinase | 1.4E+00 | 9.5E-01 | NE | NE[125] |
| P1_gp001 | Sv prime | C-terminal moiety of tail fiber gpS | 5.3E-01 | 3.2E-01 | NE | NE [126] |
| P1_gp030 | U prime | structural protein gpU prime of tail fiber |
8.6E-01 | 8.0E-01 | NE | NE [126] |
| P1_gp031 | U | tail fiber structure or assembly | <5.2E-5 | E | ||
| P1_gp032 | S | tail fiber structure or assembly | <5.2E-5 | E | ||
| P1_gp033 | R | tail fiber structure or assembly | <5.2E-5 | E | E[127] | |
| P1_gp034 | 16 | baseplate or tail tube | <5.2E-5 | E | E[128] | |
| P1_gp035 | bplA | putative baseplate structure, may correspond to gene 3 | <2.9E-5 | E | ||
| P1_gp036 | pmgA | Putative morphogenetic function | <2.9E-5 | E | E[73] | |
| P1_gp037 | sit | putative tape measure protein | <2.9E-5 | E | ||
| P1_gp038 | pmgB | Putative morphogenetic function | <2.9E-5 | E | E[73] | |
| P1_gp039 | tub | tail tube | <2.9E-5 | E | ||
| P1_gp040 | pmgC | Putative morphogenetic function | <2.9E-5 | E | E[73] | |
| P1_gp041 | simC | superimmunity | 1.7E+00 | 6.9E-01 | NE | NE[129] |
| P1_gp042 | simB | superimmunity | 3.8E+00 | 8.4E-01 | NE | NE[129] |
| P1_gp043 | simA | superimmunity | 9.0E-01 | 4.9E-01 | NE | NE[129] |
| P1_gr044 | c4 RNA | acts on icd and ant mRNA | 8.3E-01 | 9.4E-01 | NE | |
| P1_gp045 | icd | reversible inhibition of cell division | 6.0E-01 | 2.2E-01 | NE | NE[130] |
| P1_gp046 | ant1 | antagonizes C1 represssion1 | 2.0E+00 | 1.1E+00 | NE | NE[131] |
| P1_gp047 | ant2 | product antagonizes C1 | 2.3E+00 | 1.8E+00 | NE | NE[131] |
| P1_gp048 | ask | regulatory region of kilA gene; | 1.2E+00 | 4.9E-01 | NE | |
| P1_gp049 | kilA | product can kill host | 8.6E-01 | 8.0E-01 | NE | NE[131] |
| P1_gp050 | repL | initiates replication at oriL | 7.1E-01 | 3.0E-01 | NE | NE[131] |
| P1_gp051 | rlfA | possibly associated with lytic replication |
1.3E+00 | 6.1E-02 | NE | |
| P1_gp052 | rlfB | possibly associated with lytic replication |
8.8E-01 | 3.0E-02 | NE | |
| P1_gp053 | pmgF | putative morphogenetic function | 1.2E+00 | 1.0E-02 | NE | NE[73] |
| P1_gp054 | bplB | baseplate structure | <1.2E-7 | E | ||
| P1_gp055 | pmgG | putative morphogenetic function | <1.2E-7 | E | E[73] | |
| P1_gp056 | 21 | baseplate or tail tube | <1.2E-7 | E | * [128] | |
| P1_gp057 | 22 | tail sheath | <1.2E-7 | E | * [128] | |
| P1_gp058 | 23 | Major head protein | <1.2E-7 | E | * [128] | |
| P1_gp059 | parB | active partitioning of P1 plasmid during cell division |
1.3E+00 | 7.6E-01 | NE | |
| P1_gp060 | parA | active partitioning of P1 plasmid during cell division |
1.6E+00 | 1.5E+00 | NE | |
| P1_gp061 | repA | initiates replication from oriR; plasmid replication |
9.5E-01 | 6.4E-02 | NE | |
| P1_gp062 | upfA | 1.2E+00 | 8.9E-01 | NE | NE[73] | |
| P1_gp063 | mlp | membrane lipoprotein precursor | 2.4E-01 | 1.9E-01 | NE | |
| P1_gp064 | ppfA | possible periplasmic function | 1.3E+00 | 1.2E+00 | NE | |
| P1_gp065 | upfB | 1.3E+00 | 1.0E+00 | NE | NE[73] | |
| P1_gp066 | upfC | 1.1E+00 | 6.8E-01 | NE | NE[73] | |
| P1_gp067 | uhr | 8.6E-01 | 1.9E-01 | NE | NE[73] | |
| P1_gp068 | hrdC | hpothetical recombination associated protein of RdgC family |
8.7E-01 | 4.6E-01 | NE | |
| P1_gp069 | dmt-B | DNA methlytransferases; methlysates A at GATC |
1.4E+00 | 1.2E+00 | NE | NE[132] |
| P1_gp070 | dmt-A | 1.4E+00 | 7.6E-03 | NE | ||
| P1_gt071 | trnT | 9.2E-01 | 4.0E-01 | NE | ||
