이 작품은 p53lab (BMSI, A * STAR)과 JCO VIP 보조금 (A * STAR)의 핵심 예산에 의해 지원되었습니다.

HEK293 세포주 프로토콜에 사용되었고 덜벡코의 수정된 이글 배지에서 10% 태아 소 혈청, 2mM L-글루타민, 100 U/mL 페니실린/스트렙토마이신으로 보충하였다. 세포는 가습 환경에서 5% CO2로 37°C에서 배양되었다.
1. eIF4E:eIF4G604-646 보완 분석등을 통한 eIF4F 복잡한 중단에 대한 정량적 평가
<ol><li>eIF4E:eIF4G604-646 보완 분석의 세포 배양 및 일시적인 연분<ol>
<li>모든 실험에 20개 미만의 구절을 사용하여 새로 해동된 세포를 사용하십시오. 1일째에는 표준 셀 카운터를 사용하여 셀 번호를 결정하고 Trypan blue 제외방법(13)을사용하여 실행 가능한 총 셀을 계산한다.</li>
		<li>종자 6웰 플레이트0.9 - 1.2 x 106 의 HEK 293 셀의 2 mL에서 표준 성장 배지. 참고: 위에 표시된 세포주 내에서 최상의 경질 효율을 달성하기 위해 도금 된 세포가 시드 후 하루에 70-90 % 응수되도록하십시오.</li>
		<li>2일 오전, SubA-eIF4E 및 eIF4G604-646-SubB플라스미드를 이용한 공동 트랜스펙트 세포는 지질계 형 질산성 트랜스포마이트 시약(재료표참조)을 사용한다.<ol>
<li>각 배설물및 실온에서 5분 동안 배양하는 페놀 레드 없이 125 μL의 감소된 혈청 배지를 함유한 튜브에 리포솜 기반 용액의 9μL을 희석시하십시오.</li>
			<li>각 피질 튜브에 대해 125 μL의 감소된 혈청 배지에 각 플라스미드의 3 μg를 희석하여 DNA의 마스터 믹스를 준비합니다.</li>
			<li>DNA 마스터 믹스 튜브에 증강 기시약 12 μL을 추가하고 잘 섞은 다음 DNA를 즉시 추가합니다: 증강 마스터 믹스는 희석된 리포좀의 각 튜브에 1:1비율로 혼합됩니다. 실온에서 15분 동안 배양하십시오.</li>
			<li>각 우물에 DNA 지질 복합체를 추가하고 24h에 대해 5 % CO2로 37 °C 인큐베이터에서 세포를 배양합니다.</li>
		</ol>
</li>
		<li>3일 아침, PBS 1mL로 각각 헹구는 다.</li>
		<li>PBS를 제거하고 37°C에서 5분 동안 트립신의 0.3mL로 각각 의 세포를 배양한다.</li>
		<li>각 우물에 0% FCS를 함유하는 페놀 레드 없이 감소된 혈청 배지의 2mL을 첨가하여 트립신을 중화시키고 15mL 튜브로 전염된 세포를 전달한다. 참고: 페놀 레드는 루시파아제 활동을 방해할 수 있습니다. 따라서, 세포는 페놀 레드 없이 매체에서 이 단계에서 부터 처리되어야 합니다.</li>
		<li>290 x g에서 5 분 동안 셀을 회전시키고 매체를 흡인시합니다. 0% FCS를 함유하는 페놀 레드 없이 감소된 혈청 배지의 2mL에서 세포를 다시 중단한다. 1.1 단계에서 설명된 대로 계산합니다.</li>
		<li>종자 0% FCS를 함유하지 않고 96개의 불투명 플레이트에서 90,000개의 세포밀도로 HEK 293 세포를 감염하였다. 3가지 상이한 화합물에 대해 동일한 실험 내에서 3개의 기술적 복제를 얻기 위해, 가장자리의 우물을 제외한 세포가 있는 플레이트의 60웰을 시드한다.</li>
		<li>감염된 세포를 파종한 직후 10μL의 10μL를 DMSO 화합물 용액을 추가합니다(1.2단계 참조).</li>
	</ol></li>
	<li>복합 제제<ol>
<li>100% DMSO(v/v)로 관심 화합물을 용해시켜 1m 복합 스톡 솔루션을 준비한다. 각 화합물 적정에 대해 3개의 복제를 갖기 위해 1mM 복합 스톡 용액의 8μL을 사용하십시오. 참고 : 사용되는 1 mM 재고 화합물의 볼륨은 필요한 것보다 더 많은 것입니다. 이 작업은 피펫팅 오류를 고려하기 위해 수행됩니다.</li>
		<li>1m 스톡의 4μL을 각 적정점에 대해 100% DMSO의 4μL로 재고 화합물 용액의 2배 연속 희석을 수행한다. 참고: 완전한 복합 적정의 경우 시작 재고로부터 9개의 직렬 희석을 100% DMSO로 수행합니다. 여러 화합물을 테스트해야 하는 경우 이 단계와 후속 희석을 용이하게 하기 위해 96개의 웰 플레이트와 멀티채널 파이펫을 사용하십시오.</li>
