Структура и функция универсального участка внутреннего связывания рибосомы из мРНК вируса RhPV (Rhopalosiphum padi virus) тема автореферата и диссертации по химии, 02.00.10 ВАК РФ

Список сокращений.

Введение.

Обзор литературы.

Глава I. Молекулярные механизмы инициации трансляции у про- и эукариош.

1. Прокариоты.

1.1 Общий механизм инициации трансляции у прокариот.

1.2 Связывание рибосомы с мРНК и выбор инициаторного кодона.

1.3 Энхансеры трансляции.

1.4 Структура и функции индивидуальных факторов инициации.

1.4.1 IF1.

1.4.2 IF2.

1.4.3 IF3.

2. Эукариоты и Археи.,.

2.1 Археи. ф 2.2 Структура эукариотических мРНК.

2.3 Сканирующая модель инициации трансляции.

2.4 Эукариотические факторы инициации.

2.4.1 elFl.

2.4.2 elFlA.

2.4.3 eIF2.

2.4.4 eIF3.

2.4.5 eIF4A.

2.4.6 eIF4B. w 2.4.7 eIF4F.

2.4.8 eIF5.

2.4.9 eIF5B.

Глава II. Вирус Rhopalosiphum padi.

Результаты и обсуждение.

1. IRES-элемент RhPV эффективно направляет трансляцию в лизате ретикулоцитов кролика.

2. Факторы инициации 4-й группы eIF4A, 4В, 4G не являются абсолютно необходимыми для образования

48S комплекса на 5'-концевом IRES-элементе RhPV.

3. Фактор инициации elFl необходим 40S рибосомной субчастице для достижения инициаторного кодона мРНК RhPV.

4. Анализ целостности мРНК в ходе экспериментов.

5. 5'-IRES RhPV не содержит специфических сайтов связывания с компонентами инициаторного аппарата.

6. Структурный анализ 5'-НТО RhPV

7. Рибосомная 40S субчастица и фактор инициации eIF образуют стабильный комплекс с IRES-элементом RhPV.

Белковый синтез является сложным процессом, регулируемым на нескольких уровнях. Однако после попадания в цитоплазму влиять на эффективность трансляции становится возможным только на уровне стабильности мРНК и скорости образования инициаторных комплексов, и именно эти области регуляции трансляции вызывают повышенный интерес исследователей. Не последнюю роль играет и то, что многие вирусы в процессе эволюции научились перепрограммировать трансляционный аппарат клетки на преимущественное использование вирусных мРНК. Очень часто это достигается именно на стадии инициации за счет наличия в ряде вирусных мРНК сложных структур, называемых участками внутреннего связывания рибосомы или IRES-элементами (от англ. Internal Ribosome Entry Site). Ввиду сложного устройства клеток высших эукариот, до сих пор не разработаны эффективные методы анализа инициации трансляции in vivo. Поэтому, по крайней мере, в ближайшие годы наилучшим методом изучения трансляции останется реконструкция комплексов рибосома*мРНК из очищенных компонентов в сочетании с техникой тоу-принта - ингибирования обратной транскрипции рибосомными комплексами. На сегодняшний день этим методом были определены механизмы инициации трансляции на ряде клеточных и вирусных мРНК.

Как уже упоминалось, мРНК многих вирусов содержит IRES-элементы. Это сложно организованные последовательности РНК, взаимодействующие с определенными компонентами инициаторного аппарата, направляющие рибосому к инициаторному кодону. Ввиду сложности IRES-элементов неудивительно, что большинство их функционирует лишь в определенных организмах, а небольшие вариации их первичной структуры могут в значительно мере понизить или даже свести на нет их активность. В связи с этим представляют интерес те редкие IRES-элементы, которые функционируют в разных организмах, а также обладают «модульной» структурой, поскольку механизм их работы в настоящее время не совсем понятен. Одним из подобных «универсальных» IRES-элементов является IRES, находящийся в 5'-неторанслируемой области (5-НТО) мРНК вируса насекомых RhPV (Rhopalosiphum padi virus). Настоящая работа посвящена исследованию взаимодействий IRES-элемента RhPV с компонентами инициаторного аппарата и механизма его работы.

В ходе данной работы было показано, что необычный IRES-элемент, расположенный в 5'-НТО вируса RhPV, способен образовывать инициаторный 48S комплекс в присутствии «канонических» факторов инициации. Однако, в отличие от известных IRES-элементов, которым факторы группы elF4 либо не нужны вовсе, либо критически необходимы, в данном случае они стимулируют образование 48S комплекса, но не абсолютно необходимы для его образования. Подобная «частичная» зависимость от факторов 4-й группы была подтверждена результатами трансляции в присутствии доминант-негативного мутанта elF4A(R362Q), ингибирующего хеликазную активность фактора elF4F. Помимо этого, было показано, что фактор инициации elF1, участвующий в сканировании, также необходим для инициации на мРНК RhPV.

Показано, что инициация происходит на полноразмерной 5-НТО RhPV, как в присутствии факторов группы elF4, так и в их отсутствие.

Путем последовательного удаления фрагментов 5'-НТО RhPV было продемонстрировано отсутствие каких-либо специфических участков связывания факторов инициации. Оказалось, что только 200 5'-концевых нуклеотидов неспособны функционировать как IRES, в то время как любой другой достаточно протяженный фрагмент 5'-НТО мог направлять внутреннюю посадку рибосомы. Эти результаты были интерпретированы в свете полученных в этой же работе данных по вовлеченности нуклеотидов 5'-НТО RhPV в образование вторичных структур. Было выяснено, что достаточно протяженные фрагменты 5-НТО RhPV, обладающие слаборазвитой вторичной структурой, способны неспецифически привлекать компоненты инициаторного аппарата, в частности, образовывать стабильный тройной комплекс MPHK*elF3*40S.

Полученные данные объясняют, почему IRES-элемент RhPV способен функционировать в различных эукариотических клетках. Эта способность может быть использована при создании универсальных векторов для экспрессии генов в клетках самого разного происхождения.

Обзор литературы.

выводы

1. Исследован механизм образования 48S инициаторного комплекса на 5'-концевом IRES-элементе мРНК RhPV (Rhopalosiphum padi virus). Показано, что для инициации на данном IRESe необходимы факторы инициации elF1, elF2, elF3. Факторы e!F1A и elF4G с 4А существенно стимулировали образование 48S, в то время как elF4B не оказывал никакого влияния.

2. Охарактеризована вторичная структура 5'-НТО мРНК RhPV.

3. Показано, что активность IRES-элемента RhPV определяется AUG-проксимальной U-богатой последовательностью мРНК, находящейся преимущественно в одноцепоцечной конформации.

4. Установлено, что данная последовательность способна образовывать стабильный комплекс с 40S субчастицей и фактором инициации elF3.

5. Показана принципиальная возможность связывания 40S рибосомной субчастицы с неструктурированными внутренними участками мРНК с последующим образованием инициаторного комплекса.

МАТЕРИАЛЫ И МЕТОДЫ

1. Реактивы и материалы.

В работе были использованы следующие реактивы и материалы: немеченые дезоксирибонуклеозид-5'-трифосфаты, рибонукпеозид-5'-трифосфаты фирмы Pharmacia (Швеция), a-[32P]-dATP и у-[32Р]-АТР из Обнинска, [353]-метионин фирм Amersham Biosciences и ICN Radiochemicals (последний любезно предоставлен Т.В.Пестовой). 1,4-дитио-0,1-треитол (DTT); |3-меркаптоэтанол фирмы Serva (Германия); акриламид, N.N'-метиленбисакриламид, персульфат аммония и N,N,N',N'-тетраметилэтилендиамин фирм Serva (Германия), Reanal (Венгрия) и Хеликон (Россия); агароза фирмы Sigma (США), СМСТ фирмы Pierce (Франция), DMS фирмы Aldrich, PMSF (Хеликон). В качестве красителей для электрофореза использовали бромфеноловый синий фирмы Merck (Германия), кселенцианол фирмы Chemicals (Англия). Использовали неорганические реагенты фирм Sigma (США) и Merck (Германия). В работе использовали бактоагар, бактотриптон, дрожжевой экстракт фирмы DIFCO (США); ампициллин и канамицин завода "Синтез" (Пенза). Использованные в данной работе олигонуклеотиды были синтезированы на фирмах Synthol и ЛИТЕХ (обе - Россия).

Биопрепараты: обратная транскриптаза из AMV фирмы Promega (США), ингибитор рибонуклеаз фирмы Fermentas (Литва), рибонуклеазы Т1, Т2 и V1, эндонуклеазы рестрикции фирм Fermentas и Сибэнзим (Россия), полинуклеотидкиназа, ДНК-лигаза и ДНК-полимераза фага Т4, РНК-полимераза фага Т7 фирмы Fermentas, набор для секвенирования ДНК фирмы USB (США), маркеры молекулярного веса ДНК и белков фирм Fermentas и GibcoBRL (США), свободная от РНКаз ДНКаза RQ1 фирмы Promega (США).

При клонировании использовали штаммы Е. coir. JM109 - для выделения плазмид, BL21, BL21(DE3) и BL21(DE3)RIL - для получения рекомбинантных белков.

2. Плазмидные конструкции.

Плазмида pLuc была создана путем вставки содержащего последовательность люциферазы Firefly фрагмента BamHI-Xhol из плазмиды pGEM-Luc (Promega) в аналогично порезанную плазмиду pSP72 (Promega). Для создания плазмиды pRhPV-Luc, фрагмент BamHl- BamHI из плазмиды pGEM-CAT/RhPVA1/LUC [491] был лигирован в порезанную по ВатН1-сайту плазмиду pLuc. Во избежание каких-либо эффектов чужеродной нуклеотидной последовательности, остаток полилинкера pSP72 был удален путем вырезания из pRhPV-Luc фрагмента ДНК между сайтов Bsal и BamHI.

Заключение

Из представленных данных можно заключить, что функционально активной частью изучаемого IRES-элемента является слабоструктурированная 3'-концевая область. Можно утверждать также, что IRES-элемент RhPV из 5'-НТО его мРНК не содержит высокоспецифичных сайтов связывания компонентов инициаторного аппарата. Именно этим объясняется способность данного IRESa функционировать в различных системах в противоположность IRES-элементам афто-, пести- и флавивирусов, которые обладают сродством к факторам инициации и/или рибосомным субчастицам только из клеток млекопитающих, и, потому, способны направлять трансляцию только в соответствующих системах.

По всей видимости, данный IRES вместо рекрутирования трансляционного аппарата посредством одного высокоспецифичного сайта работает посредством множества тандемных низкоафинных сайтов, которые, будучи расположенными в непосредственной близости друг от друга, способствуют достаточному для эффективной трансляции повышению локальной концентрации факторов инициации (напр., elF4G и elF3) и/или рибосом вблизи инициаторного AUG-кодона. Этим объясняется уникальная возможность удалять значительные участки IRES-элемента без потери активности, что является существенным отличием от «классических» IRES-элементов, в случае которых замены или делеции даже одного нуклеотида приводят к полной потере активности. Можно предположить, что минимальный размер индивидуального сайта посадки должен быть достаточным чтобы вместить хотя бы одну 40S субчастицу и elF3, т.е. иметь размер порядка 50- 100 нуклеотидов.

Можно предположить, что 40S рибосомная субчастица (при содействии elF3) способна связывать одноцепочечный U-богатый 54RES RhPV даже в отсутствие факторов группы elF4. Образовавшийся комплекс способен связывать тройной комплекс elF2*TPHK*GTP и осуществлять зависимое от elF1 сканирование в поисках AUG-кодона. Подобный механизм очень напоминает последовательность событий в прокариотах, где первичное связывание с мРНК осуществляет в U-богатых областях рибосомный белок S1, а функции elF1 выполняет IF3.

Образование 485-комплексов в отсутствие факторов 4-й группы и АТР было описано для искусственной мРНК, содержавшей 100% неструктурированную 5-НТО, состоявшую из 19 повторов САА [235]. Однако, данный лидер не функционировал как область внутренней посадки рибосомы. По всей видимости, это объясняется тем, что авторы использовали слишком короткую последовательность (около 40 нуклеотидов). Хотя нельзя исключать возможность влияния нуклеотидного состава одноцепочечных областей на эффективность их работы в качестве IRES-элементов, о возможности направлять трансляцию в различных бесклеточных системах, а также in vivo, сообщалось для IRESob, представленных длинными богатыми пуриновыми нуклеотидами последовательностями [493].