| P1_gp072 | plp | putative lipoprotein | 1.6E+00 | 8.2E-01 | NE | |
| P1_gp073 | upl | 1.9E+00 | 5.9E-01 | NE | NE[73] | |
| P1_gp074 | tciA | tellurite or colicin resistance or inhibition of cell division | 6.5E-01 | 6.5E-02 | NE | |
| P1_gp075 | tciB | tellurite or colicin resistance or inhibition of cell division | 9.9E-01 | 1.0E-01 | NE | |
| P1_gp076 | tciC | tellurite or colicin resistance or inhibition of cell division | 1.3E+00 | 4.4E-01 | NE | |
| P1_gt117 | trnI | 1.4E+00 | 7.9E-01 | NE | ||
| P1_gp077 | ban | dnaB homolog | 1.2E+00 | 4.8E-01 | NE | NE[133] |
| P1_gp078 | dbn | downstream of ban | 1.3E+00 | 1.3E-01 | NE | NE[73] |
| P1_gp079 | 5 | baseplate | <2.1E-6 | E |
* [128] |
|
| P1_gp080 | 6 | tail length | 8.3E-03 | 1.3E-03 | E | * [128] |
| P1_gp081 | 24 | baseplate or tail stability | 4.9E-03 | 5.0E-03 | E | * [128] |
| P1_gp082 | 7 | tail stability | <8.2E-6 | E | * [128] | |
| P1_gp083 | 25 | tail stability | 1.1E-01 | 6.6E-02 | NE | * [128] |
| P1_gp084 | 26 | baseplate; | 1.2E-01 | 1.5E-01 | NE | * [128] |
| P1_gp085 | pmgL | putative morphogenetic function | 1.3E+00 | 9.4E-01 | NE | NE[73] |
| P1_gp086 | pmgM | putative morphogenetic function | 3.8E-01 | 2.1E-01 | NE | NE[73] |
| P1_gp087 | pmgN | putative morphogenetic function | 1.4E-02 | 1.5E-03 | E | NE[73] |
| P1_gp088 | pmgO | putative morphogenetic function | 1.1E+00 | 8.7E-01 | NE | NE[73] |
| P1_gp089 | pmgP | putative morphogenetic function | 7.2E-01 | 7.3E-02 | NE | NE[73] |
| P1_gp090 | ppp | protein phosphatase | 1.2E+00 | 8.0E-02 | NE | NE[73] |
| P1_gp091 | pmgQ | putative morphogenetic function | 1.4E+00 | 7.5E-01 | NE | NE[73] |
| P1_gp092 | pmgR | putative morphogenetic function | 9.4E-01 | 3.0E-01 | NE | E[73] |
| P1_gp093 | pmgS | putative morphogenetic function | 1.2E+00 | 3.2E-01 | NE | NE[73] |
| P1_gp094 | pap | acid phosphatase | 7.7E-01 | 2.3E-01 | NE | NE[73] |
| P1_gp095 | pmgT | putative morphogenetic function | 9.8E-01 | 9.7E-01 | NE | NE[73] |
| P1_gp096 | pmgU | putative morphogenetic function | 2.1E-01 | 6.4E-02 | NE | NE[73] |
| P1_gp097 | pmgV | putative morphogenetic function | 1.9E+00 | 2.0E+00 | NE | NE[73] |
| P1_gp098 | upfM | unknown protein function | NT | NE[73] | ||
| P1_gp099 | upfN | unknown protein function | 8.3E-01 | 2.4E-01 | NE | NE[73] |
| P1_gp100 | upfO | unknown protein function | 9.5E-01 | 6.4E-01 | NE | NE[73] |
| P1_gp101 | hot | DNA replication | 1.2E+00 | 1.6E+00 | NE | |
| P1_gp102 | lxr | LexA-regulated functions | 7.9E-01 | 7.7E-01 | NE | |
| P1_gp103 | humD | DNA repair | 5.4E-01 | 3.3E-01 | NE | |
| P1_gp104 | phd | anti-toxin of P1 toxin-antitoxin system | 5.5E-01 | 7.1E-02 | NE | |
| P1_gp105 | doc | toxin of P1 toxin-antitoxin system | 3.6E-01 | 1.2E-02 | NE | |
| P1_gp106 | pdcA | unknown protein function | NT | NE[73] | ||
| P1_gp107 | pdcB | unknown function | 6.8E-01 | 2.6E-01 | NE | NE[73] |
| P1_gp108 | lpa | late promoter activator | <1.2E-7 | E | * [134] | |
| P1_gp109 | pacA | DNA packaging | <1.2E-7 | E | * [135] | |
| P1_gp110 | pacB | DNA packaging | <1.2E-7 | E | * [135] | |
| P1_gp111 | c1 | lytic repressor | 1.4E+00 | 1.3E+00 | NE | |
| P1_gp112 | coi | C1 inactivator | 7.4E-01 | 8.4E-01 | NE | NE[136] |
| P1_gp113 | imcB | immunity function | 8.2E-01 | 7.3E-01 | NE | |
| P1_gp114 | imcA | immunity function | NT |
E, essential; NE, nonessential; NT, not tested.
* amber mutant reported