Изучение взаимодействия р50-мажорного белка мРНП - с РНК тема диссертации и автореферата по ВАК РФ 03.00.03, кандидат биологических наук Скабкин, Максим Александрович

• Скабкин, Максим Александрович
• кандидат биологических наук
• 2003

Оглавление диссертации кандидат биологических наук Скабкин, Максим Александрович

ВВЕДЕНИЕ.

ОБЗОР ЛИТЕРАТУРЫ

МАЖОРНЫЕ БЕЛКИ ЯДЕРНЫХ И ЦИТОПЛАЗМАТИЧЕСКИХ мРНП:

СТРОЕНИЕ И ФУНКЦИОНИРОВАНИЕ.

I. Гетерогенные ядерные рибонуклеопротеидные частицы (гяРНП).

1. История открытия гяРНП.

2. Белки гяРНП.

2.1. Общие характеристики белков гяРНП.

2.2. Домены белков гяРНП.

2.2.1. РНК-связывающий домен (RBD).

2.2.2. КН-домен.

2.2.3. Вспомогательные домены (auxiliary domains).

2.3. Коровые белки гяРНП.

2.3.1. А/В группа белков гяРНП.

2.3.2. Группа С белков гяРНП.

2.4. Прочие «не коровые» белки гяРНП.

3. Упаковка гяРНК и структура гяРНП.

4. Транспорт мРНК из ядра в цитоплазму.

II Цитоплазматические матричные рибонуклеопротеидные частицы (мРНП).

1. История открытия цитоплазматических мРНП.

2. Основные характеристики мРНП.

3. Мажорные белки цитоплазматических мРНП.

3.1. Поли(А)-связывающий белок РАВР.

3.1.1. Структура РАВР и его связывание с мРНК.

3.1.2. Функции РАВР.

3.2. Мажорный белок цитоплазматических мРНП р и его гомологи с доменами холодового шока (CSD-белки).

3.2.1. Обнаружение р50 и других членов семейства белков с доменами холодового шока.

3.2.2. Строение р50.

3.2.3. Структура генов р50 и его гомологов у позвоночных.

3.2.4. Взаимодействие р50 с РНК.

3.2.5. р50 в биогенезе и функционировании мРНК.

3.2.6. Изменение концентрации р50 в клетке и ее компартментах.

4. Структурная организация цитоплазматических мРНП.

ЭКСПЕРИМЕНТАЛЬНАЯ ЧАСТЬ

МАТЕРИАЛЫ И МЕТОДЫ

1. Выделение рекомбинантного р50 из Escherichia coli.

2. Получение фрагментов р50.

3. Выделение плазмидной ДНК из Escherichia coli.

4. Рестрикция плазмиды.

5. Аналитический электрофорез нуклеиновых кислот в геле агарозы.

6. Получение транскриптов РНК in vitro.

7. Электрофорез РНК в полиакриламидном геле в присутствии мочевины.

8. Препаративное выделение РНК из полиакриламидного геля.

9. Проведение полимеразной цепной реакции (ПЦР).

10. Мечение ДНК 32Р по 5' концу.

11. Электрофорез белков в полиакриламидном геле в присутствии SDS.

12. Сборка комплексов мРНК с р50 и их анализ центрифугированием в градиенте концентрации сахарозы.

13. Центрифугирование комплексов мРНК с р в градиенте плотности CsCl.

14. Определение четвертичной структуры р в комплексе с мРНК методом сшивки глутаровым альдегидом.

15. Исследование взаимодействия белка с РНК методом замедления подвижности РНК в геле (gel-shift assay).

16. Определение относительных контактов доменов р50 с мРНК методом ультрафиолетовых сшивок белка с Р-меченной РНК.

17. Исследование распределения белка р во фракциях градиента CsCl методом Western-dot.

18. Отжиг комплементарных цепей нуклеиновых кислот в присутствии р50.

19. Исследование обмена комплементарных цепей

РНК в присутствии р50 и его фрагментов.

РЕЗУЛЬТАТЫ.

