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A programming language for genetic data

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Essential genes and ohnologs: a quire analysis

After the whole-genome duplication event leading the evolution of S. cerevisiae and related species, each of the genes that were essential would have been duplicated. The fates of each of these genes can be identified based on the knowledge of existing ohnologs (genes related by the whole-genome duplication), synthetic lethality data, and essentiality data.

phylogeny

The analysis to trace the fates of these duplicated essential genes in the quire programming language follows.

Essential genes in which the duplicate was lost
Ohnolog pairs in which only one gene is essential
Ohnolog pairs in which both genes are essential
Ohnolog pairs that have a synthetic lethal relationship

Identifying essential genes in which the duplicate was lost

By far the most common event for any duplicated gene was that the duplicate copy was lost.

lost

We can find these genes with quire.

First, let's read a gene registry for all of the S. cerevisiae genes and a list of the essential genes. (Here we are using the list of genes reported to be essential for the reference S288c strain; a small number of genes are different in different strain backgrounds.)

scgenes      = registry( @ "scgene_registry.txt" )
essential    = genelist( @ "essential.txt", generegistry=scgenes )

Second, we read in a network in which genes related by the whole-genome duplication are reported as "ohnolog" interactions. When the network of paralogs is read in, we specify that the symmetry is "all". This means that the A:B interaction is also stored as the B:A interaction. The actual file also has other non-whole genome duplication relationships that are labeled as "paralog" interactions, so we need to filter out only the ohnolog interactions.

paralogs_net = network( @ "paralogs.txt", generegistry=scgenes, symmetry="all", format="sif" )
ohnologs_net = filter( paralogs_net, type="ohnolog" )

Because we read in the network with a symmetry of "all", we can extract all of the genes by getting the "bait" or the "prey" genes.

ohnologs = element( ohnologs_net, type="baits" )

We can then identify the essential genes that do not have duplications in S. cerevisiae identifying those essential genes that are not present in the list of ohnologs.

essential_with_deletion = essential + ohnologs -> filter( partition="10" )

"Essential genes = " + sizeof( essential )
"Essential genes not in ohnolog pairs = " + sizeof( essential_with_deletion )

And the output is:

Essential genes = 1060
Essential genes not in ohnolog pairs = 1018

Thus only 42 of the 1060 essential genes have not lost their duplicates (ohnologs) arising from the whole-genome duplication event. Here we won't list the 1018 gene not in ohnolog pairs.

Identifying ohnolog pairs in which only one gene is essential

One interesting possibility is that divergence of the one of the copies allows it to adopt a different function, since the other still supports the essential function.

oneess

We can identify these types of pairs using quire.

scgenes      = registry( @ "scgene_registry.txt" )
essential    = genelist( @ "essential.txt", generegistry=scgenes )

Second, we read in a network in which genes related by the whole-genome duplication are reported as "ohnolog" interactions. The actual file also has other non-whole genome duplication relationships that are labeled as "paralog" interactions, so we need to filter out only the ohnolog interactions.

When the network of paralogs is read in, we specify that the symmetry is "all". This means that the A:B interaction is also stored as the B:A interaction. If we had specified the symmetry as "none", we would only store the interaction as an A:B interaction. This is important in the essential gene paralog filtering that will happen later.

paralogs_net = network( @ "paralogs.txt", generegistry=scgenes, symmetry="all", format="sif" )
ohnologs_net = filter( paralogs_net, type="ohnolog" )

Third, we label all of the interactions based on which of the genes involved in the interaction are in list of essential genes and filter out those with only one essential gene. In this case, the interactions are given a gene partition label of "0:0" if neither gene is essential, "1:0" or "0:1" if one gene is essential, and "1:1" if both genes are essential.

Because we read the network in using the symmetry set to "all", filtering out those interactions with gene partition labels of "1:0" or "0:1" will give us each interaction twice. If the network had been read in with the symmetry set to "none", then we would have needed both. However, the advantage of using symmetry "all" with filtering for gene partition labels of "1:0" means that we always know that the essential gene is the first one (the "bait") and the non-essential gene is the second one (the "prey").

ohnologs_net::label( genepartition=essential )
only_one_essential = filter( ohnologs_net, genepartition="1:0" )

Fourth, and finally, we can now investigate all of the ohnolog pairs with one essential and one non-essential gene by examining the interactions in the resulting network.