		<li>2배 의 직렬 희석의 각 지점에 대해 36μL의 HPLC 급 멸균수를 추가하여 10% DMSO(v/v)에서 10배 작동 용액의 40μL을 준비합니다(즉, 100 μM ~ 0.39 μM ~ 0.39 μM 10% DMSO 스톡 시리즈는 0.039%에 10μMM의 최종 용액으로 이어질 때 0.039%의 최종 용액으로 이어질 것이다). 처리 제어는 HPLC 급 멸균 수에서 10% DMSO 전용 재고 용액을 준비합니다.</li>
		<li>10μL의 10μL을 96개의 잘 불투명한 플레이트에 추가하여 잔류 DMSO 농도가 1%(v/v)의 잔류 DMSO 농도를 100μL의 총 부피로 산출하고 5% v/v 대기 CO2로37°C에서 3시간 동안 배양한다.</li>
	</ol></li>
	<li>루시파아제 보완 및 생존 가능성 분석<ol>
<li>3h의 약물 섭취 후, 1부량의 기판과 희석 시약 19권의 희석 시약을 결합하여 루시파라기 기질 시약을 준비하기 시작한다(제조업체의 지침 참조). 참고: 루시파라제 분석은 시판되는 키트를 사용하여 수행됩니다(재료표참조).</li>
		<li>멀티채널 파이펫을 사용하여 기판 시약 25μL을 즉시 추가합니다.</li>
		<li>350 rpm에서 실온에서 궤도 셰이커에서 50 분 동안 접시를 흔들어보십시오.</li>
		<li>플레이트 판독기를 사용하여 발광을 평가합니다. 이렇게 하려면 미러 판독기를 발광 및 455에 방출 필터에 설정합니다. 측정 높이는 6.5mm로 측정 시간이 1s입니다.</li>
		<li>세포 생존가능성을 제고하기 위해 33μL의 생존가능성 분석 시약을 추가한 다음, 플레이트 판독기를 사용하여 실온에서 15분 후에 발광을 다시 측정합니다.</li>
		<li>600nm에 미러 판독기와 방출 필터를 설정하여 플레이트 판독기의 발광을 평가합니다. 측정 높이는 6.5mm로 측정 시간이 1s입니다. 참고: 생존능력은 제조업체 지침에 따라 세포 용해시에 따른 ATP의 세포내 수준을 측정하여 평가됩니다. 이 경우 생존 가능성 분석이 다른 방출 파장을 가진 다른 루시파라제를 사용하기 때문에 멀티플렉스가 가능합니다.</li>
		<li>데이터를 사용하여 데이터를 4파라미터 피팅 곡선 방정식에 맞게 곡선을 사용하여 각 화합물의 IC50 값을 결정합니다. Y = ((A-D)/(1+(x/C)^B)) + D 숫자 값 D와 A는 곡선 피팅 프로세스에서 구속되어야 합니다. eIF4E:4G 보완 분석에서 예상되는 최소한의 곡선 연삭 또는 최소한의 이론적 반응 수준에 대한 Y축의 발광 값. eIF4E:4G 보완 분석에서 예상되는 최대 곡선 연삭 또는 최대 이론적 레벨 응답에 대한 Y축의 발광 값입니다. 참고: 최소 응답에 대한 값은 1% DMSO(v/v) 대조군 처리로부터 파생되며 최대 반응의 값은 세포 생존에 영향을 미치지 않고 고원된 높은 친화성 mTOR 억제제의 최대 반응으로부터 파생된다.</li>
	</ol></li>
</ol>2. eIF4E:eIF4G604-646 분석 억제와 eIF4F 복합 중단
<ol><li>분석에 의해 측정되는 신호가 화합물에 의한 eIF4E-eIF4G 상호작용의 물리적 중단에 대응하는지 확인하기 위해, 종자 세포는 1.1단계에서 설명된 바와 같이.</li>
	<li>다음날, 배지를 페놀 레드를 함유하지 않는 감소된 혈청 배지의 1mL로 교체하고 관심 있는 화합물로 4h에 대해 배양한다. 총 부피 1mL에서 잔류 DMSO 농도를 1%(v/v)로 보장합니다. 참고: 결과와의 상관관계를 쉽게 허용하기 위해 측정된 보완 분석 분석 곡의 시작점, 중간점 및 끝점에서 복합 농도를 사용한다.</li>
	<li>Lyse 세포 및 수행 m7GTP eIF4F 및 eIF4E:4EBP1 복합체를 격리 아래로 당겨. m7GTP 풀 다운 실험을 수행하는 방법에 대한 자세한 절차는 다른 곳에서 찾을 수 있습니다14.</li>
	<li>서쪽 블롯 분석에 의해 m7GTP 바운드 eIF4G, eIF4E 및 4EBP1 단백질 수준을 검출한 다음, 보완 분석 신호 억제와 eIF4F 복잡한 중단과 상관관계가 있습니다.</li>
</ol>

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저자는 공개 할 것이 없습니다.