Наши данные не позволяют нам утверждать, что любая одноцепочечная последовательность мРНК может работать как IRES в любых in vitro или in vivo системах. Тем не менее, они показывают, что для эукариотической рибосомы не существует никаких препятствий для связывания с внутренними участками мРНК, в отсутствие специфических участков связывания. Это противоречит строгим правилам сканирующей модели в ее классическом виде, но, в тоже время, существенно дополняет ее. Таким образом, наши данные являются еще одним доказательством сходства аппаратов инициации эукариот и прокариот.

Необходимо отметить, что низкое содержание остатков гуанина и цитидина в 5'-НТО, как это имеет место в случае мРНК RhPV, не является характерным для остальных представителей рода криповирусов (CrPV, Drosophila С virus, Shrimp paralysis virus, Plautia stali intestinal virus и ряда других), которые, по всей видимости, содержат «классические» IRESbi, т.к. их 5'-НТО имеют большое содержание гуанина и цитидина, а также содержат множественные AUG-кодоны, некоторые из которых находятся в оптимальном нуклеотидном окружении. Примечательно, что 54RES CrPV, в отличие от RhPV, не функционирует в экстракте проростков пшеницы [482].

1. Gualerzi, С. О. and Роп, С. L. (1990) Initiation of mRNA translation in prokaryotes Biochemistry 29, pp.5881-5889.

2. Kozak, M. (1999) Initiation of translation in prokaryotes and eukaryotes Gene 234, pp. 187-208.

3. McCarthy, J. E. and Brimacombe, R. (1994) Prokaryotic translation: the interactive pathway leading to initiation Trends Genet. 10, pp.402-407.

4. Voorma, Н. O. (1996) Control of translation initiation in prokaryotes. In Translational Control of Gene Expression (ed. Sonenberg,N., Mathews, M.B., and Hershey J.W.B.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp.759-777.

5. Zucker, F. H. and Hershey, J. W. (1986) Binding of Escherichia coli protein synthesis initiation factor IF1 to 30S ribosomal subunits measured by fluorescence polarization Biochemistry 25, pp.36823690.

6. Gualerzi, C., Risuleo, G., and Pon, C. L. (1977) Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3 Biochemistry 16, pp.1684-1689.

7. Wintermeyer, W. and Gualerzi, C. (1983) Effect of Escherichia coli initiation factors on the kinetics of N-Acphe-tRNAPhe binding to 30S ribosomal subunits. A fluorescence stopped-flow study Biochemistry 22, pp.690-694.

8. Wu, X. Q., Iyengar, P., and RajBhandary, U. L. (1996) Ribosome-initiator tRNA complex as an intermediate in translation initiation in Escherichia coli revealed by use of mutant initiator tRNAs and specialized ribosomes EMBOJ. 15, pp.4734-4739.

9. Wu, X. Q. and RajBhandaiy, U. L. (1997) Effect of the amino acid attached to Escherichia coli initiator tRNA on its affinity for the initiation factor IF2 and on the IF2 dependence of its binding to the ribosome J.Biol.Chem. 212, pp.1891-1895.

10. Allen, G. S., Zavialov, A., Gursky, R., Ehrenberg, M., and Frank, J. (2005) The cryo-EM structure of a translation initiation complex from Escherichia coli Cell 2005. Jun.3;121. (5):703.-12. 121, pp.703-712.

11. Butler, J. S., Springer, M., Dondon, J., Graffe, M., and Grunberg-Manago, M. (1986) Escherichia coli protein synthesis initiation factor IF3 controls its own gene expression at the translational level in vivo J.Mol.Biol. 192, pp.767-780.

12. Balakin, A. G., Skripkin, E. A., Shatsky, I. N., and Bogdanov, A. A. (1992) Unusual ribosome binding properties of mRNA encoding bacteriophage lambda repressor Nucleic Acids Res. 20, pp.563571.

13. Shine, J. and Dalgarno, L. (1974) The З'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites Proc.Natl.Acad.Sci. USA 71, pp.1342-1346.

14. Steitz, J. A. and Jakes, K. (1975) How ribosomes select initiator regions in mRNA: base pair fomiation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli Proc.Natl.Acad.Sci. USA 72, pp.4734-4738.

15. Shine, J. and Dalgarno, L. (1975) Determinant of cistron specificity in bacterial ribosomes Nature 254, pp.34-38.

16. Hui, A. and de Boer, H. A. (1987) Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli Proc.Natl.Acad.Sci. U SA 84, pp.4762-4766.

17. Jacob, W. F., Santer, M., and Dahlberg, A. E. (1987) A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins Proc.Natl.Acad.Sci. USA 84, pp.4757-4761.

18. Hartz, D., McPheeters, D. S., Green, L., and Gold, L. (1991) Detection of Escherichia coli ribosome binding at translation initiation sites in the absence of tRNA J.Mol.Biol. 218, pp.99-105.

19. Tl. Hartz, D., McPheeters, D. S., Traut, R., and Gold, L. (1988) Extension inhibition analysis of translation initiation complexes Methods Enzymol. 164, pp.419-425.

20. Hartz, D., Binkley, J., Hollingsworth, Т., and Gold, L. (1990) Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3 Genes Dev. 4, pp.1790-1800.

21. Huttenhofer, A. and Noller, H. F. (1994) Footprinting mRNA-ribosome complexes with chemical probes EMBOJ. 13, pp.3892-3901.

22. Komarova, A. V., Tchufistova, L. S., Supina, E. V., and Boni, I. V. (2002) Protein SI counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation RNA 8, pp.1137-1147.

23. Pedersen, 1С., Zavialov, A. V., Pavlov, M. Y., Elf, J., Gerdes, 1С., and Ehrenberg, M. (2003) The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site Cell 112, pp.131-140.

24. Hauryliuk V. and Ehrenberg, M., личное сообщение.34. de Boer, H. A., Comstock, L. J., Hui, A., Wong, E., and Vasser, M. (1983) A hybrid promoter and portable Shine-Dalgarno regions of Escherichia coli Biochem.Soc.Symp. 48, pp.233-244.

25. Hager, P. W. and Rabinowitz, J. C. (1985) Inefficient translation of T7 late mRNA by Bacillus subtilis ribosomes. Implications for species-specific translation J.Biol.Chem. 260, pp.15163-15167.

26. Stallcup, M. R., Sharrock, W. J., and Rabinowitz, J. C. (1974) Ribsome and messenger specificity in protein synthesis by bacteria Biochem.Biophys.Res.Commun. 58, pp.92-98.

27. Stallcup, M. R., Sharrock, W. J., and Rabinowitz, J. C. (1976) Specificity of bacterial ribosomes and messenger ribonucleic acids in protein synthesis reactions in vitro J.Biol.Chem. 251, pp.2499-2510.

28. Band, L. and Henner, D. J. (1984) Bacillus subtilis requires a "stringent" Shine-Dalgarno region for gene expression DNA 3, pp.17-21.

29. Lodish, H. F. (1969) Species specificity of polypeptide chain initiation Nature 224, pp.867-870.

30. McLaughlin, J. R., Murray, C. L., and Rabinowitz, J. C. (1981) Unique features in the ribosome binding site sequence of the gram-positive Staphylococcus aureus beta-lactamase gene J.Biol.Chem. 256, pp.11283-11291.

31. Stallcup, M. R. and Rabinowitz, J. C. (1973) Initiation of protein synthesis in vitro by a clostridial system. I. Specificity in the translation of natural messenger ribonucleic acids J.Biol.Chem. 248, pp.3209-3215.

32. Calogero, R. A., Pon, C. L., Canonaco, M. A., and Gualerzi, С. O. (1988) Selection of the mRNA translation initiation region by Escherichia coli ribosomes Proc.Natl.Acad.Sci. USA 85, pp.64276431.

33. Gallie, D. R. and Kado, С. I. (1989) A translational enhancer derived from tobacco mosaic virus is functionally equivalent to a Shine-Dalgarno sequence Proc.Natl.Acad.Sci. USA 86, pp.129-132.

34. Ivey-Hoyle, M. and Steege, D. A. (1992) Mutational analysis of an inherently defective translation initiation site J.Mol.Biol. 224, pp.1039-1054.

35. Loechel, S., Inamine, J. M., and Ни, P. C. (1991) A novel translation initiation region from Mycoplasma genitalium that functions in Escherichia coli Nucleic Acids Res. 19, pp.6905-6911.

36. Porter, A. G. and Hindley, J. (1972) Characterization of extended sequences around the coat and replicase cistron ribosome binding sites in phage Q RNA FEBSLett. 26, pp.139-144.

37. Smiley, B. L., Lupski, J. R., Svec, P. S., McMacken, R., and Godson, G. N. (1982) Sequences of the Escherichia coli dnaG primase gene and regulation of its expression Proc.Natl.Acad.Sci. USA19, pp.4550-4554.

38. Melancon, P., Leclerc, D., Destroismaisons, N., and Brakier-Gingras, L. (1990) The anti-Shine-Dalgarno region in Escherichia coli 16S ribosomal RNA is not essential for the correct selection of translational starts Biochemistry 29, pp.3402-3407.

39. Roberts, M. W. and Rabinowitz, J. C. (1989) The effect of Escherichia coli ribosomal protein SI on the translational specificity of bacterial ribosomes J.Biol.Chem. 264, pp.2228-2235.

40. Sorensen, M. A., Fricke, J., and Pedersen, S. (1998) Ribosomal protein SI is required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo J.Mol.Biol. 280, pp.561-569.

41. Szer, W., Hermoso, J. M., and Leffler, S. (1975) Ribosomal protein SI and polypeptide chain initiation in bacteriaProc.Natl.Acad.Sci.USA 72, pp.2325-2329.

42. Tedin, K., Resch, A., and Blasi, U. (1997) Requirements for ribosomal protein SI for translation initiation of mRNAs with and without a 5' leader sequence Mol.Microbiol. 25, pp. 189-199.

43. Van, Dieijen G., Van Der Laken, C. J., Van Knippenberg, P. H., and van, Duin J. (1975) Function of Escherichia coli ribosomal protein SI in translation of natural and synthetic messenger RNA J.Mol.Biol. 93, pp.351-366.

44. Van, Dieijen G., Van Knippenberg, P. H., and van, Duin J. (1976) The specific role of ribosomal protein SI in the recognition of native phage RNA Eur.J.Biochem. 64, pp.511-518.

45. Farwell, M. A., Roberts, M. W., and Rabinowitz, J. C. (1992) The effect of ribosomal protein SI from Escherichia coli and Micrococcus luteus on protein synthesis in vitro by E. coli and Bacillus subtilis Mol.Microbiol. 6, pp.3375-3383.

46. Tzareva, N. V., Makhno, V. I., and Boni, I. V. (1994) Ribosome-messenger recognition in the absence of the Shine-Dalgarno interactions FEBS Lett. 337, pp.189-194.

47. Boni, I. V., Isaeva, D. M., Musychenko, M. L., and Tzareva, N. V. (1991) Ribosome-messenger recognition: mRNA target sites for ribosomal protein SI Nucleic Acids Res. 19, pp. 155-162.

48. Subramanian, A. R. (1983) Structure and functions of ribosomal protein S1 Prog.Nucleic Acid Res.Mol.Biol. 28, pp.101-142.

49. Sengupta, J., Agrawal, R. K., and Frank, J. (2001) Visualization of protein SI within the 30S ribosomal subunit and its interaction with messenger RNA Proc.Natl.Acad.Sci. USA 98, pp.1199111996.

50. Ganoza, M. C. and Fox, J. L. (1974) Isolation of a soluble factor needed for protein synthesis with various messenger ribonucleic acids other than poly(U) J.Biol.Chem. 249, pp.1037-1043.

51. Lu, J., Aoki, H., and Ganoza, M. C. (1999) Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF4A Int.J.Biochem.Cell Biol. 31, pp.215-229.