In the following for loop, the value i is assigned to each interaction in the network. In quire, the value is provided as a list data type containing the named elements bait, prey, partition, genepartition, and obs. The obs named element is a list of lists containing each observation for that interaction. These observation sublists contain the named elements pmid, type, id, obspartition and symmgen. Here, only the bait and prey named elements of the interaction list are important.

n = 1
for i in only_one_essential
    "Interaction " + n
    "\tEssential:     " + i["bait"] + " " + tolocus( i["bait"], scgenes )
    "\tNon-essential: " + i["prey"] + " " + tolocus( i["prey"], scgenes )
    ""
    n = n+1
rof

The results are:

Interaction 1
        Essential:     YDR303C RSC3
        Non-essential: YHR056C RSC30

Interaction 2
        Essential:     YOR326W MYO2
        Non-essential: YAL029C MYO4

Interaction 3
        Essential:     YMR113W FOL3
        Non-essential: YKL132C RMA1

Interaction 4
        Essential:     YOR110W TFC7
        Non-essential: YNL108C YNL108C

Interaction 5
        Essential:     YNR026C SEC12
        Non-essential: YCR067C SED4

Interaction 6
        Essential:     YKL180W RPL17A
        Non-essential: YJL177W RPL17B

Interaction 7
        Essential:     YPL228W CET1
        Non-essential: YMR180C CTL1

Interaction 8
        Essential:     YLR457C NBP1
        Non-essential: YPR174C CSA1

Interaction 9
        Essential:     YOR182C RPS30B
        Non-essential: YLR287C-A RPS30A

Interaction 10
        Essential:     YLR293C GSP1
        Non-essential: YOR185C GSP2

Interaction 11
        Essential:     YJR045C SSC1
        Non-essential: YEL030W ECM10

Interaction 12
        Essential:     YMR047C NUP116
        Non-essential: YKL068W NUP100

Interaction 13
        Essential:     YLR249W YEF3
        Non-essential: YNL014W HEF3

Interaction 14
        Essential:     YCR052W RSC6
        Non-essential: YNR023W SNF12

Interaction 15
        Essential:     YMR079W SEC14
        Non-essential: YKL091C YKL091C

Interaction 16
        Essential:     YJL026W RNR2
        Non-essential: YGR180C RNR4

Interaction 17
        Essential:     YLR223C IFH1
        Non-essential: YDR223W CRF1

Interaction 18
        Essential:     YOL066C RIB2
        Non-essential: YDL036C PUS9

Interaction 19
        Essential:     YDR341C YDR341C
        Non-essential: YHR091C MSR1

Interaction 20
        Essential:     YCL043C PDI1
        Non-essential: YDR518W EUG1

Interaction 21
        Essential:     YKL035W UGP1
        Non-essential: YHL012W YHL012W

Interaction 22
        Essential:     YML085C TUB1
        Non-essential: YML124C TUB3

Interaction 23
        Essential:     YNL162W RPL42A
        Non-essential: YHR141C RPL42B

Interaction 24
        Essential:     YLR310C CDC25
        Non-essential: YLL016W SDC25

Interaction 25
        Essential:     YLR310C CDC25
        Non-essential: YLL017W YLL017W

Interaction 26
        Essential:     YBL030C PET9
        Non-essential: YBR085W AAC3

Interaction 27
        Essential:     YKL104C GFA1
        Non-essential: YMR084W YMR084W

Interaction 28
        Essential:     YKL104C GFA1
        Non-essential: YMR085W YMR085W

Interaction 29
        Essential:     YPR162C ORC4
        Non-essential: YLR453C RIF2

Interaction 30
        Essential:     YGL225W VRG4
        Non-essential: YER039C HVG1

Interaction 31
        Essential:     YML125C PGA3
        Non-essential: YML087C AIM33

