Действие белков YB-1 и РАВР на трансляцию полиа(-) и полиа(+)мРНК YB-1 тема диссертации и автореферата по ВАК РФ 03.01.03, кандидат биологических наук Елисеева, Ирина Александровна

• Елисеева, Ирина Александровна
• кандидат биологических наук
• 2012

Оглавление диссертации кандидат биологических наук Елисеева, Ирина Александровна

СПИСОК СОКРАЩЕНИЙ.

ВВЕДЕНИЕ.

ОБЗОР ЛИТЕРАТУРЫ.

1. Структура и функции Y-бокс-связывающего белка YB-1.

1.1. Структура, доменная организация.

1.2. Особенности взаимодействия YB-1 с другими молекулами.

1.3. Функции YB-1 в ядре.

1.4. Функции YB-1 в цитоплазме.

1.5. Внеклеточные функции YB-1.

1.6. Регуляция синтеза и активности YB-1.

1.7. Участие YB-1 в эмбриональном развитии и онкологических заболеваниях

2. Структура и функции поли(А)-связывающего белка РАВРС1.

2.1. Структура, доменная организация и взаимодействие с другими молекулами.

2.2. Функции.

2.3. Регуляция синтеза и активности РАВР.

3. Участие 3' НТО в трансляции.

3.1. Регуляция с участием белков, взаимодействующих с 3' НТО.

3.2. Регуляция трансляции микрорегуляторными РНК, специфически связывающимися с 3' НТО.

МАТЕРИАЛЫ И МЕТОДЫ.

1. Плазмидные конструкции, использованные в работе.

2. Методы работы с ДНК.

2.1. Полимеразная цепная реакция (ПЦР).

2.2. Трансформация Escherichia coli плазмидной ДНК.

2.3. Выделение плазмидной ДНК из Escherichia coli.

2.4. Обработка плазмиды рестриктазой.

2.5. J1 игирование Т4 ДНК лигазой.

2.6. Получение меченого фрагмента кДНК (ДНК-зонда) для Northen-блота.

2.7. Электрофорез ДНК в геле агарозы.

3. Методы работы с РНК.

3.1. Синтез РНК in vitro.

3.2. Дефосфорилирование РНК.

3.3. Мечение РНК по 5' концу Т4 полинуклеотид киназой.

3.4. Получение РНК, биотинилированной по 3' концу.

3.5. Получение суммарной РНК из лизата ретикулоцитов кролика.

3.6. Получение суммарной РНК из клеток HeLa.

3.7. Получение суммарной кДНК.

3.8. Получение поли(А)-фрагмента.

3.9. Выделение РНК из полиакриламидного геля.

3.10. Определение стабильности мРНК (Northern-блот).

3.11. Электрофорез РНК в полиакриламидном нативном геле.

3.12. Электрофорез РНК в полиакриламидном геле в присутствии мочевины

3.13. Электрофорез РНК в геле агарозы в денатурирующих условиях.

4. Методы работы с белками.

4.1. Выделение рекомбинантного РАВР.

4.2. Выделение рекомбинантного YB-1.

4.3. Выделение рекомбинантных GST и GST-Paip2.

4.4. Обеднение ретикулоцитного лизата по РАВР.

4.5. Электрофорез белков в полиакриламидном геле в присутствии додецилсульфата натрия.

4.6. Иммуноблоттинг (Western-блот).

5. РНК-белковые методы.

5.1. Метод задержки в геле (гель-шифт).

5.2. Связывание на нитроцеллюлозных фильтрах.

5.3. Ковалентные сшивки под действием ультрафиолета (УФ-сшивки).

5.4. Выделение белков на биотинилированную РНК.

5.5. Бесклеточная система трансляции (БСТ) из ретикулоцитов кролика.

РЕЗУЛЬТАТЫ.

1. Исследование механизмов специфического действия YB-1 и РАВР на трансляцию А(-) мРНК YB-1.

