Dataset Information

A molecular network of conserved factors keeps ribosomes dormant in the egg

ABSTRACT: Ribosomes are produced in large quantities during oogenesis and stored in the egg. However, the egg and early embryo are translationally inactive. How translation is activated during embryogenesis is poorly understood. Using mass-spectrometry and cryo-EM analyses of ribosomes isolated from zebrafish and Xenopus eggs and embryos, we find that ribosomes transition from a dormant to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four factors that form two modules: a Habp4-eEF2 module that stabilizes ribosome levels and a Dap1b/Dapl1-eIF-5a module that represses translation. Dap/Dap1b is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Thus, a developmentally programmed, unique ribosome state plays a key role in ribosome storage and translational repression in the egg.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio) Xenopus Laevis (african Clawed Frog)

TISSUE(S): Egg

SUBMITTER: Manuel Matzinger

LAB HEAD: Andrea Pauli

PROVIDER: PXD026866 | Pride | 2022-11-03

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20180117_QexHF2_RSLC2_Leesch_Pauli_IMP_acetone_pellets_ribosomes_6c7per_M3.raw	Raw
	20180117_QexHF2_RSLC2_Leesch_Pauli_IMP_acetone_pellets_ribosomes_8c2per_M2.raw	Raw
	20180117_QexHF2_RSLC2_Leesch_Pauli_IMP_acetone_pellets_ribosomes_8per_M1.raw	Raw
	20180122_QexHF2_RSLC2_Leesch_Pauli_IMP_acetone_pellets_lysates_2per_LM1.raw	Raw
	20180122_QexHF2_RSLC2_Leesch_Pauli_IMP_acetone_pellets_lysates_2per_LM2.raw	Raw

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Publications

A molecular network of conserved factors keeps ribosomes dormant in the egg.

Leesch Friederike F Lorenzo-Orts Laura L Pribitzer Carina C Grishkovskaya Irina I Roehsner Josef J Chugunova Anastasia A Matzinger Manuel M Roitinger Elisabeth E Belačić Katarina K Kandolf Susanne S Lin Tzi-Yang TY Mechtler Karl K Meinhart Anton A Haselbach David D Pauli Andrea A

Nature 20230118 7945

Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed<sup>1-4</sup>. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with fou ...[more]

PMID: 36653451

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Project description:We use mRNA-seq in combination with polysome profiling to determine translational status for all mRNAs in Drosophila mature oocytes and activated eggs. Puromycin-treated lysates are used as a negative control in polysome profiling experiments. Additionally, we use ribosome footprinting to globally measure translational efficiency of mRNAs in wild type mature oocytes as well as wild type and png mutant activated eggs. Lysates of hand-dissected Drosophila mature oocytes (containing ~540 M-NM-<g of total RNA) were subjected to separation by velocity sedimentation through sucrose gradients. In this way, free mRNAs (present in RNPs fraction) or those comigrating with ribosomal subunits (40S or 60S+80S fractions) or with varying numbers of bound ribosomes (low polysomes (2-4 ribosomes), medium polysomes (5-9 ribosomes), and heavy polysomes (more than 10 ribosomes) can be separated based on their size and collected as sucrose gradient fractions. To compare quantitatively the levels of every mRNA across the polysome gradient fractions, we added 5ng of S. cerevisiae mRNA as an exogenous spike-in to each of the six fractions of interest: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes. RNA was extraced from these fractions, follwing proteinase K treatment, by hot acid phenol method. In case of unfractionated lysates, RNA was extracted using TRIzol (Invitrogen) according to manufacturerM-bM-^@M-^Ys instructions. mRNA-seq samples were prepared from 1 M-NM-<g of total RNA (in case of sucrose gradient fractions and unfractionated lysates) and subject to Illumina based sequencing. Puromycin-treated lysates of mature oocytes or 0-2h Drosophila activated eggs (containing ~540 M-NM-<g of total RNA) were also subjected to separation by velocity sedimentation through sucrose gradients. Puromycin causes premature termination of elongating ribosomes and thus it can be used to determine whether the mRNAs co-sedimenting with the polysomal peaks (defined here as M-bM-^IM-%5 ribosomes) were actively engaged in translation. As an independent approach to assess translation and obtain information on the position of ribosomes on mRNAs, we employed ribosome footprinting. In addition to analyzing the same samples, as by polysome profiling, we also analyzed png mutant activated eggs by ribosome footprinting. Ribosome footprint profiling measures the number of ribosome-protected fragments (RPFs) derived from the mRNAs of each gene, resulting in a singular value of translational efficiency (TE) for each gene (TE=RPF/RNA).