본 문서에 설명된 방법은 라이브 셀에서 eIF4G-eIF4E 상호작용의 직접 측정을 통해 eIF4F 복합 조립을 정량적으로 모니터링하기 위해 루시파라제 계 보완 분석법을 활용한다. eIF4E-eIF4G 보완 시스템의 사용에 대한 세부 정보를 제공하고 있으며, 또한 eIF4E-eIF4G 상호작용16의약물 유발 4EBP1 매개 해리를 측정하는 데 시스템이 매우 정확하다는 것을 보여주었습니다. 이 분석의 처리량을 용?...

유전자 발현의 제어는 성장 증식 및 분화와 같은 세포 프로그램의 올바른 실행에 중추적 인 역할을한다. 조절 제어 메커니즘은 유전자 전사 수준 또는 mRNA 번역 수준에서 발휘될 수 있다. 지난 10 년 동안, 그것은 점점 더 분명 해지고 있다 개시 과정의 변조에 의해 번역 제어 보다는 오히려 신장 및 종료의 후반 단계 보다는 생물학적 기능의 넓은 범위를 재생 하는 단백질의 특정 하위 집합의 합성을 미세 하 게 조절할 수 있습니다.
생존에 관여하는 mRNA의 증가된 번역, 반자율적 및 반세포 반응은 여러 암에 연루되어 왔으며 또한 비정상적인 활성화 또는 번역 개시 요인1의발현에 인과 관계가 있다.
eIF4F 컴플렉스는 번역 개시의 마스터 레귤레이터입니다. mRNAs의 5'끝에 캡 구조를 결합함으로써, eIF4F는 초기 mRNA-리보솜 모집을 구동하고 차례로 약하게 번역 진핵 mRNA2의mRNA 번역 효율을 증가시키고 있다. eIF4F는 RAS/MAPK 또는 AKT/TOR 경로의 비정상적인 활성화를 수용하는 많은 암 모델에 대해 암 관련 mRNAs의 번역을 중재하여 암세포가 eIF4F를 조절하여 자체 신생물 활성을 강화하는 것을 시사합니다. eIF4F 복합형성을 억제하여 이 피드 포워드 루프의 중단은 매우 유망한 치료 전략3,4이다.
eIF4F 복합체는 (i) eIF4E, mRNA의 5' UTR에서 발견되는 캡 결합 서브유닛, (ii) eIF4A, RNA 헬리케이스 및 (iii) eIF4G, eIF4A 와 상호 작용하는 비계 단백질로 구성되며 결국40개의서브보를 모집한다. eIF4E와 eIF4G 연결은 기능성 eIF4F 복합체의 조립을 위한 속도 제한 단계이며 eIF4E 결합 단백질(4EBP, 멤버 1, 2 및 3)에 의해 부정적으로 조절된다6. 4EBP는 표준 및 비정식 eIF4E 바인딩 시퀀스7,8,9(인간 eIF4E에 대한 aa 604-646에 걸친 영역)로 구성된 인터페이스를 통해 eIF4E에 eIF4E 결합을 결합하여 eIF4E 복합 형성을 적극적으로 방지하는 eIF4E의 풀을 감소시킵니다. 이러한 단백질 단백질 상호 작용의 상호 작용은 주로 4EBP의 라파마이신 (mTOR)의 포유 동물 표적에 의해 조절된다. 미토제닉 자극시, mTOR은 4E-BP 단백질 제품군의 구성원을 직접 인광하여 eIF4E와의 연관성을 감소시키고, 이에 따라 eIF4E-eIF4G 상호 작용 및 기능성 eIF4F 복합체의 형성을 촉진한다10.
eIF4F 복잡한 무결성을 대상으로 하는 화합물 개발에 큰 노력에도 불구하고, 라이브 셀에서 eIF4E-eIF4G 상호 작용의 직접적인 중단을 측정하는 아세약의 부족은 세포 활성 히트 화합물에 대한 검색을 제한했다. 우리는 eIF4E-eIF4G 상호 작용을 통해 eIF4F 무결성의 상태를 실시간으로 모니터링하기 위해 coelenterazine 아날로그 (예를 들어, 나노 루크 기반 보완 분석)에 따라 루시파라제 분석체를 적용했습니다. 루시파아제 보완 단백질 시스템은 최소 자기 연결 및안정성(11)에최적화된 18kDa 단백질 단편(SubA)과 11개의 아미노산 펩타이드 단편(SubB)으로 구성된다. 인간 전체 길이 eIF4E 및 eIF4E 상호작용 도메인을 인간 eiF4G1(aa 604-646)으로부터 융합 제품으로 발현하면, 두 개의 상호 작용 단백질은 SubA 및 SubB 단편을 서로 가까이에 가져오고, 세포 침투성 기판의 존재가 결국 1개의 발광을 생성하게된다는활성 루시파아제의 형성을 유도할 것이다. 우리는 다른 곳에서 eIF4E:eIF4G604-646 보완 시스템16의시공 및 검증을 보고했다.
여기서는 eIF4E:eIF4G604-646 상호 보완 시스템(요청 시 사용 가능)을 사용하여 라이브 셀에서 4EBP1 매개 eIF4E-eIF4G 중단을 정확하게 측정할 수 있는 방법을 설명합니다. 또한, 우리는 잠재적인 암 치료 약으로 현재 임상 시험을 받고 있는 몇몇 mTOR 억제제의 효력을 측정해서 그것의 유용성을입증합니다 12. 오프 타겟 효과는 종종 약물 관련 활동을 마스크하기 때문에, 우리는 또한 eIF4E:eIF4G604-646 시스템 측정의 다재다능성을 고려하기 위해 세포 생존성의 직교 측정으로 확장 될 수있는 방법을 설명합니다.