1. Исследование комплексов р50 с мРНК.

1.1. Седиментационная характеристика комплексов р50 с мРНК.

1.2. Плотностное распределение комплексов р50 с мРНК в градиенте CsCl.

1.3. Комплексы р50 с мРНК нестабильны, и белок легко переходит с одной молекулы мРНК на другую.

1.4. При низких соотношениях р50/мРНК белок связывается с мРНК как мономер, в то время как при высоких соотношениях р50 образует на мРНК мультимеры.

1.5. При низких соотношениях р50/мРНК белок связывается с мРНК двумя РНК-связывающими доменами, в то время как при высоких значениях этого соотношения белок взаимодействует с мРНК преимущественно N-концевой

частью молекулы с доменом холодового шока.

2. Влияние р50 на вторичную структуру РНК.

2.1. р50 ускоряет отжиг взаимокомплементарных цепей РНК.

2.2. р50 ускоряет обмен комплементарных цепей в молекулах

РНК и приводит к образованию наиболее протяженных дуплексов.

2.3. р50 вызывает плавление или, наоборот, отжиг

РНК в зависимости от соотношения р50/РНК.

2.4. р50 ускоряет отжиг комплементарных цепей ДНК.

2.5. Фосфорилирование in vitro белка р50 казеинкиназой II снижает его ДНК-отжигающую активность, но не влияет на отжиг РНК.

ОБСУЖДЕНИЕ РЕЗУЛЬТАТОВ.

1. р50 - основной структурообразующий белок цитоплазматических мРНП эукариотических клеток.

2. р50 - шаперон нуклеиновых кислот.

ВЫВОДЫ.

БЛАГОДАРНОСТИ.

Введение диссертации (часть автореферата) на тему «Изучение взаимодействия р50-мажорного белка мРНП - с РНК»

Молекулы мРНК эукариотической клетки синтезируются в клеточном ядре в виде предшественников, образующих фракцию гетерогенных ядерных РНК (гяРНК). Там же в ядре эти предшественники процессируются до зрелых мРНК, которые переносятся через ядерные поры в цитоплазму. В цитоплазме мРНК могут пребывать некоторое время (иногда очень длительное) в нетранслируемом состоянии или ассоциировать с рибосомами и служить матрицами для белкового синтеза. Таким образом, молекулы мРНК имеют «ядерный» и «цитоплазматический» периоды своей истории.

Ядерные предшественники и зрелые мРНК ассоциированы с белками и образуют с ними рибонуклеопротеидные частицы с уникальными свойствами. Исторически первыми в 1964 г были обнаружены и охарактеризованы частицы, содержащие цитоплазматические нетранслируемые мРНК (свободные мРНП) (Spirin, 1964). Эти частицы были названы информосомами. Затем были получены РНП, содержащие гяРНК. Эти частицы получили название гетерогенные ядерные РНП (гяРНП) (Samarina et al., 1966). Наконец, в 1968 г. было показано, что транслируемая мРНК, находящаяся в полисомах, также ассоциирована с белками (Cartouzou et al., 1968; Henshaw, 1968; Perry and Kelley, 1968). Эти полисомные мРНП могут быть выделены после диссоциации рибосом на субчастицы. гяРНП и цитоплазматические мРНП двух классов обладают близкими физико-химическими свойствами, позволяющими объединить их в один тип частиц. А.С. Спирин предложил использовать для этого типа частиц термин информосомы (Spirin, 1964; Spirin, 1969). Согласно этой терминологии можно различать три класса информосом: ядерные, свободные цитоплазматические и полисомные транслируемые. Благодаря их уникальным свойствам, эти частицы можно легко отличить от других типов клеточных РНП. Ниже перечисленны основные характеристики информосом (Preobrazhensky and Spirin, 1978).

1) Информосомы характеризуются широким седиментационным распределением, отражающим гетерогенность мРНК и ее предшественников по размерам в большинстве клеток; существует линейная корреляция между коэффициентом седиментации частиц и РНК, причем коэффициенты седиментации РНП превышают коэффициент седиментации РНК в 2,5 - 3 раза.

