- 追加された行はこの色です。
- 削除された行はこの色です。
- 細胞周期関連 へ行く。
[[研究]]
*出芽酵母細胞周期関連遺伝子の制御 [#g9538fef]
**30遺伝子 [#jfb04d31]
|Gene Name|Transcription|Translation|Degradation|Phosphorylation|Others|h
|BUB2||||||
|CDC14||||||
|CDC15||||||
|CDH1|ND|||CDK((localization: S-16,42,176,227,239)), CDC5(([[18500339]]~ activity: S-215,259))||
|CLB2|||CDC20,CDH1((&ref_paper(12152084); 25-Dbox,85-,100-KEN))|||
|PDS1|||CDC20, CDH1((8-KEN, 85-Dbox))|CDK((&ref_paper();)),[[pic:http://www.nature.com/nature/journal/v454/n7202/images/nature07050-f1.2.jpg]]||
|CLB5|||CDC20((34-Dbox))|||
|CDC20|||CDH1((tow-Dbox,585-KEN))|||
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|SWE1|||CDK,CLA4,CDC5((&ref_paper(15920482);)), HSL1|||
|SWI5|SFF||CDC4((&ref_paper(18787112);))|SRB10((&ref_paper(18787112); CDC4 interaction: S-225,231,246,250,261,300,T-320,323)), CDK((NLS: S-552,646,664))||
|||||||
*その他 [#c532e354]
|Gene Name|Transcription|Translation|Degradation|Phosphorylation|Others|h
|ACM1|MCB, SCB||CDC20, CDH1((&ref_paper(18498748);))|CDK((&ref_paper(18519589);~&ref_paper(18498748);~ Stability&localization: S-3,31,48,161,T-161))||
|ALK1|SFF||CDH1?(200-KEN,224-Dbox,[[16855400]])|||
|ALK2|||CDH1?(116-KEN,150-Dbox,[[16855400]])|||
|[[CDC5]]|SFF||CDH1((&ref_paper(11566880);~&ref_paper(18172166);~ N70, 35-KEN))|CDK((&ref_paper(16303563);~ Activation: S-242))||
|CIN8|HCM1([[16912276]])| | CDH1((&ref_paper(11694576);~ 35-Dbox,970-KEN))| | |
|FIN1| | |CDH1((&ref_paper(17173039);~ 8-Dbox))|CDK((&ref_paper(17173039);~ S-36,54,117,148,T-68))||
|HSL1|MCB, SCB||HOG1((&Ref_paper(16688223);))|CDC20,CDH1((&ref_paper(11562348);~ 94-Dbox,775-,812-KEN,))||
|MPS1|||CDC20,CDH1|||
*細胞周期用語集 [#v863e472]
-R-X-X-L-X-X-X-X-[N/D/E] Destruction (D) box APC_Cdc20の標的モチーフ
--[[D-box finder:http://bioinfo.weizmann.ac.il/~danag/d-box/main.html]]
-K-E-N (KEN box) APC_Cdh1の標的モチーフ((&ref_paper(10733526);)) KEN → AAA
-[S/T]-P-X-[K/R] CDKのより厳密なコンセンサス
-[S/T]-P CDKの緩いコンセンサス
-[D/E]-X-[S/T]-Phi-X-[D/E] Polo kinaseのコンセンサス（where 'Phi' denotes a hydrophobic residue）
-S-[pT/pS]-[P/X] Polo Box binding (PBB) site
-SCF_Cdc4の標的
--Sic1, Swi5
-APC_Cdc20の標的
--Clb5, Clb2, DBF4((&ref_paper(18591250);)),Pds1 (Securin)
-APC_Cdh1の標的
--BUB1((Mammal,&ref_paper(17158872);)),Clb1, Clb2, Cdc5, Cin8, Kip1, Hsl1, Cdc20, Ase1, Fin1, Pds1p
--A simple database search of budding yeast sequences reveals 92 proteins containing matches to both a basic D box (RxxLxxxx(NDEQ)) and a basic KEN box (KENxxx(NDEQ)), in 32 of which the two motifs are separated by fewer than 100 amino acids.([[11562348]])
-&ref_paper(18591966);~
--The current study verifies previous models of Cdh1 function in the cell cycle, strengthens the case for Cdh1 as a tumour suppressor and validates a role for Cdh1 in the nervous system.