<table><tbody><tr><td>293FT cells</td><td>Thermo Fisher Scientific</td><td>R70007</td><td></td></tr><tr><td>Cell culture microplate 96 well, F-Bottom</td><td>greiner bio-one</td><td>655083</td><td></td></tr><tr><td>Cell titer Glo 2.0</td><td>PROMEGA</td><td>G9241</td><td></td></tr><tr><td>Envision Multilabel Reader</td><td>PerkinElmer</td><td>not applcable</td><td></td></tr><tr><td>Finnpipette F2 Multichannel Pipettes 12-channels 30-300 ml</td><td>Thermo Fisher Scientific</td><td>4662070</td><td></td></tr><tr><td>Finnpipette F2 Multichannel Pipettes 12-channels 5-50 ml</td><td>Thermo Fisher Scientific</td><td>4662050</td><td></td></tr><tr><td>FUGENE6</td><td>PROMEGA</td><td>E2692</td><td></td></tr><tr><td>Lipofectamine 3000</td><td>Thermo Fisher Scientific</td><td>&lt;a href=&quot;https://www.thermofisher.com/order/catalog/product/L3000015&quot; target=&quot;_blank&quot;&gt;L3000015&lt;/a&gt;</td><td></td></tr><tr><td>NanoBiT PPI Starter Systems</td><td>PROMEGA</td><td>N2014</td><td></td></tr><tr><td>Optimem I Reduced Serum Mediun, no phenol red</td><td>Thermo Fisher Scientific</td><td>11058021</td><td></td></tr><tr><td>Orbital shaker</td><td>Eppendorf</td><td>not appicable</td><td></td></tr><tr><td>&amp;gamma;-Aminophenyl-m&lt;sup&gt;7&lt;/sup&gt;GTP (C&lt;sub&gt;10&lt;/sub&gt;-spacer)-Agarose</td><td>Jena Bioscience</td><td>AC-155S</td><td></td></tr></tbody></table>

monitoring eif4f assembly by measuring eif4e-eif4g interaction in live cells

eIF4F 복합체의 형성은 종종 인간에서 온코겐성 활성화를 겪는 신호 경로의 수렴을 위한 핵심 다운스트림 노드로 나타났습니다. eIF4F는 변환 개시의 mRNA-리보솜 모집 단계에 관여하는 캡 결합 복합체이다. 암의 많은 세포 및 전임상 모델에서 eIF4F의 규제 완화는 암 증식 및 생존에 관여하는 특정 mRNA 하위 집합의 증가된 번역으로 이어집니다. eIF4F는 캡 결합 서브유닛 eIF4E, 헬리케이스 eIF4A 및 스캐폴딩 서브유닛 eIF4G로부터 제작된 이종트리메릭 복합체이다. 활성 eIF4F 복합체의 조립에 중요한 것은 eIF4E와 eIF4G 단백질 간의 단백질 단백질 상호 작용이다. 이 문서에서는 라이브 셀에서 eIF4E-eIF4G 상호 작용 상태를 모니터링하는 eIF4F 어셈블리를 측정하는 프로토콜을 설명합니다. eIF4e:4G 세포 기반 단백질 단백질 상호 작용 분석법은 또한 eIF4F 복합 무결성의 약물 유도된 변화가 정확하고 안정적으로 평가될 수 있도록 합니다. 우리는 이 방법이 시판되는 화합물의 활성을 확인하거나 eIF4F 복합체의 형성을 효율적으로 방해하는 새로운 화합물 또는 양식의 추가 스크리닝을 위해 적용될 수 있다고 구상합니다.

eIF4E:eIF4G604-646 보편시스템의 감도를 검증하기 위해, eIF4F 복합 조립체의 4EBP1 중재 억제는 mTOR 억제제를 사용하여 평가되었다. 4EBP 단백질 제품군의 mTORC1 키나아제 의존형 인산화를 억제함으로써, mTOR 억제는 eIF4E에 4EBP1 연결을 강화하여, 따라서 eIF4F 분해15. mTOR 키나아제의 기계적으로 다른 억제제의 두 종류는 시험되었다: 라팔로그 (예를 들어, 라?...