52. Ganoza, M. C., Kiel, M. C., and Aoki, H. (2002) Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 66, pp.460-85.

53. Tanner, N. K., Cordin, O., Banroques, J., Doere, M., and Linder, P. (2003) The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis Mol.Cell 11, pp. 127138.

54. Abramson, R. D., Dever, Т. E., Lawson, T. G., Ray, В. K., Thach, R. E., and Merrick, W. C. (1987) The ATP-dependent interaction of eukaryotic initiation factors with mRNA J.Biol.Chem. 262, pp.3 826-3 832.

55. Jones, P. G., Mitta, M., Kim, Y., Jiang, W., and Inouye, M. (1996) Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli Proc.Natl.Acad.Sci. USA 93, pp.76-80.

56. Moll, I., Grill, S., Grundling, A., and Blasi, U. (2002) Effects of ribosomal proteins SI, S2 and the DeaD/CsdA DEAD-box helicase on translation of leaderless and canonical mRNAs in Escherichia coli Mol.Microbiol. 44, pp.1387-1396.

57. Toone, W. M., Rudd, К. E., and Friesen, J. D. (1991) deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB, the gene encoding ribosomal protein S2 J.Bacteriol. 173, pp.3291-3302.

58. Nishi, K., Morel-Deville, F„ Hershey, J. W., Leighton, Т., and Schnier, J. (1988) An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosomal subunit assembly Nature 336, pp.496-498.

59. Dreyfus, M. (1988) What constitutes the signal for the initiation of protein synthesis on Escherichia coli mRNAs? J.Mol.Biol. 204, pp.79-94.

60. Gold, L., Pribnow, D., Schneider, Т., Shinedling, S., Singer, B. S., and Stormo, G. (1981) Translational initiation in prokaryotes Annu.Rev.Microbiol. 35, pp.365-403.

61. Gold, L. (1988) Posttranscriptional regulatory mechanisms in Escherichia coli. Annu.Rev.Biochem. 57, pp. 199-233.

62. Stormo, G. D., Schneider, T. D., and Gold, L. M. (1982) Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 10, pp.2971-2996.

63. Fargo, D. C., Zhang, M., Gillham, N. W., and Boynton, J. E. (1998) Shine-Dalgarno-like sequences are not required for translation of chloroplast mRNAs in Chlamydomonas reinhardtii chloroplasts or in Escherichia coli Mol.Gen.Genet. 257, pp.271-282.

64. Olins, P. O., Devine, C. S., Rangwala, S. H., and Kavka, K. S. (1988) The T7 phage gene 10 leader RNA, a ribosome-binding site that dramatically enhances the expression of foreign genes in Escherichia coli Gene 1Ъ, pp.227-235.

65. Petersen, C. (1987) The functional stability of the lacZ transcript is sensitive towards sequence alterations immediately downstream of the ribosome binding site Mol.Gen.Genet. 209, pp. 179-187.

66. Olins, P. O. and Rangwala, S. H. (1989) A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of the lacZ gene in Escherichia coli J.Biol.Chem. 264,pp.16973-16976.

67. McCarthy, J. E., Schairer, H. U., and Sebald, W. (1985) Translational initiation frequency of atp genes from Escherichia coli: identification of an intercistronic sequence that enhances translation EMBO J. 4, pp.519-526.

68. McCarthy, J. E., Sebald, W., Gross, G., and Lammers, R. (1986) Enhancement of translational efficiency by the Escherichia coli atpE translational initiation region: its fusion with two human genes Gene 41, pp.201-206.

69. Golshani, A., Golomehova, V., Mironova, R., Ivanov, I. G., and AbouHaidar, M. G. (1997) Does the epsilon sequence of phage T7 function as an initiator for the translation of CAT mRNA in Escherichia coli? Biochem.Biophys.Res.Commun. 236, pp.253-256.

70. Sandler, S. J. and Clark, A. J. (1994) Mutational analysis of sequences in the recF gene of Escherichia coli K-12 that affect expression J.Bacteriol. 176, pp.4011-4016.

71. Petersen, C. (1991) Multiple determinants of functional mRNA stability: sequence alterations at either end of the lacZ gene affect the rate of mRNA inactivation J.Bacteriol. 173, pp.2167-2172.

72. Stanssens, P., Remaut, E., and Fiers, W. (1986) Inefficient translation initiation causes premature transcription termination in the lacZ gene Cell 44, pp.711-718.

73. Sprengart, M. L., Fuchs, E., and Porter, A. G. (1996) The downstream box: an efficient and independent translation initiation signal in Escherichia coli EMBO J. 15, pp.665-674.

74. Sprengart, M. L., Fatscher, H. P., and Fuchs, E. (1990) The initiation of translation in E. coli: apparent base pairing between the 16srRNA and downstream sequences of the mRNA Nucleic Acids Res. 18, pp. 1719-1723.

75. Faxen, M., Plumbridge, J., and Isaksson, L. A. (1991) Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal RNA affects expression of glnS Nucleic Acids Res. 19, pp.5247-5251.

76. Ito, K., Kawakami, K., and Nakamura, Y. (1993) Multiple control of Escherichia coli lysyl-tRNA synthetase expression involves a transcriptional repressor and a translational enhancer element Proc.Natl.Acad.Sci. USA 90, pp.302-306.

77. Nagai, H., Yuzawa, H., and Yura, T. (1991) Interplay of two cis-acting mRNA regions in translational control of sigma 32 synthesis during the heat shock response of Escherichia coli Proc.Natl.Acad.Sci.USA 88, pp. 10515-10519.

78. Shean, C. S. and Gottesman, M. E. (1992) Translation of the prophage lambda cl transcript Cell 70, pp.513-522.

79. Resch, A., Tedin, K., Graschopf, A., Haggard-Ljungquist, E., and Blasi, U. (1995) Ternary complex formation on leaderless phage mRNA FEMS Microbiol.Rev. 17, pp.151-157.

80. Chen, G. F. and Inouye, M. (1990) Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes Nucleic Acids Res. 18, pp. 1465-1473.

81. Goldman, E., Rosenberg, A. H., Zubay, G., and Studier, F. W. (1995) Consecutive low-usage leucine codons block translation only when near the 5' end of a message in Escherichia coli J.Mol.Biol. 245, pp.467-473.

82. Spanjaard, R. A., Chen, K., Walker, J. R., and van, Duin J. (1990) Frameshift suppression at tandem AGA and AGG codons by cloned tRNA genes: assigning a codon to argU tRNA and T4 tRNA(Arg) Nucleic Acids Res. 18, pp.5031-5036.

83. Resch, A., Tedin, K., Grundling, A., Mundlein, A., and Blasi, U. (1996) Downstream box-anti-downstream box interactions are dispensable for translation initiation of leaderless mRNAs EMBO J. 15, pp.4740-4748.

84. Etchegaray, J. P., Xia, В., Jiang, W., and Inouye, M. (1998) Downstream box: a hidden translational enhancer Mol.Microbiol. 27, pp.873-874.

85. Etchegaray, J. P. and Inouye, M. (1999) Translational enhancement by an element downstream of the initiation codon in Escherichia coli J.Biol.Chem. 274, pp. 10079-10085.

86. Blasi, U., O'Connor, M., Squires, C. L., and Dahlberg, A. E. (1999) Misled by sequence complementarity: does the DB-anti-DB interaction withstand scientific scrutiny? Mol.Microbiol. 33, pp.43 9-441.

87. Moll, I., Huber, M., Grill, S., Sairafi, P., Mueller, F., Brimacombe, R., Londei, P., and Blasi, U. (2001) Evidence against an Interaction between the mRNA downstream box and 16S rRNA in translation initiation J.Bacteriol. 183, pp.3499-3505.

88. La, Teana A., Brandi, A., O'Connor, M., Freddi, S., and Pon, C. L. (2000) Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box RNA 6, pp.1393-1402.

89. O'Connor, M., Asai, Т., Squires, C. L., and Dahlberg, A. E. (1999) Enhancement of translation by the downstream box does not involve base pairing of mRNA with the penultimate stem sequence of 16S rRNA Proc.Natl.Acad.Sci. USA 96, pp.8973-8978.

90. Komarova, A. V., Tchufistova, L. S., Dreyfus, M., and Boni, I. V. (2005) AU-rich sequences within 5' untranslated leaders enhance translation and stabilize mRNA in Escherichia coli J.Bacteriol. 187, pp.1344-1349.

91. Kyrpides, N. C. and Woese, C. R. (1998) Universally conserved translation initiation factors Proc.Natl.Acad.Sci. USA 95, pp.224-228.

92. Sorensen, H. P., Hedegaard, J., Sperling-Petersen, H. U., and Mortensen, К. K. (2001) Remarkable conservation of translation initiation factors: IFl/elFIA and IF2/eIF5B are universally distributed phylogenetic markers IUBMB.Life 51, pp.321-327.

93. Battiste, J. L., Pestova, Т. V., Hellen, C. U., and Wagner, G. (2000) The elFIA solution structure reveals a large RNA-binding surface important for scanning function Mol.Cell 5, pp.109-119.

94. Li, W. and Hoffman, D. W. (2001) Structure and dynamics of translation initiation factor aIF-1 A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy Protein Sci. 10, pp.24262438.

95. Sette, M., van, Tilborg P., Spurio, R., Kaptein, R., Paci, M., Gualerzi, С. O., and Boelens, R. (1997) The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motifEMBOJ. 16, pp.1436-1443.

96. Bycrofit, M., Hubbard, T. J., Proctor, M., Freund, S. M., and Murzin, A. G. (1997) The solution structure of the SI RNA binding domain: a member of an ancient nucleic acid-binding fold Cell 88, pp.23 5-242.

97. Kim, К. K., Hung, L. W., Yokota, H., Kim, R., and Kim, S. H. (1998) Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution Proc.Natl.Acad.Sci. U SA 95, pp.10419-10424.

98. Nonato, M. C., Widom, J., and Clardy, J. (2002) Crystal structure of the N-terminal segment of human eukaryotic translation initiation factor 2alpha J.Biol.Chem. 277, pp. 17057-17061.

99. Weber, M. H., Beckering, C. L., and Marahiel, M. A. (2001) Complementation of cold shock proteins by translation initiation factor IF1 in vivo J.Bacteriol. 183, pp.7381-7386.

100. Moazed, D., Samaha, R. R., Gualerzi, C., andNoller, H. F. (1995) Specific protection of 16 S rRNA by translational initiation factors J.Mol.Biol. 248, pp.207-210.

101. Dahlquist, K. D. and Puglisi, J. D. (2000) Interaction of translation initiation factor IF1 with the E. coli ribosomal A sitq J.Mol.Biol. 299, pp.1-15.

102. Banerjee, A. K. (1980) 5'-terminaI cap structure in eucaryotic messenger ribonucleic acids Microbiol.Rev. 44, pp. 175-205.

103. Dottavio-Martin, D., Suttle, D. P., and Ravel, J. M. (1979) The effects of initiation factors IF-1 and IF-3 on the dissociation of Escherichia coli 70 S ribosomes FEBS Lett. 97, pp. 105-110.

104. Pon, C. L. and Gualerzi, С. O. (1984) Mechanism of protein biosynthesis in prokaryotic cells. Effect of initiation factor IF1 on the initial rate of 30 S initiation complex formation FEBS Lett. 175, pp.203-207.

105. Celano, В., Pawlik, R. Т., and Gualerzi, С. O. (1988) Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes Eur.J.Biochem. 178, pp.351-355.

106. Moreno, J. M., Drskjotersen, L., Kristensen, J. E., Mortensen, К. K., and Sperling-Petersen, H. U. (1999) Characterization of the domains of E. coli initiation factor IF2 responsible for recognition of the ribosome FEBS Lett. 455, pp. 13 0-134.

107. Stringer, E. A., Sarkar, P., and Maitra, U. (1977) Function of initiation factor 1 in the binding and release of initiation factor 2 from ribosomal initiation complexes in Escherichia coli J.Biol.Chem. 252, pp.1739-1744.

108. Canonaco, M. A., Calogero, R. A., and Gualerzi, С. O. (1986) Mechanism of translational initiation in prokaryotes. Evidence for a direct effect of IF2 on the activity of the 30 S ribosomal subunit FEBS Lett. 207, pp. 198-204.