--It is apparent that Cdh1 loss causes genomic instability, but the precise cause of this instability is unclear.
#br
**Selected binding sites for cell-cycle transcription factors (TFs) [#u8a23564]
| ||>|Budding yeast|>|Fission yeast|h
|Name |Phase| Binding site*1| TF| Binding site*1| TF|h
|MCB| G1/S| ACGCGT| MBF| ACGCGT| MBF|
|SCB| G1/S| CRCGAAA*2| SBF| Not described| Not described|
|SFF/Forkhead| G2/M| Mcm1*3 + GTAAACAA*2 |Mcm1 + Fkh2 |GTAAACAAb| Sep1? Fkh2?|
|PCB| G2/M| Not described| Not described| GNAACR| PBF, Mbx1?|
|ECB| M/G1| YAATTA + Mcm1*3| Yox1/Yhp1 + Mcm1| Not described| Not described|
|Swi5/Ace2| M/G1| ACCAGCR*2| Swi5, Ace2| ACCAGCCNT*2| Ace2|
+Different versions of binding sites have been described, and typical sequence patterns were selected for this table to represent each binding site.
+These sites are also present in reverse orientation.
+A typical Mcm1 site is: TTWCCYAAWNNGGWAA.
N is any base; R is A or G; Y is C or T;Wis A or T.
&ref_paper(16285853);
*細胞周期で制御されている遺伝子はいくつあるのか？ [#s1d48381]
これの答えは意外に難しい。
**制御の方法は？ [#jb84ce7b]
+転写
+翻訳
+リン酸化
+分解
**調べる方法は？ [#q12251d1]
-マイクロアレイ解析
-ChIP-chip解析
-ゲノム塩基配列から保存された配列を抽出
-プロテオーム解析
**細胞周期を同調させる方法は？ [#u985029a]
+Induced synchrony, which forces cells to synchronize by some intervention such as pheromone arrest or the use of temperature-sensitive cdc mutants
+Selection synchrony, which selects a cohort of cells at the same cell cycle stage, as in the elutriation method
+Yeasat Metabolic Cycle (YMC) synchrony, which is a naturally synchronized continuous yeast culture proceeds through 5-h metabolic cycles
#br
*どんな制御因子があるのか？ [#i9e1c7db]
+転写制御
--SWI4
--SWI6
--MBP1
--HCM1
--MCM1
--FKH2
--NDD1
--SWI5
+リン酸化制御
#br
*[[マイクロアレイ解析]]によるゲノムワイドな細胞周期転写制御の解析 [#gc292c3b]
**マイクロアレイによる細胞周期によって制御される転写産物の同定の始まり [#yb0dbfdb]
-&ref_paper(9702192);~
ゲノムワイドなマイクロアレイと温度感受性変異による同調をつかって、細胞周期で制御される416の転写産物を手動データ解析により同定。この論文は（こちらの方が先に発表されたにもかかわらず）、下のSpellmanの論文ほど引用されない（私も今回調べてみて始めてこの論文の存在を知った）。
-&ref_paper(9843569);~
上の論文とやっていることは同じなのだが、クラスタリングやフーリエ解析を利用したデータ解析により800の遺伝子を同定。２番煎じになってしまったため、MCBになってしまったがデータ解析に優れているためこちらの方がより引用されている。ちなみにこちらの解析では、上の論文の416の遺伝子のうち304のみが細胞周期で変動するとされた。
#br
----
**最近の解析結果 [#gc7fc1b5]
-&ref_paper(17827275);~
--酵母の代謝周期（Yeast Metabolic Cycle:YMC）によって同調した細胞のマイクロアレイ解析と、最大エントロピーデコンボリューション法をつかってかなり高解像度に細胞周期によって変化する転写産物（Cell Cycle Regulated Transcript: CCRT)を同定している。おそらく現在一番高解像度な転写マップ。
--同定できたCCRT（Rowicka's CCRT）は、1,129個！
#br
#ref(http://www.pnas.org/content/104/43/16892/F4.large.jpg,1164x1280,30%);
#br
----
-&ref_paper(18463633);
-&ref_paper(18758238);
--clb1,2,3,4,5,6, GAL-CLB1株を用いてサイクリンの発現を止めてしまっても、転写の%%周期は起き続ける！ーCDKによる生化学振動子のほかに転写の振動子があるという発見。%%~
データを見ると、振動してはいない。順番に転写活性化が起きているだけ。「振動子がある」というのは言い過ぎ。
#br