Watch this Scientific Journal Video about Monitoring eIF4F Assembly by Measuring eIF4E-eIF4G Interaction in Live Cells at JoVE.com

Monitoring eIF4F Assembly by Measuring eIF4E-eIF4G Interaction in Live Cells

여기서, 우리는 사용자가 선별 형식으로 eIF4F 복잡한 역학의 약물 유도 된 동요를 평가 할 수 있도록 살아있는 세포에서 eIF4E-eIF4G 상호 작용을 측정하는 프로토콜을 제시한다.

라이브 셀에서 eIF4E-eIF4G 상호 작용을 측정하여 eIF4F 어셈블리 모니터링

Formation of the eIF4F complex has been shown to be the key downstream node for the convergence of signalling pathways that often undergo&#160;oncogenic ...

monitoring-eif4f-assembly-measuring-eif4e-eif4g-interaction-live

Universidad de Cartagena UDEC

Research

JoVE Journal

Cancer Research

3.0K 조회수.  A*STAR (Agency for Science, Technology and Research). 여기서, 우리는 사용자가 선별 형식으로 eIF4F 복잡한 역학의 약물 유도 된 동요를 평가 할 수 있도록 살아있는 세포에서 eIF4E-eIF4G 상호 작용을 측정하는 프로토콜을 제시한다.

비디오: Monitoring eIF4F Assembly by Measuring eIF4E-eIF4G Interaction in Live Cells

Analysis of Cap-binding Proteins in Human Cells Exposed to Physiological Oxygen Conditions

Translational control is a focal point of gene regulation, especially during periods of cellular stress. Cap-dependent translation via the eIF4F complex is by far the most common pathway to initiate protein synthesis in eukaryotic cells, but stress-specific variations of this complex are now emerging. Purifying cap-binding proteins with an affinity resin composed of Agarose-linked m7GTP (a 5' mRNA cap analog) is a useful tool to identify factors involved in the regulation of translation initiation. Hypoxia (low oxygen) is a cellular stress encountered during fetal development and tumor progression, and is highly dependent on translation regulation. Furthermore, it was recently reported that human adult organs have a lower oxygen content (physioxia 1-9% oxygen) that is closer to hypoxia than the ambient air where cells are routinely cultured. With the ongoing characterization of a hypoxic eIF4F complex (eIF4FH), there is increasing interest in understanding oxygen-dependent translation initiation through the 5' mRNA cap. We have recently developed a human cell culture method to analyze cap-binding proteins that are regulated by oxygen availability. This protocol emphasizes that cell culture and lysis be performed in a hypoxia workstation to eliminate exposure to oxygen. Cells must be incubated for at least 24 hr for the liquid media to equilibrate with the atmosphere within the workstation. To avoid this limitation, pre-conditioned media (de-oxygenated) can be added to cells if shorter time points are required. Certain cap-binding proteins require interactions with a second base or can hydrolyze the m7GTP, therefore some cap interactors may be missed in the purification process. Agarose-linked to enzymatically resistant cap analogs may be substituted in this protocol. This method allows the user to identify novel oxygen-regulated translation factors involved in cap-dependent translation.

Here, we present human cell culture protocols to analyze translation initiation factors that bind the 5' cap of mRNA during physiological oxygen conditions. This method utilizes an Agarose-linked m7GTP cap analog and is suitable to investigate cap-binding factors and their interacting partners.

생리 산소 조건에 노출 된 인간 세포의 캡 결합 단백질의 분석

Translational control is a focal point of gene regulation, especially during periods of cellular stress. Cap-dependent translation via the eIF4F complex ...

연구

유전학

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for example, during cellular differentiation, morphogenesis, and functional stimulation (such as activation of immune cells), or after exposure to drugs and other factors from the local environment. Depending on the stimulus and cell type, these changes occur rapidly and at any possible level of gene regulation. Displaying all molecular processes of a responding cell to a certain type of stimulus/drug is one of the hardest tasks in molecular biology. Here, we describe a protocol that enables the simultaneous analysis of multiple layers of gene regulation. We compare, in particular, transcription factor binding (Chromatin-immunoprecipitation-sequencing (ChIP-seq)), de novo transcription (4-thiouridine-sequencing (4sU-seq)), mRNA processing, and turnover as well as translation (ribosome profiling). By combining these methods, it is possible to display a detailed and genome-wide course of action.
Sequencing newly transcribed RNA is especially recommended when analyzing rapidly adapting or changing systems, since this depicts the transcriptional activity of all genes during the time of 4sU exposure (irrespective of whether they are up- or downregulated). The combinatorial use of total RNA-seq and ribosome profiling additionally allows the calculation of RNA turnover and translation rates. Bioinformatic analysis of high-throughput sequencing results allows for many means for analysis and interpretation of the data. The generated data also enables tracking co-transcriptional and alternative splicing, just to mention a few possible outcomes.
The combined approach described here can be applied for different model organisms or cell types, including primary cells. Furthermore, we provide detailed protocols for each method used, including quality controls, and discuss potential problems and pitfalls.