109. Meinnel, Т., Sacerdot, C., Graffe, M.s Blanquet, S., and Springer, M. (1999) Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules J.Mol.Biol. 290, pp.825-837.

110. Howe, J. G. and Hershey, J. W. (1983) Initiation factor and ribosome levels are coordinately controlled in Escherichia coli growing at different rates J.Biol.Chem. 258, pp.1954-1959.

111. Bae, W., Xia, В., Inouye, M., and Severinov, It. (2000) Escherichia coli CspA-family RNA chaperones are transcription antitenninators Proc.Natl.Acad.Sci. 97, pp.7784-7789.

112. Giuliodori, A. M., Brandi, A., Gualerzi, С. O., and Pon, C. L. (2004) Preferential translation of cold-shock mRNAs during cold adaptation RNA 10, pp.265-276.

113. Caldas, Т., Laalami, S., and Richarme, G. (2000) Chaperone properties of bacterial elongation factor EF-G and initiation factor IF2 J.Biol.Chem. 275, pp.855-860.

114. Meunier, S., Spurio, R., Czisch, M., Wechselberger, R., Guenneugues, M., Gualerzi, С. O., and Boelens, R. (2000) Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2 EMBO J. 19, pp.1918-1926.

115. Pestova, Т. V., Kolupaeva, V. G., Lomakin, I. В., Pilipenko, E. V., Shatsky, I. N., Agol, V. I., and Hellen, C. U. (2001) Molecular mechanisms of translation initiation in eukaryotes Proc.Natl.Acad.Sci.USA 98, pp.7029-7036.

116. Roll-Mecak, A., Shin, B. S., Dever, Т. E., and Burley, S. It. (2001) Engaging the ribosome: universal IFs of translation Trends Biochem.Sci. 26, pp.705-709.

117. Roll-Mecak, A., Cao, C., Dever, Т. E., and Burley, S. It. (2000) X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding Cell 103, pp.781-792.

118. Sundari, R. M., Stringer, E. A., Schulman, L. H., and Maitra, U. (1976) Interaction of bacterial initiation factor 2 with initiator tRNA J.Biol.Chem. 251, pp.3338-3345.

119. La, Teana A., Gualerzi, С. O., and Dahlberg, A. E. (2001) Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA RNA 7, pp.1173-1179.

120. Tomsic, J., Vitali, L. A., Daviter, Т., Savelsbergh, A., Spurio, R., Striebeck, P., Wintermeyer, W., Rodnina, M. V., and Gualerzi, С. O. (2000) Late events of translation initiation in bacteria: a kinetic analysis EMBO J. 19, pp.2127-2136.

121. Antoun, A., Pavlov, M. Y., Andersson, It., Tenson, Т., and Ehrenberg, M. (2003) The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis EMBO J. 22, pp.55935601.

122. Lin, Q., Yu, N. J., and Spremulli, L. L. (1996) Expression and functional analysis of Euglena Gracilis chloroplast initiation factor 3 Plant Mol.Biol. 32, pp.937-945.

123. Yu, N. J. and Spremulli, L. L. (1997) Structural and mechanistic studies on chloroplast translational initiation factor 3 from Euglena gracilis Biochemistry 36, pp.14827-14835.

124. Yu, N. J. and Spremulli, L. L. (1998) Regulation of the activity of chloroplast translational initiation factor 3 by NH2- and COOH-terminal extensions J.Biol.Chem. 273, pp.3871-3877.

125. Garcia, C., Fortier, P. L., Blanquet, S., Lallemand, J. Y., and Dardel, F. (1995) 1H and 15N resonance assignments and structure of the N-terminal domain of Escherichia coli initiation factor 3 Eur.J.Biochem. 228, pp.395-402.

126. Biou, V., Shu, F., and Ramakrishnan, V. (1995) X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix EMBO J. 14, pp.4056-4064.

127. Fortier, P. L., Schmitter, J. M., Garcia, C., and Dardel, F. (1994) The N-terminal half of initiation factor IF3 is folded as a stable independent domain Biochimie 16, pp.376-383.

128. Kycia, J. H., Biou, V., Shu, F., Gerchman, S. E., Graziano, V., and Ramakrishnan, V. (1995) Prokaryotic translation initiation factor IF3 is an elongated protein consisting of two crystallizable domains Biochemistry 34, pp.6183-6187.

129. Sette, M., Spurio, R., van, Tilborg P., Gualerzi, С. O., and Boelens, R. (1999) Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy RNA 5, pp.82-92.

130. Petrelli, D., LaTeana, A., Garofalo, C., Spurio, R., Pon, C. L., and Gualerzi, С. O. (2001) Translation initiation factor IF3: two domains, five functions, one mechanism? EMBOJ. 20, pp.45604569.

131. Shapkina, T. G., Dolan, M. A., Babin, P., and Wollenzien, P. (2000) Initiation factor 3-induced structural changes in the 30 S ribosomal subunit and in complexes containing tRNA(f)(Met) and mRNA J.Mol.Biol. 299, pp.615-628.

132. Tedin, K., Moll, I., Grill, S., Resch, A., Graschopf, A., Gualerzi, С. O., and Blasi, U. (1999) Translation initiation factor 3 antagonizes authentic start codon selection on leaderless mRNAs Mol.Microbiol. 31, pp.67-77.

133. Gualerzi, C., Pon, C. L., and Kaji, A. (1971) Initiation factor dependent release of aminoacyl-tRNAs from complexes of 30S ribosomal subunits, synthetic polynucleotide and aminoacyl tRNA Biochem.Biophys.Res.Commun. 45, pp.1312-1319.

134. Haggerty, T. J. and Lovett, S. T. (1997) IF3-mediated suppression of a GUA initiation codon mutation in the recJ gene of Escherichia coli J.Bacteriol. 179, pp.6705-6713.

135. Pon, C. L. and Gualerzi, C. (1974) Effect of initiation factor 3 binding on the 30S ribosomal subunits of Escherichia coli Proc.Natl.Acad.Sci. USA 71, pp.4950-4954.

136. Sussman, J. K., Simons, E. L., and Simons, R. W. (1996) Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo Mol.Microbiol. 21, pp.347-360. .

137. Hartz, D., McPheeters, D. S., and Gold, L. (1989) Selection of the initiator tRNA by Escherichia coli initiation factors Genes Dev. 3, pp.1899-1912.

138. La, Teana A., Pon, C. L., and Gualerzi, С. O. (1993) Translation of mRNAs with degenerate initiation triplet AUU displays high initiation factor 2 dependence and is subject to initiation factor 3 repressionProc.Natl.AcadSci.USA 90, pp.4161-4165.

139. La, Teana A., Gualerzi, С. O., and Brimacombe, R. (1995) From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors RNA 1, pp.772-782.

140. Hirokawa, G., Kiel, M. C., Muto, A., Selmer, M., Raj, V. S., Liljas, A., Igarashi, K., Kaji, H., and Kaji, A. (2002) Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic EMBO J. 21, pp.2272-2281.

141. Karimi, R., Pavlov, M. Y., Buckingham, R. H., and Ehrenberg, M. (1999) Novel roles for classical factors at the interface between translation termination and initiation Mol.Cell 3, pp.601-609.

142. Petrelli, D., Garofalo, C., Lammi, M., Spurio, R., Pon, C. L., Gualerzi, С. O., and La, Teana A. (2003) Mapping the active sites of bacterial translation initiation factor IF3 J.Mol.Biol. 331, pp.541-556.

143. Betlach, M., Friedman, J., Boyer, H. W., and Pfeifer, F. (1984) Characterization of a halobacterial gene affecting bacterio-opsin gene expression Nucleic Acids Res. 12, pp.7949-7959.

144. Osada, Y., Saito, R., and Tomita, M. (1999) Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes Bioinformatics. 15, pp.578-581.

145. Saito, R. and Tomita, M. (1999) Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation Gene 238, pp.79-83.

146. Condo, I., Ciammaruconi, A., Benelli, D., Ruggero, D., and Londei, P: (1999) Cis-acting signals controlling translational initiation in the thermophilic archaeon Sulfolobus solfataricus Mol.Microbiol. 34, pp.377-384.

147. Kyrpides, N. C., Olsen, G. J., IClenk, H. P., White, O., and Woese, C. R. (1996) Methanococcus jannaschii genome: revisited Microb.Comp Genomics 1, pp.329-338.

148. Keeling, P. J. and Doolittle, W. F. (1995) An archaebacterial elF-1 A: new grist for the mill Mol.Microbiol. 17, pp.399-400.

149. Kyrpides, N. C. and Woese, C. R. (1998) Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families Proc.Natl.Acad.Sci. USA 95, pp.3726-3730.

150. Yatime, L., Schmitt, E., Blanquet, S., and Mechulam, Y. (2004) Functional molecular mapping of archaeal translation initiation factor 2 J.Biol. Chem. 279, pp. 15984-15993.

151. Magdolen, V., Klier, H., Wohl, Т., IClink, F., Hirt, H., Hauber, J., and Lottspeich, F. (1994) The function of the hypusine-containing proteins of yeast and other eukaryotes is well conserved Mol.Gen.Genet. 244, pp.646-652.

152. Yang, W. and Hinnebusch, A. G. (1996) Identification of a regulatory subcomplex in the guanine nucleotide exchange factor eIF2B that mediates inhibition by phosphorylated eIF2 Mol.Cell Biol. 16, pp.6603-6616.

153. Pedulla, N„ Palermo, R., Hasenohrl, D., Blasi, U., Cammarano, P., and Londei, P. (2005) The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor Nucleic Acids Res. 33, pp.1804-1812.

154. Tahara, M., Ohsawa, A., Saito, S., and Kimura, M. (2004) In vitro phosphorylation of initiation factor 2 alpha (aIF2 alpha) from hyperthermophilic archaeon Pyrococcus horikoshii OT3 J.Biochem. (Tokyo) 135, pp.479-485.

155. Grill, S., Gualerzi, С. O., Londei, P., and Blasi, U. (2000) Selective stimulation of translation of leaderless mRNA by initiation factor 2: evolutionary implications for translation EMBO J. 19, pp.41014110.

156. Londei, P. (2005) Evolution of translational initiation: new insights from the archaea FEMS Microbiol.Rev. 29, pp. 185-200.

157. Shatkin, A. J. (1976) Capping of eucaryotic mRNAs Cell 9, pp.645-653.

158. Lim, L. and Canellakis, E. S. (1970) Adenine-rich polymer associated with rabbit reticulocyte messenger RNA Nature 227, pp.710-712.

159. Jacobson A. (1996) Poly(A) metabolism and translation: the closed-loop model, pp.451-480.

160. Palmer, T. D., Miller, A. D., Reeder, R. H., and McStay, B. (1993) Efficient expression of a protein coding gene under the control of an RNA polymerase I promoter Nucleic Acids Res. 21, pp.34513457.

161. Sachs, A. and Wahle, E. (1993) Poly(A) tail metabolism and function in eucaryotes J.Biol.Chem. 268, pp.22955-22958.

162. Sherman, F., McICnight, G., and Stewart, J. W. (1980) AUG is the only initiation codon in eukaryotes Biochim.Biophys.Acta 609, pp.343-346.

163. Boeck, R., Curran, J., Matsuoka, Y., Compans, R., and Kolakofsky, D. (1992) The parainfluenza virus type 1 Р/С gene uses a very efficient GUG codon to start its С' protein J. Virol. 66, pp. 1765-1768.

164. Gordon, K., Futterer, J., and Hohn, T. (1992) Efficient initiation of translation at non-AUG triplets in plant cells Plant J. 2, pp.809-813.

165. Peabody, D. S. (1989) Translation initiation at non-AUG triplets in mammalian cells J.Biol.Chem. 264, pp.5031-5035.

166. Grunert, S. and Jackson, R. J. (1994) The immediate downstream codon strongly influences the efficiency of utilization of eukaryotic translation initiation codons EMBOJ. 13, pp.3618-3630.