2) Все три класса информосом имеют высокое весовое соотношение белок/РНК, равное 3 для ядерных и свободных цитоплазматических РНП и 2 для полисомных; это обуславливает уникальную плавучую плотность в CsCl, равную 1,39 -1,4 г/см3 для ядерных и свободных цитоплазматических РНП и 1,45 г/см3 для полисомных транслируемых мРНП.

3) РНК информосом обладает чрезвычайно высокой чувствительностью к эндорибонуклеазам, что свидетельствует о ее поверхностном расположении в частицах.

Несмотря на сходство основных физико-химических свойств информосом трех классов, набор белков в этих частицах существенно различается, поскольку различаются те функции, которые выполняют эти белки. Белки гяРНП принимают участие в синтезе предшественников мРНК и их процессинге до зрелых мРНК, включая кэпирование 5' конца, укорачивание 3' конца и его последующее полиаденилирование и, наконец, вырезание интронов и соединение экзонов в процессе, получившем название сплайсинг. Белки гяРНП также участвуют в транспорте мРНК из ядра в цитоплазму через ядерные поры. Белки цитоплазматических мРНП регулируют трансляцию, определяют время жизни индивидуальных молекул мРНК и их локализацию в определенных местах цитоплазмы. Таким образом, мРНК при транспорте из ядра в цитоплазму и переходе в полисомы в значительной степени «переодеваются». Вместе с тем, некоторые белки, ассоциированные с мРНК в ядре, выходят вместе с ней в цитоплазму и потом снова возвращаются в ядро. Такие белки получили название челночных белков.

Многочисленные белки, входящие в состав информосом, можно условно подразделить на три группы. Первую группу составляют белки, специфически связывающиеся только с некоторыми мРНК, имеющими участки узнавания для этих белков, например, белки, участвующие в селективной регуляции активности и стабильности мРНК, а также определяющие специфическую локализацию мРНК в клетке. Ко второй группе можно отнести белки, присутствующие на всех или большинстве мРНК, но в единичных копиях и ограниченное время, например ферменты, участвующие в процессинге мРНК, факторы трансляции. В третью группу входят белки, ассоциированные с большинством или всеми мРНК и представленные на них в большом количестве копий. Именно эти белки обнаруживаются как мажоры в суммарных препаратах белков информосом ядра и цитоплазмы. Они выявляются в препаратах информосом из разных клеток и тканей организма и, скорее всего, определяют уникальные физико-химические свойства информосом. Среди мажорных белков ядерных информосом наиболее хорошо изучены белки А1/В2, А2/В1 и С1/С2, а среди цитоплазматических мРНП - р50 и поли(А)-связывающий белок РАВР (goly(A) binding protein). Белки первой и второй группы, напротив, представлены многочисленными минорами в суммарных препаратах информосом, и их набор может сильно варьировать в зависимости от источника получения.

Описанию строения и функционирования минорных белков ядерных и цитоплазматических мРНП посвящено множество обзорных статей, регулярно появляющихся как в отечественной, так и в зарубежной литературе. К сожалению, рассмотрению мажорных белков было уделено гораздо меньше внимания в обзорной литературе, несмотря на растущее ежегодно количество новых данных, касающихся их строения и функционирования. В связи с этим нам показалось очень важным и интересным проанализировать как недавние, так и ранее полученные результаты по этой теме в представленном здесь обзоре литературы, озаглавленном «Мажорные белки ядерных и цитоплазматических мРНП: строение и функционирование».

ОБЗОР ЛИТЕРАТУРЫ

МАЖОРНЫЕ БЕЛКИ ЯДЕРНЫХ И ЦИТОПЛАЗМАТИЧЕСКИХ мРНП: СТРОЕНИЕ И ФУНКЦИОНИРОВАНИЕ

I. Гетерогенные ядерные рибонуклеопротеидные частицы (гяРНП)

Заключение диссертации по теме «Молекулярная биология», Скабкин, Максим Александрович

выводы

1. При насыщении 9S а-глобиновой мРНК мажорным белком мРНП, р50, образуются гомогенные частицы с коэффициентом седиментации около 28S, что примерно соответствует величине коэффициента седиментации природных мРНП (информосом) с мРНК использованного размера.