This protocol describes the combinatorial use of ChIP-seq, 4sU-seq, total RNA-seq, and ribosome profiling for cell lines and primary cells. It enables tracking changes in transcription-factor binding, de novo transcription, RNA processing, turnover and translation over time, and displaying the overall course of events in activated and/or rapidly changing cells.

바인딩, 전사, 번역, 및 회전율 세포 활성화 중 글로벌 이벤트를 표시 하는 녹음 방송 요인의 실시간 분석

Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for ...

An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

Cap-dependent protein synthesis is the predominant translation pathway in eukaryotic cells. While various biochemical and genetic approaches have allowed extensive studies of cap-dependent translation and its regulation, high resolution kinetic characterization of this translation pathway is still lacking. Recently, we developed an in vitro assay to measure cap-dependent translation kinetics with single-molecule resolution. The assay is based on fluorescently labeled antibody binding to nascent epitope-tagged polypeptide. By imaging the binding and dissociation of antibodies to and from nascent peptide&#8211;ribosome&#8211;mRNA complexes, the translation progression on individual mRNAs can be tracked. Here, we present a protocol for establishing this assay, including mRNA and PEGylated slide preparations, real-time imaging of translation, and analysis of single molecule trajectories. This assay enables tracking of individual cap-dependent translation events and resolves key translation kinetics, such as initiation and elongation rates. The assay can be widely applied to distinct translation systems and should broadly benefit in vitro studies of cap-dependent translation kinetics and translational control mechanisms.

An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

Tracking individual translation events allows for high-resolution kinetic studies of cap-dependent translation mechanisms. Here we demonstrate an in vitro single-molecule assay based on imaging interactions between fluorescently labeled antibodies and epitope-tagged nascent peptides. This method enables single-molecule characterization of initiation and peptide elongation kinetics during active in vitro cap-dependent translation.

캡 의존형 번역 역학 분석을 위한 생체외 단일 분자 이미징 분석

Cap-dependent protein synthesis is the predominant translation pathway in eukaryotic cells. While various biochemical and genetic approaches have allowed ...

생화학

Monitoring Kinase and Phosphatase Activities Through the Cell Cycle by Ratiometric FRET

F&ouml;rster resonance energy transfer (FRET)-based reporters1 allow the assessment of endogenous kinase and phosphatase activities in living cells. Such probes typically consist of variants of CFP and YFP, intervened by a phosphorylatable sequence and a phospho-binding domain. Upon phosphorylation, the probe changes conformation, which results in a change of the distance or orientation between CFP and YFP, leading to a change in FRET efficiency (Fig 1). Several probes have been published during the last decade, monitoring the activity balance of multiple kinases and phosphatases, including reporters of PKA2, PKB3, PKC4, PKD5, ERK6, JNK7, Cdk18, Aurora B9 and Plk19. Given the modular design, additional probes are likely to emerge in the near future10. 
Progression through the cell cycle is affected by stress signaling pathways 11. Notably, the cell cycle is regulated differently during unperturbed growth compared to when cells are recovering from stress12.Time-lapse imaging of cells through the cell cycle therefore requires particular caution. This becomes a problem particularly when employing ratiometric imaging, since two images with a high signal to noise ratio are required to correctly interpret the results. Ratiometric FRET imaging of cell cycle dependent changes in kinase and phosphatase activities has predominately been restricted to sub-sections of the cell cycle8,9,13,14.
Here, we discuss a method to monitor FRET-based probes using ratiometric imaging throughout the human cell cycle. The method relies on equipment that is available to many researchers in life sciences and does not require expert knowledge of microscopy or image processing.

FRET-based reporters are increasingly used to monitor kinase and phosphatase activities in live cells. Here we describe a method on how to use FRET-based reporters to assess cell cycle-dependent changes in target phosphorylation.

안달 Ratiometric하여 세포주기를 통해 키나제와 인산 가수 분해 효소 활동을 모니터링

F&ouml;rster resonance energy transfer (FRET)-based reporters1 allow the assessment of endogenous kinase and phosphatase activities in living cells. Such ...

생물학

Quantification of Efferocytosis by Single-cell Fluorescence Microscopy

Studying the regulation of efferocytosis requires methods that are able to accurately quantify the uptake of apoptotic cells and to probe the signaling and cellular processes that control efferocytosis. This quantification can be difficult to perform as apoptotic cells are often efferocytosed piecemeal, thus necessitating methods which can accurately delineate between the efferocytosed portion of an apoptotic target versus residual unengulfed cellular fragments. The approach outlined herein utilizes dual-labeling approaches to accurately quantify the dynamics of efferocytosis and efferocytic capacity of efferocytes such as macrophages. The cytosol of the apoptotic cell is labeled with a cell-tracking dye to enable monitoring of all apoptotic cell-derived materials, while surface biotinylation of the apoptotic cell allows for differentiation between internalized and non-internalized apoptotic cell fractions. The efferocytic capacity of efferocytes is determined by taking fluorescent images of live or fixed cells and quantifying the amount of bound versus internalized targets, as differentiated by streptavidin staining. This approach offers several advantages over methods such as flow cytometry, namely the accurate delineation of non-efferocytosed versus efferocytosed apoptotic cell fractions, the ability to measure efferocytic dynamics by live-cell microscopy, and the capacity to perform studies of cellular signaling in cells expressing fluorescently-labeled transgenes. Combined, the methods outlined in this protocol serve as the basis for a flexible experimental approach that can be used to accurately quantify efferocytic activity and interrogate cellular signaling pathways active during efferocytosis.