167. Kozak, M. (1989) Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems Mol.Cell Biol. 9, pp.5073-5080.

168. Kozak, M. (1983) Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles Microbiol.Rev. 47, pp. 1-45.

169. Matveeva, О. V. and Shabalina, S. A. (1993) Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA Nucleic Acids Res. 21, pp.1007-1011.

170. Mauro, V. P. and Edelman, G. M. (1997) rRNA-like sequences occur in diverse primary transcripts: implications for the control of gene expression Proc.Natl.Acad.Sci. U SA 94, pp.422-427.

171. Verrier, S. B. and Jean-Jean, O. (2000) Complementarity between the mRNA 5' untranslated region and 18S ribosomal RNA can inhibit translation RNA 6, pp.584-597.

172. Yueh, A. and Schneider, R. J. (2000) Translation by ribosome shunting on adenovirus and hsp70 mRNAs facilitated by complementarity to 18S rRNA Genes Dev. 14, pp.414-421.

173. Cavener, D. R. and Ray, S. C. (1991) Eukaryotic start and stop translation sites Nucleic Acids Res. 19, pp.3185-3192.

174. Joshi, C. P., Zhou, H., Huang, X., and Chiang, V. L. (1997) Context sequences of translation initiation codon in plants Plant Mol.Biol. 35, pp.993-1001.

175. Kozak, M. (1984) Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs Nucleic Acids Res. 12, pp.857-872.

176. Kozak, M. (1987) An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs Nucleic Acids Res. 15, pp.8125-8148.

177. Pesole, G., Gissi, C., Grillo, G., Licciulli, F., Liuni, S., and Saccone, C. (2000) Analysis of oligonucleotide AUG start codon context in eukariotic mRNAs Gene 261, pp.85-91.

178. Pesole, G., Bernardi, G., and Saccone, C. (1999) Isochore specificity of AUG initiator context of human genes FEBS Lett. 464, pp.60-62.

179. Hamilton, R., Watanabe, С. K., and de Boer, H. A. (1987) Compilation and comparison of the sequence context around the AUG startcodons in Saccharomyces cerevisiae mRNAs Nucleic Acids Res. 15, pp.3581-3593.

180. Kozak, M. (1978) How do eucaryotic ribosomes select initiation regions in messenger RNA? Cell 15, pp. 1109-1123.

181. Kozak, M. (1980) Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes Cell 22, pp.7-8.

182. Kozak, M. (1989) The scanning model for translation: an update J.Cell Biol. 108, pp.229-241.

183. Olsen, D. S., Savner, E. M., Mathew, A., Zhang, F., Krishnamoorthy, Т., Phan, L., and Hinnebusch, A. G. (2003) Domains of elFIA that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo EMBO J. 22, pp.193-204.

184. Fekete, C. A., Applefield, D. J., Blakely, S. A., Shirokikh, N., Pestova, Т., Lorsch, J. R., and Hinnebusch, A. G. (2005) The elFIA C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo EMBO J. 24, pp.3588-3601.

185. Kozak, M. (2002) Pushing the limits of the scanning mechanism for initiation of translation Gene 299, pp. 1-34.

186. Hellen, C. U. and Sarnow, P. (2001) Internal ribosome entry sites in eukaryotic mRNA molecules Genes Dev. 15, pp. 1593-1612.

187. Benne, R. and Hershey, J. W. (1978) The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes J.Biol.Chem. 253, pp.3078-3087.

188. Hershey, J. W., Asano, K., Naranda, Т., Vornlocher, H. P., Hanachi, P., and Merrick, W. C. (1996) Conservation and diversity in the structure of translation initiation factor EIF3 from humans and yeast Biochimie 78, pp.903-907.

189. Trachsel, H., Erni, В., Schreier, M. PI., and Staehelin, T. (1977) Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors J.Mol.Biol. 116,pp.755-767.

190. Thomas, A., Spaan, W., van, Steeg H., Voorma, H. O., and Benne, R. (1980) Mode of action of protein synthesis initiation factor eIF-1 from rabbit reticulocytes FEBS Lett. 116, pp.67-71.

191. Fletcher, С. M., Pestova, Т. V., Hellen, C. U., and Wagner, G. (1999) Structure and interactions of the translation initiation factor elFl EMBO J. 18, pp.2631-2637.

192. Dallas, A. and Noller, H. F. (2001) Interaction of translation initiation factor 3 with the 30S ribosomal subunit Mol.Cell 8, pp.855-864.

193. Lomakin, I. В., Kolupaeva, V. G., Marintchev, A., Wagner, G., and Pestova, Т. V. (2003) Position of eukaryotic initiation factor elFl on the 40S ribosomal subunit determined by directed hydroxyl radical probing Genes Dev. 17, pp.2786-2797.

194. Yoon, H. J. and Donahue, T. F. (1992) The suil suppressor locus in Saccharomyces cerevisiae encodes a translation factor that functions during tRNA(iMet) recognition of the start codon Mol.Cell Biol. 12, pp.248-260.

195. Pestova, Т. V. and Kolupaeva, V. G. (2002) The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection Genes Dev. 16, pp.2906-2922.

196. Pestova, Т. V., Borukhov, S. I., and Hellen, C. U. (1998) Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons Nature 394, pp.854-859.

197. Cui, Y., Dinman, J. D., ICinzy, T. G., and Peltz, S. W. (1998) The Mof2/Suil protein is a general monitor of translational accuracy Mol.Cell Biol. 18, pp.1506-1516.

198. Algire, M. A., Maag, D., and Lorsch, J. R. (2005) P(i) Release from eIF2, Not GTP Hydrolysis, Is the Step Controlled by Start-Site Selection during Eukaryotic Translation Initiation Mol.Cell 20, pp.251-262.

199. Majumdar, R. and Maitra, U. (2005) Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation EMBO J. 24, pp.3737-3746.

200. Maag, D., Fekete, C. A., Gryczynski, Z., and Lorsch, J. R. (2005) A conformational change in the eukaryotic translation preinitiation complex and release of elFl signal recognition of the start codon Mol.Cell 17, pp.265-275.

201. Bandyopadhyay, A. and Maitra, U. (1999) Cloning and characterization of the p42 subunit of mammalian translation initiation factor 3 (eIF3): demonstration that eIF3 interacts with eIF5 in mammalian cells Nucleic Acids Res. 27, pp.1331-1337.

202. Wei, C. L., Kainuma, M., and Hershey, J. W. (1995) Characterization of yeast translation initiation factor 1A and cloning of its essential genq J.Biol.Chem. 270, pp.22788-22794.

203. Marintchev, A., Kolupaeva, V. G., Pestova, Т. V., and Wagner, G. (2003) Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners Proc. Natl. A cad. Sci. USA 100, pp.1535-1540.

204. Schreier, M. H. and Staehelin, T. (1973) Initiation of eukaryotic protein synthesis: (Met-tRNA f -40S ribosome) initiation complex catalysed by purified initiation factors in the absence of mRNA Nat.New Biol. 242, pp.35-38.

205. Goumans, H., Thomas, A., Verhoeven, A., Voorma, H. O., and Benne, R. (1980) The role of eIF-4C in protein synthesis initiation complex formation Biochim.Biophys.Acta 608, pp.39-46.

206. Chaudhuri, J., Chowdhury, D., and Maitra, U. (1999) Distinct functions of eukaryotic translation initiation factors elFIA and eIF3 in the formation of the 40 S ribosomal preinitiation complex

207. J.Biol.Chem. 274, pp.17975-17980.

208. Kolupaeva, V. G.,Unbehaun, A., Lomakin, I. В., Hellen, C. U., and Pestova, Т. V. (2005) Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association RNA 11, pp.470-486.

209. Kainuma, M. and Hershey, J. W. (2001) Depletion and deletion analyses of eucaryotic translation initiation factor 1A in Saccharomyces cerevisiae Biochimie. 83, pp.505-514.

210. Barrieux, A. and Rosenfeld, M. G. (1977) Characterization of GTP-dependent Met-tRNAf binding protein J.Biol.Chem. 252, pp.3843-3847.

211. Pestova, Т. V. and Hellen, C. U. (2003) Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA Genes Dev. 17, pp.181-186.

212. Wilson, J. E., Pestova, Т. V., Hellen, C. U., and Sarnow, P. (2000) Initiation of protein synthesis from the A site of the ribosome Cell 102, pp.511-520.

213. Schwab, S. R., Li, К. C., Kang, C., and Shastri, N. (2003) Constitutive display of cryptic translation products by MHC class I molecules Science 301, pp. 1367-1371.

214. Trachsel, H. and Staehelin, T. (1978) Binding and release of eukaryotic initiation factor eIF-2 and GTP during protein synthesis initiation Proc.Natl.Acad.Sci. USA 75, pp.204-208.

215. Chaudhuri, J., Si, K., and Maitra, U. (1997) Function of eukaryotic translation initiation factor 1A (elFIA) (formerly called eIF-4C) in initiation of protein synthesis J.Biol.Chem. 272, pp.7883-7891.

216. Majumdar, R., Bandyopadhyay, A., and Maitra, U. (2003) Mammalian translation initiation factor elFl functions with elFIA and eIF3 in the formation of a stable 40 S preinitiation complex J.Biol.Chem. 278, pp.6580-6587.

217. Benkowski, L. A., Ravel, J. M., and Browning, K. S. (1995) mRNA binding properties of wheat germ protein synthesis initiation factor 2 Biochem.Biophys.Res.Commun. 214, pp.1033-1039.

218. Flynn, A., Shatsky, I. N., Proud, C. G., and Kaminski, A. (1994) The RNA-binding properties of protein synthesis initiation factor eIF-2 Biochim.Biophys.Acta 1219, pp.293-301.

219. Gonsky, R., Itamar, D., Harary, R., and Kaempfer, R. (1992) Binding of ATP and messenger RNA by the beta-subunit of eukaryotic initiation factor 2 Biochimie 74, pp.427-434.

220. Laurino, J. P., Thompson, G. M., Pacheco, E., and Castilho, B. A. (1999) The beta subunit of eukaryotic translation initiation factor 2 binds mRNA through the lysine repeats and a region comprising the C2-C2 motif Mol.Cell Biol. 19, pp.173-181.

221. Roy, R., Ghosh-Dastidar, P., Das, A., Yaghmai, В., and Gupta, N. K. (1981) Protein synthesis in rabbit reticulocytes. Co-eIF-2A reverses mRNA inhibition of ternary complex (Met-tRNAf.eIF-2.GTP) formation by eIF-2 J.Biol.Chem. 256, pp.4719-4722.

222. Barrieux, A. and Rosenfeld, M. G. (1978) mRNA-induced dissociation of initiation factor 2 J.Biol.Chem. 253, pp.6311-6314.

223. Choi, S. Y., Scherer, B. J., Schnier, J., Davies, M. V., Kaufman, R. J., and Hershey, J. W. (1992) Stimulation of protein synthesis in COS cells transfected with variants of the alpha-subunit of initiation factor eIF-2 J.Biol.Chem. 267, pp.286-293.

224. Mouat, M. F. and Manchester, K. (1998) An alpha subunit-deficient form of eukaryotic protein synthesis initiation factor eIF-2 from rabbit reticulocyte lysate and its activity in ternary complex formation Mol.Cell Biochem. 183, pp.69-78.

225. Nika, J., Rippel, S., and Hannig, E. M. (2001) Biochemical analysis of the eIF2beta gamma complex reveals a structural function for eIF2alpha in catalyzed nucleotide exchange J.Biol.Chem. 276, pp.1051-1056.

226. Raychaudhuri, P., Chaudhuri, A., and Maitra, U. (1985) Formation and release of eukaryotic initiation factor 2 X GDP complex during eukaryotic ribosomal polypeptide chain initiation complex formation J.Biol. Chem. 260, pp.2140-2145.

227. Chakrabarti, A. and Maitra, U. (1992) Release and recycling of eukaryotic initiation factor 2 in the formation of an 80 S ribosomal polypeptide chain initiation complex. J.Biol.Chem. 267, pp.1296412972.

228. Ramaiah, К. V., Dhindsa, R. S., Chen, J. J., London, I. M., and Levin, D. (1992) Recycling and phosphorylation of eukaryotic initiation factor 2 on 60S subunits of SOS initiation complexes and polysomes Proc.Natl.Acad.Sci.USA 89, pp.12063-12067.