#ref(http://www.nature.com/nature/journal/v453/n7197/images/nature06955-f4.2.jpg,800x336,70%)
#br
----
-[[細胞周期で制御を受ける遺伝子データベース:http://www.cyclebase.org/index.action]]
割と見やすくてよいが、上記の論文のデータがアップデートされていない。
#br
*出芽酵母のゲノムを細胞周期制御モチーフからみる [#n214e3b8]
SGDの[[Pattern Matching:http://seq.yeastgenome.org/cgi-bin/PATMATCH/nph-patmatch]]を使って、細胞周期制御に関わる蛋白質のモチーフを検索する(Sep.30 2008)
|Motif | Unique hit| Total hit |h
|KEN box (KEN) | 871 | 1025 |
|D-box (RxxLxxxx[DEN]) | 1686 | 2246 |
|D-box (RxxLxxxx[DENQ])| 1951 | 2741 |
|CDK ([ST]Px[KR]) | 1440 | 2108 |
|Moc1 (LFP) | 498 | 529 |
|Moc2 ([ST]Pxx[KR]) | 1639 | 2254 |
|Total ORF | 5884 | |
#br
Mocにあるように適当な配列を用いて検索をかけても、多くの蛋白質がヒットする。単純にモチーフからだけではどの遺伝子が制御されているのか結論を出すのは難しい。そこで、これらの組み合わせ（Rowicka's CCRT, CDK, D_hit, KEN_hit）で見てみる。
#br
| Name | CCRT | CDK | D_hit | KEN |h
| ACC1 | G1 | 4 | 1 | 1 |
| AFR1 | M | 1 | 1 | 1 |
| ALK1* | G2 | 1 | 1 | 1 |
| ALK2* | S | 2 | 1 | 1 |
| ATF1 | G2/M | 1 | 1 | 1 |
| BFR1 | S | 1 | 1 | 1 |
| BNR1 | G1/S | 2 | 1 | 1 |
| BUD3 | G2 | 5 | 2 | 1 |
| CDC20* | M | 1 | 1 | 1 |
| CDC5* | G2 | 1 | 2 | 1 |
| CSR1 | G1(P) | 1 | 1 | 1 |
| ERM6 | G2 | 1 | 1 | 1 |
| FAA3 | G2/M | 1 | 1 | 1 |
| FKH2 | G1(P) | 3 | 1 | 1 |
| GPT2 | G2/M | 1 | 1 | 1 |
| HPC2 | S | 4 | 1 | 1 |
| HSL1* | S | 2 | 4 | 3 |
| IQG1* | M | 4 | 3 | 2 |
| ISW1 | G1(P) | 1 | 3 | 3 |
| KAR3 | S | 2 | 2 | 1 |
| KEL1 | S | 2 | 1 | 2 |
| KEL2 | G1/S | 1 | 1 | 1 |
| KIP1 | S | 1 | 1 | 1 |
| LTE1 | G1(P) | 8 | 1 | 1 |
| MMS4 | G1/S | 3 | 1 | 1 |
| MPS1* | M | 1 | 1 | 1 |
| MSC7 | G1(P) | 1 | 1 | 1 |
| MYO2 | S | 1 | 1 | 1 |
| NTE1 | S | 1 | 1 | 1 |
| NUM1 | G1 | 2 | 2 | 13 |
| PDS1* | S | 3 | 1 | 1 |
| SGS1 | S | 1 | 1 | 2 |
| SIR4 | G2 | 5 | 1 | 1 |
| SKM1 | G1/S | 1 | 1 | 1 |
| SPC72 | G1 | 1 | 1 | 1 |
| SPT16 | M/G1 | 1 | 1 | 2 |
| STH1 | S | 1 | 1 | 3 |
| STU1 | G1/S | 1 | 1 | 1 |
| STU2 | S | 1 | 1 | 1 |
| SUM1 | G1(P) | 1 | 1 | 1 |
| SVL3 | S | 1 | 2 | 1 |
| SWI4 | M | 2 | 1 | 1 |
| SWI5 | G2/M | 8 | 1 | 1 |
| TOS2 | G1/S | 1 | 1 | 1 |
| TRA1 | G1(P) | 4 | 5 | 4 |
| UBP7 | G1 | 1 | 3 | 1 |
| ULS1 | M/G1 | 2 | 1 | 2 |
| VAC17 | G2 | 2 | 1 | 1 |
| YCS4 | S | 1 | 1 | 1 |
| YHP1 | S | 2 | 1 | 1 |
| YLR057W | G1(P) | 1 | 1 | 1 |
CENTER: *CDH1のターゲットであることがわかっている遺伝子。
*Morgan's CDK substrate [#u7fe32c5]
| Protein | Clb5/Clb2 | Biological Process |h
| Ace2 | 1.3 | Required for G1-specific transcription |
| Ady3 | 3.4 | Protein of unknown function |
| Arg1 | 0.7 | Argininosuccinate synthetase |
| Ase1 | 15.8 | Microtubule binding protein required for spindle stability |
| Ash1 | 1.7 | Daughter cell-localized transcription factor |
| Atg20 | 0.5 | Protein of unknown function |
| Axl2 | 2.0 | Required for axial budding pattern |
| Bbp1 | 3.1 | Spindle pole body component |