Efferocytosis, the phagocytic removal of apoptotic cells, is required to maintain homeostasis and is facilitated by receptors and signaling pathways that allow for the recognition, engulfment, and internalization of apoptotic cells. Herein, we present a fluorescence microscopy protocol for the quantification of efferocytosis and the activity of efferocytic signaling pathways.

단일 세포 형광 현미경 검사 법에 의해 Efferocytosis의 정량화

Studying the regulation of efferocytosis requires methods that are able to accurately quantify the uptake of apoptotic cells and to probe the signaling ...

면역학 및 감염병학

Identification of Protein Interacting Partners Using Tandem Affinity Purification

A critical and often limiting step in understanding the function of host and viral proteins is the identification of interacting cellular or viral protein partners. There are many approaches that allow the identification of interacting partners, including the yeast two hybrid system, as well as pull down assays using recombinant proteins and immunoprecipitation of endogenous proteins followed by mass spectrometry identification1. Recent studies have highlighted the utility of double-affinity tag mediated purification, coupled with two specific elution steps in the identification of interacting proteins. This approach, termed Tandem Affinity Purification (TAP), was initially used in yeast2,3 but more recently has been adapted to use in mammalian cells4-8.
As proof-of-concept we have established a tandem affinity purification (TAP) method using the well-characterized eukaryotic translation initiation factor eIF4E9,10.The cellular translation factor eIF4E is a critical component of the cellular eIF4F complex involved in cap-dependent translation initiation10. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence8. To forgo the need for the generation of clonal cell lines, we developed a rapid system that relies on the expression of the TAP-tagged bait protein from an episomally maintained plasmid based on pMEP4 (Invitrogen). Expression of tagged murine eIF4E from this plasmid was controlled using the cadmium chloride inducible metallothionein promoter.
Lysis of the expressing cells and subsequent affinity purification via binding to rabbit IgG agarose, TEV protease cleavage, binding to streptavidin linked agarose and subsequent biotin elution identified numerous proteins apparently specific to the eIF4E pull-down (when compared to control cell lines expressing the TAP tag alone). The identities of the proteins were obtained by excision of the bands from 1D SDS-PAGE and subsequent tandem mass spectrometry. The identified components included the known eIF4E binding proteins eIF4G and 4EBP-1. In addition, other components of the eIF4F complex, of which eIF4E is a component were identified, namely eIF4A and Poly-A binding protein. The ability to identify not only known direct binding partners as well as secondary interacting proteins, further highlights the utility of this approach in the characterization of proteins of unknown function.

Tandem affinity purification is a robust approach for the identification of protein binding partners. As proof of concept, this methodology was applied to the well-characterized translation initiation factor eIF4E to co-precipitate the host cell factors involved in translation initiation. This method is easily adapted to any cellular or viral protein.

탠덤 동질 정제를 사용하여 단백질 나누기 파트너의 식별

A critical and often limiting step in understanding the function of host and viral proteins is the identification of interacting cellular or viral protein ...

FRET Microscopy for Real-time Monitoring of Signaling Events in Live Cells Using Unimolecular Biosensors

F&ouml;rster resonance energy transfer (FRET) microscopy continues to gain increasing interest as a technique for real-time monitoring of biochemical and signaling events in live cells and tissues. Compared to classical biochemical methods, this novel technology is characterized by high temporal and spatial resolution. FRET experiments use various genetically-encoded biosensors which can be expressed and imaged over time in situ or in vivo1-2. Typical biosensors can either report protein-protein interactions by measuring FRET between a fluorophore-tagged pair of proteins or conformational changes in a single protein which harbors donor and acceptor fluorophores interconnected with a binding moiety for a molecule of interest3-4. Bimolecular biosensors for protein-protein interactions include, for example, constructs designed to monitor G-protein activation in cells5, while the unimolecular sensors measuring conformational changes are widely used to image second messengers such as calcium6, cAMP7-8, inositol phosphates9 and cGMP10-11. Here we describe how to build a customized epifluorescence FRET imaging system from single commercially available components and how to control the whole setup using the Micro-Manager freeware. This simple but powerful instrument is designed for routine or more sophisticated FRET measurements in live cells. Acquired images are processed using self-written plug-ins to visualize changes in FRET ratio in real-time during any experiments before being stored in a graphics format compatible with the build-in ImageJ freeware used for subsequent data analysis. This low-cost system is characterized by high flexibility and can be successfully used to monitor various biochemical events and signaling molecules by a plethora of available FRET biosensors in live cells and tissues. As an example, we demonstrate how to use this imaging system to perform real-time monitoring of cAMP in live 293A cells upon stimulation with a &beta;-adrenergic receptor agonist and blocker.