229. Thomas, N. S., Matts, R. L., Levin, D. H., and London, I. M. (1985) The 60 S ribosomal subunit as a carrier of eukaryotic initiation factor 2 and the site of reversing factor activity during protein synthesis J.Biol.Chem. 260, pp.9860-9866.

230. Proud, C. G. (1992) Protein phosphorylation in translational control Curr.Top.CellRegul. 32, pp.243-369.

231. Webb, B. L. and Proud, C. G. (1997) Eukaryotic initiation factor 2B (eIF2B) Int.J.Biochem.Cell Biol. 29, pp.1127-1131.

232. Goss, D. J., Parkhurst, L. J., Mehta, H. В., Woodley, C. L., and Wahba, A. J. (1984) Studies on the role of eukaryotic nucleotide exchange factor in polypeptide chain initiation J.Biol.Chem. 259, pp.7374-7377.

233. Pavitt, G. D., Yang, W., and Hinnebusch, A. G. (1997) Homologous segments in three subunits of the guanine nucleotide exchange factor eIF2B mediate translational regulation by phosphorylation of eIF2 Mol.CellBiol. 17, pp.1298-1313.

234. Rowlands, A. G., Panniers, R., and Henshaw, E. C. (1988) The catalytic mechanism of guanine nucleotide exchange factor action and competitive inhibition by phosphorylated eukaryotic initiation factor 2 J.Biol.Chem. 263, pp.5526-5533.

235. Oldfield, S., Jones, B. L., Tanton, D., and Proud, C. G. (1994) Use of monoclonal antibodies to study the structure and function of eukaryotic protein synthesis initiation factor eIF-2B Eur.J.Biochem. 221, pp.399-410.

236. Kaufman, R. J. (2000) Double-stranded RNA-activated protein kinase PKR. In Translational Control of Gene Expression (ed. Sonenberg,N., Mathews, M.B., and Hershey J.W.B.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. pp.503-528.

237. Chen J-J. (2000) Heme-regulated eIF2alpha kinase. In Translational Control of Gene Expression (ed. Sonenberg,N., Mathews,M.B., and Hershey J.W.B.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. pp.529-546.

238. Flynn, A., Oldfield, S., and Proud, C. G. (1993) The role of the beta-subunit of initiation factor eIF-2 in initiation complex formation Biochim.Biophys.Acta 1174, pp.117-121.

239. Pathak, V. K., Nielsen, P. J., Trachsel, H., and Hershey, J. W. (1988) Structure of the beta subunit of translational initiation factor eIF-2 Cell 54, pp.633-639.

240. Donahue, T. F., Cigan, A. M., Pabich, E. K., and Valavicius, В. C. (1988) Mutations at a Zn(II) finger motif in the yeast eIF-2 beta gene alter ribosomal start-site selection during the scanning process Cell 54, pp.621-632.

241. Ye, X. and Cavener, D. R. (1994) Isolation and characterization of the Drosophila melanogaster gene encoding translation-initiation factor eIF-2 beta Gene 142, pp.271-274.

242. Roll-Mecak, A., Alone, P., Cao, C., Dever, Т. E., and Burley, S. K. (2004) X-ray structure of translation initiation factor eIF2gamma: implications for tRNA and eIF2alpha binding J.Biol.Chem. 279, pp.10634-10642.

243. Castilho-Valavicius, В., Thompson, G. M., and Donahue, T. F. (1992) Mutation analysis of the Cys-X2-Cys-X19-Cys-X2-Cys motif in the beta subunit of eukaryotic translation initiation factor 2 Gene Expr. 2, pp.297-309.

244. Huang, H. K., Yoon, H., Hannig, E. M., and Donahue, T. F. (1997) GTP hydrolysis controls stringent selection of the AUG start codon during translation initiation in Saccharomyces cerevisiae Genes Dev. 11, pp.2396-2413.

245. Dorris, D. R., Erickson, F. L., and Hannig, E. M. (1995) Mutations in GCD11, the structural gene for eIF-2 gamma in yeast, alter translational regulation of GCN4 and the selection of the start site for protein synthesis EMBO J. 14, pp.2239-2249.

246. Hashimoto, N. N., Carnevalli, L. S., and Castilho, B. A. (2002) Translation initiation at non-AUG codons mediated by weakened association of eukaryotic initiation factor (elF) 2 subunits BiochemJ. 367, pp.359-368.

247. Colthurst, D. R. and Proud, C. G. (1986) Eukaryotic initiation factor 2 from rat liver: no apparent function for the beta-subunit in the formation of initiation complexes Biochim.Biophys.Acta 868, pp.7786.

248. Mitsui, It., Datta, A., and Ochoa, S. (1981) Removal of beta subunit of the eukaryotic polypeptide chain initiation factor 2 by limited proteolysis Proc.Natl.Acad.Sci. USA 78, pp.4128-4132.

249. Trachsel, H. (1996) Binding of initiator methionyl-tRNA to ribosomes. In Translational Control of Gene Expression (ed. Sonenberg,N., Mathews,M.B., and Hershey J.W.B.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp.113-138.

250. Gaspar, N. J., Itinzy, T. G., Scherer, B. J., Humbelin, M., Hershey, J. W., and Merrick, W. C. (1994) Translation initiation factor eIF-2. Cloning and expression of the human cDNA encoding the gamma-subunit J.Biol.Chem. 269, pp.3415-3422.

251. Aravind, L. and Koonin, E. V. (2000) Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system Genome Res. 10, pp.1172-1184.

252. Schmitt, E., Blanquet, S., and Mechulam, Y. (2002) The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors EMBO J. 21, pp.1821-1832.

253. Ito, Т., Marintchev, A., and Wagner, G. (2004) Solution structure of human initiation factor eIF2alpha reveals homology to the elongation factor eEFIB Structure.(Camb.) 12, ррЛ693-1704.

254. Thompson, H. A., Sadnik, I., Scheinbuks, J., and Moldave, It. (1977) Studies on native ribosomal subunits from rat liver. Purification and characterization of a ribosome dissociation factor Biochemistry 16, pp.2221-2230.

255. Trachsel, H. and Staehelin, T. (1979) Initiation of mammalian protein synthesis. The multiple functions of the initiation factor eIF-3 Biochim.Biophys.Acta 565, pp.305-314.

256. Freienstein, C. and Blobel, G. (1975) Nonribosomal proteins associated with eukaryotic native small ribosomal subunits Proc.Natl.Acad.Sci. USA 72, pp.3392-3396.

257. Mayeur, G. L., Fraser, C. S., Peiretti, F., Block, It. L., and Hershey, J. W. (2003) Characterization of eIF3k: a newly discovered subunit of mammalian translation initiation factor elF3 Eur.J.Biochem. 270, pp.4133-4139.

258. Bommer, U. A., Lutsch, G., Stahl, J., and Bielka, H. (1991) Eukaryotic initiation factors eIF-2 and eIF-3: interactions, structure and localization in ribosomal initiation complexes Biochimie 73, pp.1007-1019.

259. Srivastava, S., Verschoor, A., and Frank, J. (1992) Eukaryotic initiation factor 3 does not prevent association through physical blockage of the ribosomal subunit-subunit interface J.Mol.Biol. 226, pp.301304.

260. Tolan, D. R., Hershey, J. W., and Traut, R. T. (1983) Crosslinking of eukaryotic initiation factor eIF3 to the 40S ribosomal subunit from rabbit reticulocytes Biochimie 65, pp.427-436.

261. Valasek, L., Mathew, A. A., Shin, B. S., Nielsen, It. H., Szamecz, В., and Hinnebusch, A. G. (2003) The yeast eIF3 subunits TIF32/a, NIPl/c, and eIF5 make critical connections with the 40S ribosome in vivo Genes Dev. 17, pp.786-799.

262. Westermann, P. and Nygard, O. (1983) The spatial arrangement of the complex between eukaryotic initiation factor eIF-3 and 40 S ribosomal subunit. Cross-linking between factor and ribosomal proteins Biochim.Biophys.Acta 741, pp.103-108.

263. Seal, S. N., Schmidt, A., and Marcus, A. (1989) Ribosome binding to inosine-substituted mRNAs in the absence of ATP and mRNA factors J.Biol.Chem. 264, pp.7363-7368.

264. Asano, K., Phan, L., Anderson, J., and Hinnebusch, A. G. (1998) Complex formation by all five homologues of mammalian translation initiation factor 3 subunits from yeast Saccharomyces cerevisiae J.Biol.Chem. 273, pp. 18573-18585.

265. Phan, L., Schoenfeld, L. W., Valasek, L„ Nielsen, К. H., and Hinnebusch, A. G. (2001) A subcomplex of three eIF3 subunits binds elFl and eIF5 and stimulates ribosome binding of mRNA and tRNA(i)Met EMBO J. 20, pp.2954-2965.

266. Valasek, L., Nielsen, К. H., and Hinnebusch, A. G. (2002) Direct eIF2-eIF3 contact in the multifactor complex is important for translation initiation in vivo EMBO J. 21, pp.5886-5898.

267. Hui, D. J., Bhasker, C. R., Merrick, W. C., and Sen, G. C. (2003) Viral stress-inducible protein p56 inhibits translation by blocking the interaction of eIF3 with the ternary complex eIF2.GTP.Met-tRNAi J.Biol.Chem. 278, pp.39477-39482.

268. Hui, D. J., Terenzi, F., Merrick, W. C., and Sen, G. C. (2005) Mouse p56 blocks a distinct function of eukaryotic initiation factor 3 in translation initiation J.Biol.Chem. 280, pp.3433-3440.

269. Hui, D. J., Terenzi, F., Merrick, W. C., and Sen, G. C. (2004) Mouse P56 blocks a distinct function of eIF3 in translation initiation J.Biol.Chem. 280, pp.3433-3440.

270. Guo, J., Hui, D. J., Merrick, W. C., and Sen, G. C. (2000) A new pathway of translational regulation mediated by eukaryotic initiation factor 3 EMBO J. 19, pp.6891-6899.

271. Miyamoto, S., Patel, P., and Hershey, J. W. (2005) Changes in ribosomal binding activity of eIF3 correlate with increased translation rates during activation of T lymphocytes J.Biol.Chem. 280, pp.2825128264.

272. Burks, E. A., Bezerra, P. P., Le, H., Gallie, D. R., and Browning, K. S. (2001) Plant initiation factor 3 subunit composition resembles mammalian initiation factor 3 and has a novel subunit J.Biol.Chem. 276, pp.2122-2131.

273. Imataka, H., Olsen, H. S., and Sonenberg, N. (1997) A new translational regulator with homology to eukaryotic translation initiation factor 4G EMBOJ. 16, pp.817-825.

274. Methot, N., Song, M. S., and Sonenberg, N. (1996) A region rich in aspartic acid, arginine, tyrosine, and glycine (DRYG) mediates eukaryotic initiation factor 4B (eIF4B) self-association and interaction with eIF3 Mol.Cell Biol. 16, pp.5328-5334.

275. Peterson, D. Т., Merrick, W. C., and Safer, B. (1979) Binding and release of radiolabeled eukaryotic initiation factors 2 and 3 during 80 S initiation complex formation J.Biol.Chem. 254, pp.25092516.

276. Wei, Z., Zhang, P., Zhou, Z., Cheng, Z., Wan, M., and Gong, W. (2004) Crystal structure of human eIF3k, the first structure of eIF3 subunits J.Biol.Chem. 279, pp.34983-34990.

277. Rogers, G. W„ Jr., Komar, A. A., and Merrick, W. C. (2002) elF4A: the godfather of the DEAD box helicases Prog.Nucleic Acid Res.Mol.Biol. 72, pp.307-331.

278. Tanner, N. K. and binder, P. (2001) DExD/H box RNA helicases: from generic motors to specific dissociation functions Mol.Cell 8, pp.251-262.

279. Yoder-Hill, J., Pause, A., Sonenberg, N., and Merrick, W. C. (1993) The p46 subunit of eukaryotic initiation factor (eIF)-4F exchanges with eIF-4A J.Biol.Chem. 268, pp.5566-5573.