2. Одного белка р50 достаточно, для формирования с мРНК частиц с плавучей плотностью в CsCl 1,4 г/см3, что соответствует величине плавучей плотности основного плотностного компонента природных мРНП.

3. При низком соотношении р50/мРНК исходно мультимерный р50 связывается с мРНК в виде мономера. При увеличении соотношения р50/мРНК р50 образует на мРНК мультимеры. По мере увеличения соотношения р50/мРНК увеличивается относительный контакт с РНК N-концевой части молекулы р50 с доменом холодового шока и уменьшается относительный контакт с РНК С-концевого домена р50.

4. р50 ускоряет отжиг и обмен комплементарных цепей РНК и способствует образованию наиболее протяженных и совершенных дуплексов.

5. В зависимости от соотношения р50/РНК р50 может вызывать отжиг двойных спиралей РНК (при низких соотношениях р50/мРНК) или, наоборот, их плавление (при высоких значениях этого соотношения).

6. р50 вызывает отжиг комплементарных цепей ДНК, и эта активность белка ингибируется фосорилированием его казеинкиназой II.

БЛАГОДАРНОСТИ

Должен признаться, что эта глава самая приятная для написания и не только потому, что последняя. Здесь я могу поблагодарить тех людей, кто помог мне сделать эту работу, кто воспитывал меня, как научного сотрудника, всех тех, кто создавал приятную творческую атмосферу.

Прежде всего, я глубоко благодарен моему научному руководителю Льву Павловичу Овчинникову. Он взял меня в свою лабораторию еще совершенно необученным и «зеленым». В том, что я сегодня собой представляю, как научный работник, огромная его заслуга. Он пристально и внимательно руководил каждым этапом моей исследовательской работы. Неоценим его вклад и в написании текста диссертации. Особенно я хочу его поблагодарить за создание уникальной творческой и рабочей атмосферы в лаборатории и за выбор в свое время интересной научной темы - изучение белка р50.

Я искренне благодарен Валентину Устинову, который обучил меня множеству методов молекулярной биологии и биохимии и который воспитал во мне аккуратность не только в постановке экспериментов, но и в поддержании порядка на рабочем столе.

Я исключительно признателен Оле Скабкиной за постоянное ее внимание к моей работе и за бесконечное количество консультаций, которые она мне бескорыстно давала не только на работе, но и дома. Также я благодарю ее за ту огромную поддержку, которую она мне всегда оказывала, особенно в трудные для меня моменты.

Я очень благодарен Валентине Евдокимовой за то, что она научила меня «много думать» прежде, чем начинать «много капать». Кроме того, я также благодарю ее за обучение меня многим методам биохимии и молекулярной биологии.

В этой работе есть большой вклад моих коллег - Алексея Сорокина и Константина Чернова. Они помогали мне при выполнении многих экспериментов и им я очень признателен.

Отдельное большое спасибо Елене Соболевой и Елене Кунаевой за огромную помощь в работе, за очень внимательное ко мне отношение и за постоянную заботу о всей лаборатории. Особенно хочу отметить их незаменимый труд и постоянную готовность облегчить работу экспериментатора. Также я благодарю за помощь Нину Гришину.

Я очень признателен моим более старшим коллегам: Елене Давыдовой, Олегу Денисенко, Петру Симоненко, Альберту Ситикову и Елизавете Ковригиной, за внимание, которое они мне уделяли и за постоянную помощь и полезные советы.

Спасибо большое Марии Матыгиной, Максиму Некрасову, Надежде Поповой, Сергею Гурьянову, Дмитрию Лябину и Кириллу Стасевичу за дружеское отношение и готовность всегда помочь.

Я очень признателен Евгении Викторовне Серебровой за помощь в написании диссертационной работы.

Благодарю также всех сотрудников Института белка РАН, с которыми я работал и общался.

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