1.1. Регуляторный элемент необходим для специфической регуляции трансляции мРНК YB-1 под действием YB-1 и РАВР.

1.2. YB-1 ингибирует, а РАВР не влияет на трансляцию мРНК YB-1 с удаленным сайтом связывания РАВР.

1.3. YB-1 и РАВР не влияют на трансляцию мРНК YB-1 с удаленным сайтом связывания YB-1.

1.4. YB-1 ингибирует, а РАВР не влияет на трансляцию мРНК YB-1 с разделенными сайтами связывания РАВР и YB-1.

2. Исследование механизмов специфического действия YB-1 и РАВР на трансляцию полиаденилированной мРНК YB-1.

2.1. Полиаденилирование мРНК YB-1 стимулирует ее трансляцию в лизате ретикулоцитов кролика.

2.2. Полиаденилирование мРНК YB-1 не изменяет набора белков, сшивающихся с 3' НТО мРНК YB-1 в лизате ретикулоцитов кролика.

2.3. YB-1 ингибирует трансляцию А(+) так же как и А(-) мРНК YB-1.

2.4. РАВР не стимулирует трансляцию полиаденилированной мРНК YB-1 в лизате ретикулоцитов кролика.

2.5. В условиях недостатка РАВР трансляция как А(-), так и А50 мРНК YB-1 зависит от количества РАВР.

2.6. Регуляторный элемент в 3' НТО мРНК YB-1 взаимодействует с поли(А)-фрагментом в присутствии белков лизата ретикулоцитов кролика.

2.7. Влияние РАВР на трансляцию полиаденилированной мРНК YB-1 зависит от длины участка РНК между регуляторным элементом и поли(А)-хвостом.

ОБСУЖДЕНИЕ РЕЗУЛЬТАТОВ.

1. Роль YB-1 и РАВР в регуляции трансляции неполиаденилированной мРНК YB-1.

2. Возможные механизмы действия YB-1 и РАВР на трансляцию полиаденилированной мРНК YB-1.

3. Регуляция трансляции мРНК YB-1 и ее место в общей регуляции белкового синтеза.

ВЫВОДЫ.

Введение диссертации (часть автореферата) на тему «Действие белков YB-1 и РАВР на трансляцию полиа(-) и полиа(+)мРНК YB-1»

Многофункциональный Y-бокс-связывающий белок 1 (YB-1) - это ДНК- и РНК-связывающий белок с эволюционно консервативным доменом холодового шока. YB-1 принимает участие во многих клеточных процессах, включая пролиферацию, дифференцировку и ответ на стрессовые воздействия (Eliseeva et al.,

2011). Нокаут гена YB-1 приводит к нарушениям эмбрионального развития и пренатальной гибели животных (Lu et al., 2005; Uchiumi et al, 2006). Участие YB-1 в широком спектре внутри- и внеклеточных процессов объясняется, прежде всего, его уникальной способностью взаимодействовать как с ДНК и РНК, так и с различными белками (Eliseeva et al., 2011; Скабкин и др., 2004). Связываясь с поврежденной ДНК, YB-1 принимает участие в репарации ДНК (Guay et al., 2008 b; Pestryakov et al., 2012). Связываясь с определенными нуклеотидными последовательностями в промоторах генов, YB-1 позитивно или негативно регулирует транскрипцию генов, продукты которых участвуют в делении клеток, апоптозе, иммунном ответе, развитии множественной лекарственной устойчивости и др. (Kohno et al., 2003; Eliseeva et al., 2011).