Interaction 32
        Essential:     YOL120C RPL18A
        Non-essential: YNL301C RPL18B

Interaction 33
        Essential:     YAL038W CDC19
        Non-essential: YOR347C PYK2

Interaction 34
        Essential:     YNR016C ACC1
        Non-essential: YMR207C HFA1

Interaction 35
        Essential:     YEL034W HYP2
        Non-essential: YJR047C ANB1

Interaction 36
        Essential:     YLR029C RPL15A
        Non-essential: YMR121C RPL15B

Interaction 37
        Essential:     YOR204W DED1
        Non-essential: YPL119C DBP1

Interaction 38
        Essential:     YBR049C REB1
        Non-essential: YDR026C NSI1

Interaction 39
        Essential:     YOR167C RPS28A
        Non-essential: YLR264W RPS28B

Interaction 40
        Essential:     YGL075C MPS2
        Non-essential: YPL200W CSM4

Interaction 41
        Essential:     YKL141W SDH3
        Non-essential: YMR118C SHH3

Interaction 42
        Essential:     YLR277C YSH1
        Non-essential: YOR179C SYC1

Interaction 43
        Essential:     YKL203C TOR2
        Non-essential: YJR066W TOR1

Interaction 44
        Essential:     YML065W ORC1
        Non-essential: YLR442C SIR3

Several different kinds of diversification can be observed in this list.

(1) Some ohnolog pairs contain genes that have adopted different functions and one of the pair has lost the "essential" function. For example, in the TOR2/TOR1 pair, both genes encode protein kinases that play a role in nutrient sensing, but only TOR2 maintains an essential role in actin polarization. In the ORC4/RIF2 pair, ORC4 is an essential gene that encodes a subunit of the DNA replication origin recognition complex (Orc1-6), whereas RIF2 encodes a protein that binds Rap1 and helps control telomere length and telomeric silencing. Remarkably, Rif2 does not appear to interact with any of the Orc1-6 subunits. Similarly, ORC1 encodes a member of the origin-recognition complex, whereas SIR3 is involved in transcriptional silencing and is recruited to DNA through interaction with Rap1. In the RSC6/SNF12 pair, RSC6 encodes a subunit of the RSC chromatin remodeling complex, and SNF12 encodes a subunit of the SWI/SNF chromatin remodeling complex.

(2) Some ohnolog pairs contain genes in which one gene in the pair is split: GFA1/YMR084W-YMR085W * and CDC25/SDC25-YLL017W. In strains related to S288c, YMR084W-YMR085W exists as a single full-length gene and as do SDC25-YLL017W*. This sort of mutagenic loss of the copy is unsurprising in a situation where there are two redundant genes.

(3) Some ohnolog pairs appear to have alternative regulation: RNR2/RNR4, TUB1/TUB3, and CDC19/PYK2. In some cases, such as RPL15A/RPL15B, one of the genes is very poorly expressed, which is conceptually similar to the mutagenic copy loss of genes in category 2.

(4) Some ohnolog pairs appear to have changes in subcellular localization: ACC1/HFA1, FOL3/RMA1, and YDR341C/MSR1.

Identifying ohnolog pairs in which both genes are essential

In cases where an essential gene plays an essential role in two different processes, it's possible to envision that gene duplication could allow each copy to specialize for each process. In this case, each of the duplicates would be expected to be essential.

twoess

We can identify these types of pairs using quire.

scgenes      = registry( @"scgene_registry.txt" )
essential    = genelist( @"essential.txt", generegistry=scgenes )

When the network of paralogs is read in, we specify that the symmetry is "none", unlike the cases described above. This means that the A:B interaction are only stored as the B:A interaction. If we had specified the symmetry as "all", we would store the interaction both A:B and B:A interactions. This would duplicate all of the interactions we are going to label below.

paralogs_net = network( @ QUIRE_DIR+ "scerevisiae/paralogs.txt", generegistry=scgenes, symmetry="none", format="sif" )
ohnologs_net = filter( paralogs_net, type="ohnolog" )

ohnologs_net::label( genepartition=essential )
two_essential = filter( ohnologs_net, genepartition="1:1" )

sizeof( two_essential )