| Bck2 | 0.4 | Protein involved in the SIT4 pathway for CLN activation |
| Bem1 | 0.9 | Required for cell polarization and bud formation |
| Bem3 | 1.5 | GTPase-activating protein Cdc42p and Rho1p |
| Bna3 | 1.7 | Arylformamidase |
| Bni1 | 4.3 | Involved in cytoskeletal control |
| Bsp1 | 2.2 | Organization of actin cytoskeleton |
| Bud4 | 0.4 | Required for axial budding |
| Bud6 | 0.4 | Required for bipolar budding |
| Caf120 | 1.2 | Transcriptional regulation |
| Cdc20 | 2.3 | APC-activating factor in anaphase |
| Cdc5 | 1.1 | Protein kinase required for mitotic exit |
| Cdc6 | 758.6 | pre-replicative complex formation and maintenance |
| Cdh1 | 5.6 | APC activating factor in M/G1 |
| Chs2 | 0.4 | Responsible for primary septum disk during cytokinesis |
| Cnn1 | 45.7 | Protein of unknown function |
| Csr2 | 0.6 | Protein of unknown function |
| Cst9 | 1.4 | Required for synaptonemal complex formation |
| Cyc2 | 0.8 | Cytochrome-c mitochondrial import factor |
| Dbf2 | 2.2 | Protein kinase required for mitotic exit |
| Dbf20 | 2.4 | Protein kinase required for mitotic exit |
| Dbf4 | 1.9 | Regulatory subunit for Cdc7p protein kinase |
| Ddc1 | 13.1 | DNA damage checkpoint protein |
| Dna2 | 0.6 | DNA helicase |
| Dna43 | 1.5 | DNA replication initiation / DNA strand elongation |
| Dnf2 | 1.2 | Protein of unknown function |
| Dpb2 | 10.5 | DNA polymerase epsilon subunit |
| Eco1 | 2.5 | Required for establishment of sister chromatid cohesion |
| Elm1 | 0.7 | Protein kinase regulating pseudohyphal growth |
| Far1 | 3.3 | Cln-specific Cdk1 inhibitor |
| Fin1 | 13.8 | Intermediate filament protein |
| Fkh2 | 3.5 | Transcription factor regulating G2/M gene expression |
| Fmt1 | 1.6 | Mitochondrial methionyl-tRNA transformylase |
| Frt2 | 20.3 | ER protein of unknown function |
| Fun21 | 0.7 | Protein of unknown function |
| Fun30 | 0.9 | Involved in resistance to UV radiation |
| Fus1 | 3.0 | Required for cell fusion during mating |
| Gin4 | 1.9 | Protein kinase required for septin organization |
| Hcm1 | 2.0 | Member of the forkhead family of DNA-binding proteins |
| Hdr1 | 0.8 | Protein involved in meiotic segregation |
| Hos4 | 1.0 | Protein of unknown function |
| Icy2 | 0.8 | Protein of unknown function |
| Ifh1 | 0.9 | Involved in regulation of ribosomal RNA expression |
| Ino2 | 1.3 | Transcription factor required for derepression of phospholipid synthetic genes |
| Ipl1 | 1.8 | Protein kinase involved in chromosome segregation |
| Jsn1 | 1.7 | RNA-binding protein |
| Kar3 | 5.9 | Kinesin-like protein required for proper spindle assembly |
| Kar9 | 4.8 | Involved in mitotic spindle orientation |
| Kel1 | 5.1 | Involved in cell fusion and morphology |