280. Nielsen, P. J. and Trachsel, H. (1988) The mouse protein synthesis initiation factor 4A gene family includes two related functional genes which are differentially expressed EMBO J. 7, pp.20972105.

281. Morgan, R. and Sargent, M. G. (1997) The role in neural patterning of translation initiation factor eIF4AII; induction of neural fold genes Development 124, pp.2751-2760.

282. Le, H., Browning, K. S., and Gallie, D. R. (1998) The phosphorylation state of the wheat translation initiation factors eIF4B, eIF4A, and eIF2 is differentially regulated during seed development and germination J.Biol.Chem. 273, pp.20084-20089.

283. Webster, C., Gaut, R. L., Browning, It. S., Ravel, J. M., and Roberts, J. K. (1991) Hypoxia enhances phosphorylation of eukaryotic initiation factor 4A in maize root tips J.Biol.Chem. 266, pp.23341-23346.

284. Ray, В. K., Lawson, T. G., Kramer, J. C., Cladaras, M. H., Grifo, J. A., Abramson, R. D., Merrick, W. C., and Thach, R. E. (1985) ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors J.Biol.Chem. 260, pp.7651-7658.

285. Balasta, M. L., Carberry, S. E., Friedland, D. E., Perez, R. A., and Goss, D. J. (1993) Characterization of the ATP-dependent binding of wheat germ protein synthesis initiation factors elF-(iso)4F and eIF-4A to mRNA J.Biol.Chem. 268, pp.18599-18603.

286. Seal, S. N., Schmidt, A., and Marcus, A. (1983) Eukaryotic initiation factor 4A is the component that interacts with ATP in protein chain initiation Proc.Natl.Acad.Sci. USA 80, pp.6562-6565.

287. Rozen, F., Edery, I., Meerovitch, It., Dever, Т. E., Merrick, W. C., and Sonenberg, N. (1990) Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F Mol.Cell Biol. 10, pp.1134-1144.

288. Rogers, G. W., Jr., Richter, N. J., Lima,.W. F., and Merrick, W. C. (2001) Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F J.Biol.Chem. 276, pp.30914-30922.

289. Rogers, G. W., Jr., Lima, W. F., and Merrick, W. C. (2001) Further characterization of the helicase activity of eIF4A. Substrate specificity J.Biol.Chem. 276, pp.12598-12608.

290. Richter-Cook, N. J., Dever, Т. E., Hensold, J. O., and Merrick, W. C. (1998) Purification and characterization of a new eukaryotic protein translation factor. Eukaryotic initiation factor 4H J.Biol.Chem. 273, pp.7579-7587.

291. Bi, X., Ren, J., and Goss, D. J. (2000) Wheat germ translation initiation factor eIF4B affects eIF4A and eIFiso4F helicase activity by increasing the ATP binding affinity of eIF4A Biochemistry 39, pp.5758-5765.

292. Blum, S., Schmid, S. R., Pause, A., Buser, P., Linder, P., Sonenberg, N., and Trachsel, H. (1992) ATP hydrolysis by initiation factor 4A is required for translation initiation in Saccharomyces cerevisiae Proc.Natl.Acad.Sci. USA 89, pp.7664-7668.

293. Grifo, J. A., Abramson, R. D., Satler, C. A., and Merrick, W. C. (1984) RNA-stimulated ATPase activity of eukaryotic initiation factors J.Biol.Chem. 259, pp.8648-8654.

294. Lax, S. R., Browning, K. S., Maia, D. M., and Ravel, J. M. (1986) ATPase activities of wheat germ initiation factors 4A, 4B, and 4F J.Biol.Chem. 261, pp.15632-15636.

295. Lorsch, J. R. and Herschlag, D. (1998) The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide Biochemistry 37, pp.21802193.

296. Lorsch, J. R. and Herschlag, D. (1998) The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes Biochemistry 37, pp.2194-2206.

297. Peck, M. L. and Herschlag, D. (1999) Effects of oligonucleotide length and atomic composition on stimulation of the ATPase activity of translation initiation factor elF4 A RNA 5, pp.1210-1221.

298. Metz, A. M., Wong, К. C., Malmstrom, S. A., and Browning, K. S. (1999) Eukaryotic initiation factor 4B from wheat and Arabidopsis thaliana is a member of a multigene family Biochem.Biophys.Res.Commun. 266, pp.314-321.

299. Milburn, S. C., Hershey, J. W., Davies, M. V, ICelleher, K., and Kaufman, R. J. (1990) Cloning and expression of eukaryotic initiation factor 4B cDNA: sequence determination identifies a common RNA recognition motif EMBO J. 9, pp.2783-2790.

300. Sha, M., Balasta, M. L., and Goss, D. J. (1994) An interaction of wheat germ initiation factor 4B with oligoribonucleotides J.Biol.Chem. 269, pp.14872-14877.

301. Hughes, D. L., Dever, Т. E., and Merrick, W. C. (1993) Further biochemical characterization of rabbit reticulocyte eIF-4B ArchBiochem.Biophys. 301, pp.311-319.

302. Methot, N., Pickett, G., Keene, J. D., and Sonenberg, N. (1996) In vitro RNA selection identifies RNA ligands that specifically bind to eukaryotic translation initiation factor 4B: the role of the RNA remotif RNA 2, pp.38-50.

303. Methot, N., Pause, A., Hershey, J. W., and Sonenberg, N. (1994) The translation initiation factor eIF-4B contains an RNA-binding region that is distinct and independent from its ribonucleoprotein consensus sequence Mol.Cell Biol. 14, pp.2307-2316.

304. Niederberger, N., Trachsel, H., and Altmann, M. (1998) The RNA recognition motif of yeast translation initiation factor Tif3/eIF4B is required but not sufficient for RNA strand-exchange and translational activity RNA 4, pp. 1259-1267.

305. Altmann, M., Muiier, P. P., Wittmer, В., Ruchti, F., banker, S., and Trachsel, H. (1993) A Saccharomyces cerevisiae homologue of mammalian translation initiation factor 4B contributes to RNA helicase activity EMBO J. 12, pp.3997-4003.

306. Coppolecchia, R., Buser, P., Stotz, A., and binder, P. (1993) A new yeast translation initiation factor suppresses a mutation in the eIF-4A RNA helicase EMBO J. 12, pp.4005-4011.

307. Ray, B. It., bawson, T. G., Abramson, R. D., Merrick, W. C., and Thach, R. E. (1986) Recycling of messenger RNA cap-binding proteins mediated by eukaryotic initiation factor 4B J.Biol.Chem. 261, pp.11466-11470.

308. Duncan, R. F. and Hershey, J. W. (1989) Protein synthesis and protein phosphorylation during heat stress, recovery, and adaptation J. Cell Biol. 109, pp. 1467-1481.

309. Gailie, D. R., be, H„ Caldwell, C., Tanguay, R. b., Hoang, N. X., and Browning, K. S. (1997) The phosphorylation state of translation initiation factors is regulated developmentally and following heat shock in wheat J.Biol.Chem. 272, pp.1046-1053.

310. Morley, S. J. and Traugh, J. A. (1990) Differential stimulation of phosphorylation of initiation factors eIF-4F, eIF-4B, eIF-3, and ribosomal protein S6 by insulin and phorbol esters J.Biol.Chem. 265, pp.10611-10616.

311. Bonneau, A. M. and Sonenberg, N. (1987) Involvement of the 24-kDa cap-binding protein in regulation of protein synthesis in mitosis J.Biol.Chem. 262, pp.11134-11139.

312. Duncan, R. and Hershey, J. W. (1984) Heat shock-induced translational alterations in Heba cells. Initiation factor modifications and the inhibition of translation J.Biol.Chem. 259, pp.11882-11889.

313. Duncan, R. and Hershey, J. W. (1985) Regulation of initiation factors during translational repression caused by serum depletion. Abundance, synthesis, and turnover rates J.Biol.Chem. 260, pp.5486-5492.

314. Bushell, M., Wood, W., Clemens, M. J., and Morley, S. J. (2000) Changes in integrity and association of eukaryotic protein synthesis initiation factors during apoptosis Eur.J.Biochem. 267, pp.1083-1091.

315. Young, Т. E. and Gailie, D. R. (2000) Programmed cell death during endosperm development PlantMol.Biol. 44, pp.283-301.402. bodish, H. F. (1976) Translational control of protein synthesis Annu.Rev.Biochem. 45, pp.39-72.

316. Korneeva, N. b., bamphear, B. J., Hennigan, F. L., Merrick, W. C., and Rhoads, R. E. (2001) Characterization of the two eIF4A-binding sites on human eIF4G-l J.Biol.Chem. 276, pp.2872-2879.

317. Dominguez, D., Altmann, M., Benz, J., Baumann, U., and Trachsel, H. (1999) Interaction of translation initiation factor eIF4G with eIF4A in the yeast Saccharomyces cerevisiae J.Biol.Chem. 274, pp.26720-26726.

318. Sonenberg, N., Morgan, M. A., Merrick, W. C., and Shatkin, A. J. (1978) A polypeptide in eukaryotic initiation factors that crosslinks specifically to the 5'-terminal cap in mRNA Proc.Natl.Acad.Sci. USA 75, pp.4843-4847.

319. Sonenberg, N., Rupprecht, It. M., Hecht, S. M., and Shatkin, A. J. (1979) Eukaryotic mRNA cap binding protein: purification by affinity chromatography on sepharose-coupled m7GDP Proc.Natl.Acad.ScLUSA 16, pp.4345-4349.

320. Haghighat, A. and Sonenberg, N. (1997) eIF4G dramatically enhances the binding of eIF4E to the mRNA 5'-cap structure J.Biol.Chem. 272, pp.21677-21680.

321. Gross, J. D., Moerke, N. J., von der, Haar Т., Lugovskoy, A. A., Sachs, А. В., McCarthy, J. E., and Wagner, G. (2003) Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E Cell 115, pp.739-750.

322. Hershey, P. E., McWhirter, S. M., Gross, J. D, Wagner, G., Alber, Т., and Sachs, A. B. (1999) The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4Gl J.Biol.Chem. 274, pp.21297-21304.

323. Mamane, Y., Petroulakis, E., Rong, L., Yoshida, K., Ler, L. W., and Sonenberg, N. (2004) eIF4E~from translation to transformation Oncogene 2004.Apr 23, pp.3172-3179.

324. Lazaris-Karatzas, A., Montine, K. S., and Sonenberg, N. (1990) Malignant transformation by a eukaryotic initiation factor subunit that binds to mRNA 5' cap Nature 345, pp.544-547.

325. Koromilas, A. E., Lazaris-Karatzas, A., and Sonenberg, N. (1992) mRNAs containing extensive secondary structure in their 5' non-coding region translate efficiently in cells overexpressing initiation factor eIF-4E EMBO J. 11, pp.4153-4158.

326. Shantz, L. M., Hu, R. H., and Pegg, A. E. (1996) Regulation of ornithine decarboxylase in a transformed cell line that overexpresses translation initiation factor eIF-4E Cancer Res. 56, pp.32653269.

327. Gingras, A. C., Raught, В., and Sonenberg, N. (1999) eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation Anmi.Rev.Biochem. 68, pp.913-963.

328. Haghighat, A., Mader, S., Pause, A., and Sonenberg, N. (1995) Repression of cap-dependent translation by 4E-binding protein 1: competition with p220 for binding to eukaryotic initiation factor-4E EMBOJ. 14, pp.5701-5709.

329. Ling, J., Morley, S. J., and Traugh, J. A. (2005) Inhibition of cap-dependent translation via phosphorylation of eIF4G by protein kinase Pak2 EMBOJ. 24, pp. 4094-105.

330. Rosenwald, I. В., Lazaris-Karatzas, A., Sonenberg, N., and Schmidt, E. V. (1993) Elevated levels of cyclin D1 protein in response to increased expression of eukaryotic initiation factor 4E Mol.Cell Biol 13, pp.7358-7363.

331. Pyronnet, S. (2000) Phosphorylation of the cap-binding protein eIF4E by the MAPK-activated protein kinase Mnkl Biochem.Pharmacol. 60, pp.1237-1243.

332. Waskiewicz, A. J., Flynn, A., Proud, C. G., and Cooper, J. A. (1997) Mitogen-activated protein kinases activate the serine/threonine kinases Mnkl and Mnk2 EMBO J. 16, pp.1909-1920.