And the output is zero, as there are no ohnolog pairs where both genes are essential. To confirm this, we can count the number of ohnolog pairs with no essential genes, add it to the 44 ohnolog pairs identified above with one essential gene, and ensure that it matches the total number of ohnolog pairs.

no_essential = filter( ohnologs_net, genepartition="0:0" )

"Count = " + sizeof( no_essential ) + " + 44 + " + sizeof( two_essential ) + " = " + ( sizeof(no_essential) + 44 )
"Total = " + sizeof( ohnologs_net )

And the output is:

Count = 506 + 44 + 0 = 550
Total = 550

Identifying ohnolog pairs that have a synthetic lethal relationship

A final interesting possibility is that S. cerevisiae has retained both copies of the gene in the ohnolog pair. In this case, the gene that was essential in the pre-WGD species is now no long essential; however, simultaneous deletion of both copies should be lethal. Hence the genes in the ohnolog pair should show a synthetic lethal interaction.

We can identify these types of pairs using quire.

First, let's read a gene registry for all of the S. cerevisiae genes.

scgenes      = registry( @"scgene_registry.txt" )

When the network of paralogs is read in, we specify that the symmetry is "none". This means that the A:B interaction is not also stored as the B:A interaction. Because the paralog file was created non-redundantly, this means that after combining with the synthetic lethal network, we don't see both the A:B and B:A version of each interaction.

paralogs_net = network( @ "paralogs.txt", generegistry=scgenes, symmetry="none", format="sif" )
ohnologs_net = filter( paralogs_net, type="ohnolog" )

Third, we need to read in the synthetic lethal interaction data for genes in S. cerevisiae. We will do this reading in a (modified) version of the BioGRiD interaction database, and extract out those interactions corresponding to "Synthetic Lethality". We will read in the data with a symmetry type of "all" to ensure that we don't miss overlaps with the ohnolog network.

biogridfile = "BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.5.168-modified.tab2.txt"
biogrid_net = network( @ biogridfile, format="biogrid_tab2", generegistry=scgenes, symmetry="all", sourcename="biogrid", organismbait="559292", organismprey="559292" )

sl_net = filter( biogrid_net, type="Synthetic Lethality" )

Fourth, we will extract out the gene pairs that are both synthetic lethal and ohnologs by adding together the two networks and extracting those interactions in common. Interactions in common have a partition of "11", which means that they were present in the ohnolog network (first "1") and in the synthetic lethality network (second "1").

sl_ohnologs = ohnologs_net + sl_net -> filter( partition="11" )

sizeof( sl_ohnologs )

This analysis gives us 110 gene pairs (we would have 220 gene pairs with both A:B and B:A version of each interaction if we had read the ohnolog network with a symmetry of "all"). We can output these with the following for loop:

n = 1
for i in sl_ohnologs
        "Interaction " + n
        "\tGene A: " + i["bait"] + " " + tolocus( i["bait"], scgenes )
        "\tGene B: " + i["prey"] + " " + tolocus( i["prey"], scgenes )
        ""
        n = n+1
rof