| Kel2 | 0.4 | Protein involved in cell fusion and morphology |
| Kip2 | 0.7 | Kinesin-like protein required for proper spindle assembly |
| Kip3 | 2.1 | Kinesin-like protein required for proper spindle assembly |
| Lre1 | 1.5 | Protein of unknown function |
| Lrs4 | 2.5 | Involved in rDNA silencing |
| Lte1 | 0.3 | GDP exchange factor involved in mitotic exit |
| Luv1 | 1.6 | Involved in protein sorting in the late Golgi |
| Mcm2 | 0.8 | Subunit of MCM complex at origins of DNA replication |
| Mcm3 | 16.2 | Subunit of MCM complex at origins of DNA replication |
| Mcm6 | 0.7 | Subunit of MCM complex at origins of DNA replication |
| Mih1 | 6.1 | Phosphatase that dephosphorylates Y19 on Cdk1 |
| Mlp1 | 0.7 | Myosin-like protein |
| Mmr1 | 2.3 | Protein of unknown function |
| Mms4 | 0.8 | DNA damage repair protein |
| Mob1 | 0.8 | Regulatory subunit of Dbf2, required for mitotic exit |
| Mpc54 | 2.0 | Component of the meiotic plaque |
| Mps2 | 18.3 | Required for spindle pole body assembly and normal chromosome segregation |
| Mpt1 | 1.4 | Component of RNA polymerase II transcription factor TFIID |
| Msb1 | 1.5 | Required for establishment of cell polarity |
| Msh6 | 1.0 | DNA repair protein |
| Nbp1 | 1.7 | Essential protein required for G2/M transition |
| Ndd1 | 2.6 | Interacts with Fkh2 to control G2/M gene expression |
| Net1 | 0.4 | Control of the Cdc14 phosphatase |
| Nth1 | 3.6 | Neutral trehalase |
| Nup1 | 0.9 | Nuclear pore protein (nucleoporin) |
| Nup60 | 2.7 | Nuclear pore protein (nucleoporin) |
| Orc1 | 2.4 | Required in pre-replicative complex formation |
| Orc2 | 26.9 | Required in pre-replicative complex formation |
| Orc6 | 67.9 | Required in pre-replicative complex formation |
| Pak1 | 1.7 | Kinase that suppresses DNA pol. alpha mutations |
| Pcl7 | 1.0 | Pho85 cyclin |
| Pin2 | 1.2 | Protein of unknown function |
| Pkh2 | 1.2 | protein kinase with similarity to 3-phosphoinositide-dependent protein kinase |
| Plm2 | 1.5 | Required for plasmid maintenance |
| Pol1 | 1.0 | DNA polymerase I alpha subunit |
| Pom152 | 1.0 | Nuclear pore membrane glycoprotein |
| Ptk2 | 0.6 | Protein kinase required for polyamine transport |
| Pxl1 | 0.9 | Involved in polarized growth |
| Rad9 | 0.5 | DNA damage checkpoint protein |
| Rav1 | 1.9 | Involved in regulation of (H+)-ATPase in vacuolar membrane |
| Rbs1 | 1.3 | Protein of unknown function |
| Rfc1 | 0.4 | Subunit of RFC complex required for DNA replication |
| Rlf2 | 1.1 | Involved in nucleosome assembly |
| Rrp6 | 1.7 | Involved in 5.8S ribosomal RNA 3' end processing |
| Rts1 | 2.0 | PP2A regulatory subunit |
| Sac7 | 1.3 | GTPase-activating protein for Rho1p |