333. Scheper, G. C. and Proud, C. G. (2002) Does phosphorylation of the cap-binding protein eIF4E play a role in translation initiation? Eur.J.Biochem. 269, pp.5350-5359.

334. Scheper, G. С., van, ICollenburg В., Hu, J., Luo, Y., Goss, D. J., and Proud, C. G. (2002) Phosphorylation of eukaryotic initiation factor 4E markedly reduces its affinity for capped mRNA J.Biol.Chem. 277, pp.3303-3309.

335. Lang, V., Zanchin, N. I., Lunsdorf, H., Tuite, M., and McCarthy, J. E. (1994) Initiation factor eIF-4E of Saccharomyces cerevisiae. Distribution within the cell, binding to mRNA, and consequences of its overproduction J.Biol. Chem. 269, pp.6117-6123.

336. Lejbkowicz, F., Goyer, C., Darveau, A., Neron, S., Lemieux, R., and Sonenberg, N. (1992) A fraction of the mRNA 5' cap-binding protein, eukaryotic initiation factor 4E, localizes to the nucleus Proc.Natl.Acad.Sci. USA 89, pp.9612-9616.

337. Dostie, J., Ferraiuolo, M., Pause, A., Adam, S. A., and Sonenberg, N. (2000) A novel shuttling protein, 4E-T, mediates the nuclear import of the mRNA 5' cap-binding protein, eIF4E EMBO J. 19, pp.3142-3156.

338. Dostie, J., Lejbkowicz, F., and Sonenberg, N. (2000) Nuclear eukaryotic initiation factor 4E (eIF4E) colocalizes with splicing factors in speckles J.CellBiol. 148, pp.239-247.

339. Etchison, D. and Smith, It. (1990) Variations in cap-binding complexes from uninfected and poliovirus-infected HeLa cells J.Biol.Chem. 265, pp.7492-7500.

340. Itorneeva, N. L., Lamphear, B. J., Hennigan, F. L., and Rhoads, R. E. (2000) Mutually cooperative binding of eukaiyotic translation initiation factor (elF) 3 and eIF4A to human eIF4G-l J.Biol.Chem. 215, pp.41369-41376.

341. Imataka, H., Gradi, A., and Sonenberg, N. (1998) A newly identified N-terminal amino acid sequence of human eIF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation EMBO J. 17, pp.7480-7489.

342. Gailie, D. R. (1998) A tale of two termini: a functional interaction between the termini of an mRNA is a prerequisite for efficient translation initiation Gene 216, pp.1-11.

343. Wells, S. E., Hillner, P. E., Vale, R. D., and Sachs, A. B. (1998) Circularization of mRNA by eukaryotic translation initiation factors Mol.Cell 2, pp.135-140.

344. Bi, X. and Goss, D. J. (2000) Wheat germ poly(A)-binding protein increases the ATPase and the RNA helicase activity of translation initiation factors eIF4A, eIF4B, and eIF-iso4F J.Biol.Chem. 275, pp. 17740-17746.

345. Keiper, B. D., Gan, W., and Rhoads, R. E. (1999) Protein synthesis initiation factor 4G Int.J.Biochem.CellBiol. 31, pp.37-41.

346. Byrd, M. P., Zamora, M., and Lloyd, R. E. (2002) Generation of multiple isoforms of eukaryotic translation initiation factor 4GI by use of alternate translation initiation codons Mol.Cell Biol. 22, pp.4499-4511.

347. Morley, S. J., Curtis, P. S., and Pain, V. M. (1997) eIF4G: translation's mystery factor begins to yield its secrets RNA 3, pp. 1085-1104.

348. Han, B. and Zhang, J. T. (2002) Regulation of gene expression by internal ribosome entry sites or cryptic promoters: the eIF4G story Mol.CellBiol.2002. 22, pp.7372-7384.

349. Henis-Itorenblit, S., Shani, G., Sines, Т., Marash, L., Shohat, G., and Kimchi, A. (2002) The caspase-cleaved DAP5 protein supports internal ribosome entry site-mediated translation of death proteins Proc.Natl.Acad.Sci.U S A 99, pp.5400-5405. ' '

350. Hundsdoerfer, P., Thoma, C., and Hentze, M. W. (2005) Eukaryotic translation initiation factor 4GI and p97 promote cellular internal ribosome entry sequence-driven translation Proc.Natl.Acad.Sci.USA 102, pp.13421-13426.

351. Yamanaka, S., Zhang, X. Y., Maeda, M., Miura, K., Wang, S., Farese, R. V., Jr., Iwao, H., and Innerarity, T. L. (2000) Essential role of NATl/p97/DAP5 in embryonic differentiation and the retinoic acid pathway EMBO J. 19, pp.5533-5541.

352. Craig, A. W., Haghighat, A., Yu, А. Т., and Sonenberg, N. (1998) Interaction of polyadenylate-binding protein with the eIF4G homologue PAIP enhances translation Nature 392, pp.520-523.

353. Gallie, D. R. and Browning, K. S. (2001) eIF4G functionally differs from eIFiso4G in promoting internal initiation, cap-independent translation, and translation of structured mRNAs J.Biol.Chem. 276, pp.36951-36960.

354. Das, S., Ghosh, R., and Maitra, U. (2001) Eukaiyotic translation initiation factor 5 functions as a GTPase-activating protein J.Biol.Chem. 276, pp.6720-6726.

355. Paulin, F. E., Campbell, L. E., O'Brien, K., Loughlin, J., and Proud, C. G. (2001) Eukaryotic translation initiation factor 5 (eIF5) acts as a classical GTPase-activator protein Curr.Biol. 11, pp.55-59.

356. Das, K., Chevesich, J., and Maitra, U. (1993) Molecular cloning and expression of cDNA for mammalian translation initiation factor 5 Proc.Natl.Acad.Sci. US A 90, pp.3058-3062.

357. Raychaudhuri, P., Chaudhuri, A., and Maitra, U. (1985) Eukaryotic initiation factor 5 from calf liver is a single polypeptide chain protein of Mr = 62,000 J.Biol.Chem. 260, pp.2132-2139.

358. Das, S., Maiti, Т., Das, K., and Maitra, U. (1997) Specific interaction of eukaryotic translation initiation factor 5 (eIF5) with the beta-subunit of eIF2 J.Biol.Chem. 272, pp.31712-31718.

359. Chakravarti, D. and Maitra, U. (1993) Eukaryotic translation initiation factor 5 from Saccharomyces cerevisiae. Cloning, characterization, and expression of the gene encoding the 45,346-Da protein J.Biol.Chem. 268, pp.10524-10533.

360. Si, K., Das, K., and Maitra, U. (1996) Characterization of multiple mRNAs that encode mammalian translation initiation factor 5 (eIF-5) J.Biol.Chem. 271, pp.16934-16938.

361. Ghosh, S., Chevesich, J., and Maitra, U. (1989) Further characterization of eukaryotic initiation factor 5 from rabbit reticulocytes. Immunochemical characterization and phosphorylation by casein kinase II J.Biol.Chem. 264, pp.5134-5140.

362. Homma, M. It., Wada, I., Suzuki, Т., Yamaki, J., Кrcbs, E. G., and Homma, Y. (2005) CK2 phosphorylation of eukaiyotic translation initiation factor 5 potentiates cell cycle progression Proc.Natl.Acad.Sci. USA 102, pp.15688-15693.

363. Majumdar, R., Bandyopadhyay, A., Deng, H., and Maitra, U. (2002) Phosphorylation of mammalian translation initiation factor 5 (eIF5) in vitro and in vivo Nucleic Acids Res. 30, pp.1154-1162.

364. Maiti, Т., Bandyopadhyay, A., and Maitra, U. (2003) Casein kinase II phosphorylates translation initiation factor 5 (eIF5) in Saccharomyces cerevisiae Yeast 20, pp.97-108.

365. Pestova, Т. V., Lomakin, I. В., Lee, J. H., Choi, S. It., Dever, Т. E., and Hellen, C. U. (2000) The joining of ribosomal subunits in eukaryotes requires el F5!'. Nature 403, pp.332-335.

366. Merrick, W. C., Itemper, W. M., and Anderson. W. (1975) Purification and characterization of homogeneous initiation factor M2A from rabbit reticulocytes J.Biol.Chem. 250, pp.5556-5562.

367. Peterson, D. Т., Safer, В., and Merrick, W. С. (1979) Role of eukaryotic initiation factor 5 in the formation of 80 S initiation complexes J.Biol.Chem. 254. pp.7730-7735.

368. Chakrabarti, A. and Maitra, U. (1991) Function of eukaryotic initiation factor 5 in the formation of an 80 S ribosomal polypeptide chain initiation complex,/. В iol. Chem. 266, pp.14039-14045.

369. Choi, S. К., Lee, J. H., Zoll, W. L., Merrick, W. C., and Dever, Т. E. (1998) Promotion of met-tRNAiMet binding to ribosomes by yIF2, a bacterial IF2 homolog in yeast Science 280, pp.1757-1760.

370. Lee, J. Д, Pestova, Т. V., Shin, B. S., Cao, C., Choi, S. K., and Dever, Т. E. (2002) Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation Proc.Natl.Acad.Sci. USA 99, pp.16689-16694.

371. Shin, B. S., Maag, D., Roll-Mecak, A., Arefin, M. S., Burley, S. K., Lorsch, J. R., and Dever, T. E. (2002) Uncoupling of initiation factor eIF5B/IF2 GTPase and translational activities by mutations that lower ribosome affinity Cell 111, pp.1015-1025.

372. Boileau, G., Butler, P., Hershey, J. W., and Traut, R. R. (1983) Direct cross-links between initiation factors 1, 2, and 3 and ribosomal proteins promoted by 2-iminothiolane Biochemistry 22, pp.3162-3170.

373. Mayo, M. A. (2002) Names of viruses and virus species an editorial note Arch. Virol. 147, pp.1463-1464.

374. All. D'Arcy, C. J., Burnett, P. A., and Hewings, A. D (1981) Detection, biological effects, and transmission of a virus from the aphid Rhopalosiphum padi. EMBO Rep. 114, pp.268-272.

375. Gildow, F. E and D'Arcy, C. J. (1990) Cytopathology and experimental host range of Rhopalosiphum padi virus, a small isometric RNA virus infecting cereal grain aphids. J. Invertebr. Pathol. 55, pp.245-257.

376. Domier, L. L., McCoppin, N. K., and D'Arcy, C. J. (2000) Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2. Virology 268, pp.264-271.

377. Kanamori, Y. and Nakashima, N. (2001) A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA 7, pp.266-274.

378. Moon, J. S., Domier, L. L., McCoppin, N. It., D'Arcy, C. J., and Jin, H. (1998) Nucleotide sequence analysis shows that Rhopalosiphum padi virus is a member of a novel group of insect-infecting RNA viruses. EMBO Rep. 243, pp.54-65.

379. Wilson, J. E., Powell, M. J., Hoover, S. E., and Sarnow, P. (2000) Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites Mol.Cell Biol. 20, pp.49904999.

380. Sasaki, J. and Nakashima, N. (2000) Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proc.Natl.Acad.Sci. U SA 97, pp.1512-1515.

381. Hatakeyama, Y., Shibuya, N., Nishiyama, Т., and Nakashima, N. (2004) Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts. RNA 10, pp.779-786.

382. Costantino, D. and Kieft, J. S. (2005) A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA 11, pp.332-343.

383. Jan, E. and Sarnow, P. (2002) Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J.Mol.Biol. 324, pp.889-902.

384. Jan, E., Kinzy, T. G., and Sarnow, P. (2003) Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis. Proc.Natl.Acad.Sci. U SA. 100, pp.15410-15415.

385. Thompson, S. R., Gulyas, K. D., and Sarnow, P. (2001) Internal initiation in Saccharomyces cerevisiae mediated by an initiator tRNA/eIF2-independent internal ribosome entry site element. Proc.Natl.Acad.Sci. USA 98, pp.12972-12977.

386. Cevallos, R. C. and Sarnow, P. (2005) Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J. Virol. 79, pp.677-683.