This gives us the result:

~~~
Interaction 1
Gene A: YBR048W RPS11B
Gene B: YDR025W RPS11A

Interaction 2
Gene A: YLR264W RPS28B
Gene B: YOR167C RPS28A

Interaction 3
Gene A: YGR118W RPS23A
Gene B: YPR132W RPS23B

Interaction 4
Gene A: YNL301C RPL18B
Gene B: YOL120C RPL18A

Interaction 5
Gene A: YLR448W RPL6B
Gene B: YML073C RPL6A

Interaction 6
Gene A: YMR246W FAA4
Gene B: YOR317W FAA1

Interaction 7
Gene A: YDL083C RPS16B
Gene B: YMR143W RPS16A

Interaction 8
Gene A: YML124C TUB3
Gene B: YML085C TUB1

Interaction 9
Gene A: YHR021C RPS27B
Gene B: YKL156W RPS27A

Interaction 10
Gene A: YBR031W RPL4A
Gene B: YDR012W RPL4B

Interaction 11
Gene A: YBR169C SSE2
Gene B: YPL106C SSE1

Interaction 12
Gene A: YGL071W AFT1
Gene B: YPL202C AFT2

Interaction 13
Gene A: YDR099W BMH2
Gene B: YER177W BMH1

Interaction 14
Gene A: YIL105C SLM1
Gene B: YNL047C SLM2

Interaction 15
Gene A: YGR085C RPL11B
Gene B: YPR102C RPL11A

Interaction 16
Gene A: YIL149C MLP2
Gene B: YKR095W MLP1

Interaction 17
Gene A: YBR161W CSH1
Gene B: YPL057C SUR1

Interaction 18
Gene A: YHL001W RPL14B
Gene B: YKL006W RPL14A

Interaction 19
Gene A: YMR186W HSC82
Gene B: YPL240C HSP82

Interaction 20
Gene A: YER056C-A RPL34A
Gene B: YIL052C RPL34B

Interaction 21
Gene A: YGL076C RPL7A
Gene B: YPL198W RPL7B

Interaction 22
Gene A: YIL133C RPL16A
Gene B: YNL069C RPL16B

Interaction 23
Gene A: YOR054C VHS3
Gene B: YKR072C SIS2

Interaction 24
Gene A: YMR230W RPS10B
Gene B: YOR293W RPS10A

Interaction 25
Gene A: YDR471W RPL27B
Gene B: YHR010W RPL27A

Interaction 26
Gene A: YLR287C-A RPS30A
Gene B: YOR182C RPS30B

Interaction 27
Gene A: YMR199W CLN1
Gene B: YPL256C CLN2

Interaction 28
Gene A: YGR109C CLB6
Gene B: YPR120C CLB5

Interaction 29
Gene A: YDL229W SSB1
Gene B: YNL209W SSB2

Interaction 30
Gene A: YGR214W RPS0A
Gene B: YLR048W RPS0B

Interaction 31
Gene A: YOR234C RPL33B
Gene B: YPL143W RPL33A

Interaction 32
Gene A: YDR144C MKC7
Gene B: YLR120C YPS1

Interaction 33
Gene A: YBR181C RPS6B
Gene B: YPL090C RPS6A

Interaction 34
Gene A: YDR436W PPZ2
Gene B: YML016C PPZ1

Interaction 35
Gene A: YMR121C RPL15B
Gene B: YLR029C RPL15A

Interaction 36
Gene A: YOR231W MKK1
Gene B: YPL140C MKK2

Interaction 37
Gene A: YAL028W FRT2
Gene B: YOR324C FRT1

Interaction 38
Gene A: YER131W RPS26B
Gene B: YGL189C RPS26A

Interaction 39
Gene A: YCR031C RPS14A
Gene B: YJL191W RPS14B

Interaction 40
Gene A: YDR450W RPS18A
Gene B: YML026C RPS18B

Interaction 41
Gene A: YKL068W NUP100
Gene B: YMR047C NUP116

Interaction 42
Gene A: YLR441C RPS1A
Gene B: YML063W RPS1B

Interaction 43
Gene A: YAL030W SNC1
Gene B: YOR327C SNC2

Interaction 44
Gene A: YGR070W ROM1
Gene B: YLR371W ROM2

Interaction 45
Gene A: YDR502C SAM2
Gene B: YLR180W SAM1

Interaction 46
Gene A: YJL129C TRK1
Gene B: YKR050W TRK2

Interaction 47
Gene A: YBR118W TEF2
Gene B: YPR080W TEF1

Interaction 48
Gene A: YDR490C PKH1
Gene B: YOL100W PKH2

Interaction 49
Gene A: YDR500C RPL37B
Gene B: YLR185W RPL37A

Interaction 50
Gene A: YBR191W RPL21A
Gene B: YPL079W RPL21B

Interaction 51
Gene A: YGL135W RPL1B
Gene B: YPL220W RPL1A

Interaction 52
Gene A: YDR385W EFT2
Gene B: YOR133W EFT1

Interaction 53
Gene A: YER019C-A SBH2
Gene B: YER087C-B SBH1

Interaction 54
Gene A: YMR192W GYL1
Gene B: YPL249C GYP5

Interaction 55
Gene A: YDR312W SSF2
Gene B: YHR066W SSF1