YB-1 взаимодействует с мРНК на всех этапах ее биогенеза и функционирования (Dong et al., 2009; Evdokimova et al., 2006; Skabkin et al., 2004; Svitkin et al., 2009). В ядре он участвует в регуляции альтернативного сплайсинга пре-мРНК (Chansky et al., 2001; Raffetseder et al, 2003). В цитоплазме упаковывает мРНК в мРНП, регулирует ее трансляционную активность, стабильность и взаимодействие с актиновым и тубулиновым цитоскелетами (Chernov et al., 2008 b; Davydova et al., 1997; Evdokimova et al., 2001; Ruzanov et al., 1999; Skabkin et al., 2004). Считается, что YB-1 может регулировать функциональную активность мРНК как напрямую, связываясь со специфическими нуклеотидными последовательностями (Giorgini et al., 2001; Skabkina et al., 2005), так и опосредованно. Во втором случае YB-1 за счет своей РНК-шаперонной активности помогает мРНК образовать правильную вторичную структуру, необходимую для узнавания другими регуляторными белками (Skabkin et al., 2001).

Принимая во внимание, что YB-1 участвует в регуляции многих клеточных процессов, следует ожидать, что его количество строго контролируется. Было показано, что регуляция содержания YB-1 к клетке осуществляется как на уровне транскрипции (Shiota et al., 2008; Yokoyama et al., 2003 b) и трансляции (Fukuda et al, 2004; Hsieh et al, 2012; Kato et al, 2010; Skabkina et al, 2003, 2005; Thoreen et al,

2012), так и за счет изменения стабильности белка (Chibi et al., 2008; Lutz et al, 2006; Sorokin et al, 2005).

Ранее в нашей лаборатории было показано, что специфическая регуляция синтеза YB-1 может происходить под действием двух мажорных белков мРНП: YB-1 и поли(А)-связывающего белка РАВР. YB-1 избирательно ингибирует трансляцию неполиаденилированной (А(-)) мРНК УВ-1 (авторегуляция) при сравнительно низких концентрациях этого белка, оптимальных для трансляции большинства других клеточных мРНК. РАВР, наоборот, стимулирует трансляцию этой мРНК. Как ингибирование под действием УВ-1, так и стимуляция под действием РАВР наблюдаются на стадии инициации трансляции, на этапе присоединения к мРНК УВ-1 438-преинициаторного комплекса или на предыдущем этапе взаимодействия мРНК с факторами инициации трансляции (БкаЫапа et а1, 2003, 2005). С другой стороны, в 3' нетранслируемой области (НТО) мРНК УВ-1 была обнаружена нуклеотидная последовательность с повышенным сродством к УВ-1 и РАВР. Было показано, что сайты связывания двух белков на этой последовательности перекрываются, а белки УВ-1 и РАВР конкурируют за связывание с ней. Кроме того, было обнаружено, что фрагмент мРНК УВ-1 с этой последовательностью ингибирует трансляцию мРНК УВ-1, а также других мРНК на стадии инициации. Эта нуклеотидная последовательность была названа регуляторным элементом.

Тем не менее, механизмы регуляции трансляции мРНК УВ-1 все еще изучены недостаточно. Данная работа посвящена дальнейшему изучению молекулярных механизмов регуляции трансляции мРНК УВ-1. Для этого были поставлены следующие экспериментальные задачи:

1) выяснить, действительно ли регуляторный элемент (1127-1204 нт) в 3' НТО А(-) мРНК УВ-1 строго необходим для регуляции трансляции под действием УВ-1 и РАВР;

2) выяснить, оказывает ли УВ-1 прямое негативное действие на трансляцию А(-) мРНК УВ-1;

3) выяснить, оказывает ли РАВР прямое позитивное действие на трансляцию А(-) мРНК УВ-1\

4) изучить как влияют УВ-1 и РАВР на трансляцию полиаденилированной (А(+)) мРНК УВ-1\

5) проверить, взаимодействует ли регуляторный элемент в 3' НТО мРНК УВ-1 с поли(А)-фрагментом;

6) выяснить, как зависит влияние РАВР на трансляцию А(+) мРНК УВ-1 от длины и нуклеотидной последовательности участка РНК между регуляторным элементом и поли(А)-хвостом (1329-1503нт).