F&#246;rster resonance energy transfer (FRET) microscopy is a powerful technique for real-time monitoring of signaling events in live cells using various biosensors as reporters. Here we describe how to build a customized epifluorescence FRET imaging system from commercially available components and how to use it for FRET experiments.

Unimolecular 바이오 센서를 사용하여 라이브 세포에서 이벤트를 신호의 실시간 모니터링을위한 현미경을 안달

F&ouml;rster resonance energy transfer (FRET) microscopy  continues to gain increasing interest as a technique for real-time monitoring  of biochemical ...

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants. Low affinity interactions can be preserved through the use of less-stringent buffer conditions and remain readily identifiable. This protocol discusses the labeling of tissue culture cells with stable isotope labeled amino acids, transfection and immunoprecipitation of an affinity tagged protein of interest, followed by the preparation for submission to a mass spectrometry facility. This protocol then discusses how to analyze and interpret the data returned from the mass spectrometer in order to identify cellular partners interacting with a protein of interest. As an example this technique is applied to identify proteins binding to the eukaryotic translation initiation factors: eIF4AI and eIF4AII.

SILAC immunoprecipitation experiments represent a powerful means for discovering novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants, and low affinity interactions preserved through use of less-stringent buffer conditions.

SILAC - 면역 정량 프로테오믹스를 사용하여 포유 동물 세포에있는 단백질 상호 작용 파트너의 식별

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel ...

Xenopus laevis as a Model to Identify Translation Impairment

Protein synthesis is a fundamental process to gene expression impacting diverse biological processes notably adaptation to environmental conditions. The initiation step, which involves the assembly of the ribosomal subunits at the mRNA initiation codon, involved initiation factor including eIF4G1. Defects in this rate limiting step of translation are linked to diverse disorders. To study the potential consequences of such deregulations, Xenopus laevis oocytes constitute an attractive model with high degrees of conservation of essential cellular and molecular mechanisms with human. In addition, during meiotic maturation, oocytes are transcriptionally repressed and all necessary proteins are translated from preexisting, maternally derived mRNAs. This inexpensive model enables exogenous mRNA to become perfectly integrated with an effective translation. Here is described a protocol for assessing translation with a factor of interest (here eIF4G1) using stored maternal mRNA that are the first to be polyadenylated and translated during oocyte maturation as a physiological readout. At first, mRNA synthetized by in vitro transcription of plasmids of interest (here eIF4G1) are injected in oocytes and kinetics of oocyte maturation by Germinal Vesicle Breakdown detection is determined. The studied maternal mRNA target is the serine/threonine-protein-kinase mos. Its polyadenylation and its subsequent translation are investigated together with the expression and phosphorylation of proteins of the mos signaling cascade involved in oocyte maturation. Variations of the current protocol to put forward translational defects are also proposed to emphasize its general applicability. In light of emerging evidence that aberrant protein synthesis may be involved in the pathogenesis of neurological disorders, such a model provides the opportunity to easily assess this impairment and identify new targets.

Xenopus laevis as a Model to Identify Translation Impairment

Protein synthesis control occurs mainly at the translation initiation step, deficiencies in which are linked to diverse disorders. To better understand their etiology, we described here a protocol using Xenopus laevis oocytes assessing the translation of mos transcript in the presence of a mutant of translation initiation factor eIF4G1.

Xenopus의 번역 손상을 식별 할 수있는 모델로 laevis의

Protein synthesis is a fundamental process to gene expression impacting diverse biological processes notably adaptation to environmental conditions. The ...

A High Resolution Method to Monitor Phosphorylation-dependent Activation of IRF3

The IRF3 transcription factor is critical for the first line of defense against pathogens mainly through interferon &#946; and antiviral gene expression. A detailed analysis of IRF3 activation is essential to understand how pathogens induce or evade the innate antiviral response. Distinct activated forms of IRF3 can be distinguished based on their phosphorylation and monomer vs dimer status. In vivo discrimination between the different activated species of IRF3 can be achieved through the separation of IRF3 phosphorylated forms based on their mobility shifts on SDS-PAGE. Additionally, the levels of IRF3 monomer and dimer can be monitored using non-denaturing electrophoresis. Here, we detail a procedure to reach the highest resolution to gain the most information regarding IRF3 activation status. This is achieved through the combination of a high resolution SDS-PAGE and a native-PAGE coupled to immunoblots using multiple total and phosphospecific antibodies. This experimental strategy constitutes an affordable and sensitive approach to acquire all the necessary information for a complete analysis of the phosphorylation-mediated activation of IRF3.

Here we describe a procedure allowing a detailed analysis of the phosphorylation-dependent activation of the IRF3 transcription factor. This is achieved through the combination of a high resolution SDS-PAGE and a native-PAGE coupled to immunoblots using multiple phosphospecific antibodies.

고해상도 방법 IRF3의 인산화에 의존 활성화를 모니터링하려면

The IRF3 transcription factor is critical for the first line of defense against pathogens mainly through interferon &#946; and antiviral gene expression. ...