Interaction 56
Gene A: YIL148W RPL40A
Gene B: YKR094C RPL40B

Interaction 57
Gene A: YJL177W RPL17B
Gene B: YKL180W RPL17A

Interaction 58
Gene A: YDL191W RPL35A
Gene B: YDL136W RPL35B

Interaction 59
Gene A: YBL027W RPL19B
Gene B: YBR084C-A RPL19A

Interaction 60
Gene A: YNL096C RPS7B
Gene B: YOR096W RPS7A

Interaction 61
Gene A: YDL061C RPS29B
Gene B: YLR388W RPS29A

Interaction 62
Gene A: YGL049C TIF4632
Gene B: YGR162W TIF4631

Interaction 63
Gene A: YNL098C RAS2
Gene B: YOR101W RAS1

Interaction 64
Gene A: YMR194W RPL36A
Gene B: YPL249C-A RPL36B

Interaction 65
Gene A: YMR109W MYO5
Gene B: YKL129C MYO3

Interaction 66
Gene A: YDL082W RPL13A
Gene B: YMR142C RPL13B

Interaction 67
Gene A: YHR135C YCK1
Gene B: YNL154C YCK2

Interaction 68
Gene A: YGR192C TDH3
Gene B: YJR009C TDH2

Interaction 69
Gene A: YDL175C AIR2
Gene B: YIL079C AIR1

Interaction 70
Gene A: YJL136C RPS21B
Gene B: YKR057W RPS21A

Interaction 71
Gene A: YIR033W MGA2
Gene B: YKL020C SPT23

Interaction 72
Gene A: YDR447C RPS17B
Gene B: YML024W RPS17A

Interaction 73
Gene A: YDL192W ARF1
Gene B: YDL137W ARF2

Interaction 74
Gene A: YMR104C YPK2
Gene B: YKL126W YPK1

Interaction 75
Gene A: YDL161W ENT1
Gene B: YLR206W ENT2

Interaction 76
Gene A: YGR124W ASN2
Gene B: YPR145W ASN1

Interaction 77
Gene A: YJR094W-A RPL43B
Gene B: YPR043W RPL43A

Interaction 78
Gene A: YBR189W RPS9B
Gene B: YPL081W RPS9A

Interaction 79
Gene A: YER027C GAL83
Gene B: YGL208W SIP2

Interaction 80
Gene A: YER031C YPT31
Gene B: YGL210W YPT32

Interaction 81
Gene A: YGR108W CLB1
Gene B: YPR119W CLB2

Interaction 82
Gene A: YBL079W NUP170
Gene B: YER105C NUP157

Interaction 83
Gene A: YGR032W GSC2
Gene B: YLR342W FKS1

Interaction 84
Gene A: YDL188C PPH22
Gene B: YDL134C PPH21

Interaction 85
Gene A: YEL022W GEA2
Gene B: YJR031C GEA1

Interaction 86
Gene A: YDR303C RSC3
Gene B: YHR056C RSC30

Interaction 87
Gene A: YOR226C ISU2
Gene B: YPL135W ISU1

Interaction 88
Gene A: YBL085W BOI1
Gene B: YER114C BOI2

Interaction 89
Gene A: YBL068W PRS4
Gene B: YER099C PRS2

Interaction 90
Gene A: YNL302C RPS19B
Gene B: YOL121C RPS19A

Interaction 91
Gene A: YBL087C RPL23A
Gene B: YER117W RPL23B

Interaction 92
Gene A: YGR143W SKN1
Gene B: YPR159W KRE6

Interaction 93
Gene A: YDR309C GIC2
Gene B: YHR061C GIC1

Interaction 94
Gene A: YIL131C FKH1
Gene B: YNL068C FKH2

Interaction 95
Gene A: YBR082C UBC4
Gene B: YDR059C UBC5

Interaction 96
Gene A: YLR450W HMG2
Gene B: YML075C HMG1

Interaction 97
Gene A: YMR242C RPL20A
Gene B: YOR312C RPL20B

Interaction 98
Gene A: YHL033C RPL8A
Gene B: YLL045C RPL8B

Interaction 99
Gene A: YNL299W TRF5
Gene B: YOL115W PAP2

Interaction 100
Gene A: YHR203C RPS4B
Gene B: YJR145C RPS4A

Interaction 101
Gene A: YHR141C RPL42B
Gene B: YNL162W RPL42A

Interaction 102
Gene A: YHL003C LAG1
Gene B: YKL008C LAC1

Interaction 103
Gene A: YER074W RPS24A
Gene B: YIL069C RPS24B

Interaction 104
Gene A: YEL034W HYP2
Gene B: YJR047C ANB1

Interaction 105
Gene A: YDR409W SIZ1
Gene B: YOR156C NFI1

Interaction 106
Gene A: YBL039C URA7
Gene B: YJR103W URA8

Interaction 107
Gene A: YGR092W DBF2
Gene B: YPR111W DBF20

Interaction 108
Gene A: YBL072C RPS8A
Gene B: YER102W RPS8B

Interaction 109
Gene A: YFR031C-A RPL2A
Gene B: YIL018W RPL2B

Interaction 110
Gene A: YER062C GPP2
Gene B: YIL053W GPP1
~~~