ОБЗОР ЛИТЕРАТУРЫ

В первых двух разделах литературного обзора будут рассмотрены вопросы функционирования двух мажорных белков цитоплазматических мРНП, принимающих участие в регуляции трансляции мРНК YB-1: YB-1 и РАВР. Поскольку наибольший интерес для данной диссертации представляют сведения об участии этих белков в регуляции трансляции, основное внимание будет уделено именно этим функциям. В третьей части обзора литературы будут обсуждаться механизмы регуляции инициации трансляции, в которых принимает участие 3' нетранслируемая область мРНК.

Заключение диссертации по теме «Молекулярная биология», Елисеева, Ирина Александровна

выводы

В бесклеточной системе трансляции из ретикулоцитов кролика показано, что

1. Регуляторный элемент в 3' НТО неполиаденилированной мРНК УВ-1 строго необходим для негативной регуляции трансляции этой мРНК под действием УВ-1 и позитивной под действием РАВР.

2. УВ-1 обладает прямым негативным действием на трансляцию мРНК УВ-1, в то время как позитивный эффект РАВР обусловлен вытеснением УВ-1 с регуляторного элемента.

3. Фрагмент мРНК УВ-1 с регуляторным элементом образует комплекс с поли(А)-фрагментом в присутствии белков лизата ретикулоцитов кролика.

4. Влияние РАВР на трансляцию полиаденилированной мРНК УВ-1 зависит от длины участка РНК между регуляторным элементом и поли(А)-хвостом. Трансляция полиаденилированной мРНК УВ-1 с укороченным спейсером стимулируется РАВР, в то время, как трансляция полноразмерной мРНК или мРНК с заменой удаленного участка на неспецифическую последовательность не стимулируется поли(А)-связывающим белком.

5. На основании полученных данных предложена модель регуляции трансляции полиаденилированной мРНК УВ-1 за счет образования 3' концевой циклической структуры, препятствующей позитивному действию РАВР на трансляцию этой мРНК.

БЛАГОДАРНОСТИ

В заключение я приношу слова благодарности всем, кто помогал мне в данной работе. В первую очередь, я признательна Льву Павловичу Овчинникову за предоставленную возможность выполнить данную работу в лаборатории регуляции биосинтеза белка, а также за поддержку, помощь, проявленное внимание и дельные советы.

Безмерно благодарна Дмитрию Лябину, моему «микрошефу», за чуткость, доброту, понимание, помощь в овладении множеством экспериментаторских навыков.

Спасибо Вячеславу Адамовичу Колбу за внимание к моей работе, ценные советы и конструктивную критику.

Огромное спасибо Кате Ким, Насте Селютиной, Диме Кретову, Саше Доронину, Даше Мордовкиной, Лире Нигматтулиной, Эльвире Мавлявиевой, Сергею Гурьянову, Максиму Скабкину, Ольге Скабкиной, Диме Полякову, Насте Ишутиновой за практическое и моральное содействие, за готовность всегда прийти на помощь и за создание дружеской атмосферы в лаборатории.

Отдельные слова благодарности хочется произнести в адрес Елены Алексеевны Соболевой и Нины Михайловны Гришиной за техническую помощь, их незаменимый труд и создание уюта в лаборатории.

Отдельное спасибо Евгении Викторовне Серебровой за неоценимую помощь в написании статей, автореферата и диссертационной работы.

А также, огромное спасибо хочется сказать всем моим близким и родным людям: Ване Кулаковскому, Ане Елисеевой, Татьяне Владимировне Кулаковской, Ренате Александровне Кулаковской, Кате Кулаковской, Александр Прокопьевич и Валентине Николаевне Елисеевой за поддержку во время выполнения и написания этой работы.

Благодарю также всех сотрудников Института белка РАН, с которыми я общалась, а также моих друзей и коллег за веру в мою работу и задушевные разговоры.

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