| Sec3 | 1.7 | Component of exocyst complex |
| Sfb3 | 0.9 | Involved in transport of protein from the ER to the Golgi |
| Sld2 | 14.2 | Required for initiation of DNA replication |
| Sld3 | 2.1 | Involved in initiation of DNA replication |
| Slk19 | 1.8 | Kinetochore protein required for spindle assembly |
| Smc4 | 2.7 | Subunit of the condensin protein complex |
| Spa2 | 0.8 | Involved in cell polarity and cell fusion during mating |
| Spc110 | 54.2 | Spindle pole body component |
| Src1 | 0.2 | Protein of unknown function |
| Srm1 | 1.5 | GDP/GTP exchange factor for Gsp1p and Gsp2p |
| Ssk1 | 0.6 | Involved in osmosensory signal transduction |
| Stb1 | 2.5 | Involved in transcription regulation at Start |
| Stu2 | 0.9 | SPB component regulatin microtubule dynamics |
| Swe1 | 1.7 | Protein kinase that phosphorylates Cdk1 on Y19 |
| Swi5 | 2.4 | G1-specific transcription factor |
| Swi6 | 1.0 | G1-specific transcription factor |
| Tfg1 | 3.3 | RNA polymerase II transcription initiation factor TFIIF (factor g) |
| Tus1 | 0.6 | Protein with similarity to GDP-GTP exchange factors |
| Ufe1 | 1.3 | t-SNARE homolog of the endoplasmic reticulum |
| Ulp2 | 5.3 | Degrades conjugated ubiquitin-like protein Smt3p |
| Whi5 | 1.6 | Regulation of progression through Start |
| Xbp1 | 1.9 | Stress-induced transcriptional repressor |
| YDL025C | 0.9 | Protein kinase of unknown function |
| YDL089W | 0.6 | Protein of unknown function |
| YDR348C | 1.8 | Protein of unknown function |
| Yen1 | 364.4 | Protein of unknown function |
| YER158C | 1.2 | Protein of unknown function |
| YGR035C | 0.5 | Protein of unknown function |
| YHL035C | 1.2 | Protein of unknown function |
| YHR149C | 1.0 | Protein of unknown function |
| YJL084C | 1.3 | Protein of unknown function |
| YJR054W | 4.8 | Protein of unknown function |
| YKR078W | 0.3 | Protein of unknown function |
| YLR187W | 1.5 | Protein of unknown function |
| YLR278C | 0.9 | Protein of unknown function |
| YML119W | 0.5 | Protein of unknown function |
| YNL058C | 1.2 | Protein of unknown function |
| YNL321W | 3.1 | Member of the calcium permease family of membrane transporters |
| YNR047W | 4.3 | Protein kinase of unknown function |
| YOL036W | 2.6 | Protein of unknown function |
| YOL070C | 0.6 | Protein of unknown function |
| YOR066W | 1.9 | Protein of unknown function |
| YOR315W | 0.5 | Protein of unknown function |
| YPL267W | 1.6 | Protein of unknown function |
| Yrf1-3 | 1.4 | Protein of unknown function |
| Yrf1-6 | 0.7 | Protein of unknown function |
| Yta7 | 1.4 | Protein of unknown function |
| Zip1 | 3.4 | Structural protein of the synaptonemal complex |
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