There is a very clear signal of ohnologs that duplicate genes encoding protein components of both the small and large ribosomal subunits (RPS0A/B, RPS1A/B, RPS4A/B, RPS6A/B, RPS7A/B, RPS8A/B, RPS9A/B, RPS10A/B, RPS11A/B, RPS14A/B, RPS16A/B, RPS17A/B, RPS18A/B, RPS19A/B, RPS21A/B, RPS23A/B, RPS24A/B, RPS26A/B, RPS27A/B, RPS28A/B, RSP29A/B, RPS30A/B, RPL1A/B, RPL2A/B, RPL4A/B, RPL6A/B, RPL7A/B, RPL8A/B, RPL11A/B, RPL13A/B, RPL14A/B, RPL15A/B, RPL17A/B, RPL18A/B, RPL19A/B, RPL20A/B, RPL21A/B, RPL23A/B RPL27A/B, RPL33A/B, RPL34A/B, RPL35A/B, RPL36A/B, RPL37A/B, RPL40A/B, RPL43A/B). Remarkably, RPL15A/B appears as both a synthetic lethal pair and as a pair in which one of the genes is essential, which likely also represent differences between S. cerevisiae strains.

Additionally, the ohnolog pair RSC3/RSC30 appears as a pair in which only one of the two genes is essential (RSC3) or both of the genes are redundant. This is due to differences in essential genes among different S. cerevisiae strains. In the S288c background, RSC3 is essential, whereas it is not in the W303 background.

Others: ANB1/HYP2, AFT1/2, AIR1/2, ARF1/2, ASN1/2 BMH1/2, BOI1/2, CLB1/2, CLB5/6, CLN1/2, CSH1/SUR1, DBF2/20, EFT1/2, ENT1/2, FAA1/4, FHK1/2, FKS1/GSC2, FRT1/2, GAL83/SIP2 GEA1/2, GIC1/2, GPP1/2, GYL1/GYP5, HSC82/HSP82, HMG1/2, ISU1/2, KRE6/SKN1, LAC1/LAG1 MGA2/SPT23, MKC7/YPS1, MKK1/2, MLP1/2, MYO3/5, NFI1/SIZ1 NUP100/NUP116, NUP170/157, PAP2/TRF5, PKH1/2, PPH21/22 PPZ1/2, PRS2/4, RAS1/2, ROM1/2, RSC3/30, SAM1/2, SBH1/2, SIS2/VHS3, SLM1/2, SNC1/2, SSB1/2, SSE1/2, SSF1/2, TIF4631/4632 TEF1/2, TDH2/3, TRK1/2, TUB1/3, UBC4/5, URA7/8, YCK1/2, YPK1/2, YPT31/32

Posted by 2021-03-18 Labels: essential genes

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