The yeast ribosomal protein S7 and its genes.

Ribosomal protein S7 of Saccharomyces cerevisiae is encoded by two genes RPS7A and RPS7B. The sequence of each copy was determined; their coding regions differ in only 14 nucleotides, none of which leads to changes in the amino acid sequence. The predicted protein consists of 261 amino acids, making it the largest protein of the 40 S ribosomal subunit. It is highly basic near the NH2 terminus, as are most ribosomal proteins. Protein S7 is homologous to both human and rat ribosomal protein S4. RPS7A and RPS7B contain introns of 257 and 269 nucleotides, respectively, located 11 nucleotides beyond the initiator AUG. The splicing of the introns is efficient. Either RPS7A or RPS7B will support growth. However, deletion of both genes is lethal. RPS7A maps distal to CDC11 on chromosome X, and RPS7B maps distal to CUP1 on chromosome VIII.     

Structural comparison of two yeast tRNA Glu 3 genes.

DNA sequences in a 1.7 kb Pst fragment from yeast have been determined. This fragment is part of a yeast 7.4 kb Hind III segment cloned ino pBR322 (pY 5). The fragment carries a single gene for a glutamate tRNA. The coding portion of this gene is identical in sequence to that of the tRNA Glu 3 gene from pY 20 [1]. The flanking regions differ in their sequences, but possible secondary structures within the 5'-flanking regions bear similar features. Sequence homologies between pY 5 and pY 20 were detected far outside the tRNA genes. More surprisingly, extended sequence homologies were seen between the flanking regions of the pY 20 tRNA Glu 3 gene and a tRNA Ser gene [2,3]. We have also checked the known tRNA genes for structural similarities. Hybridization studies indicate that portions of the Pst fragment are repeated within the yeast genome.     

Structural and functional analyses of a yeast mitochondrial ribosomal protein homologous to ribosomal protein S15 of Escherichia coli.

We have purified a small subunit mitochondrial ribosomal protein, MRPS28p, from the yeast, Saccharomyces cerevisiae. Sequence from the amino terminus of MRPS28p was used to design a degenerate oligonucleotide that was complementary to the MRPS28 gene. The MRPS28 gene was isolated and its sequence determined. The MRPS28 sequence encodes a 28 kDa protein that has a region of homology with ribosomal protein S15 of E. coli. This region spans the entire length of the E. coli protein, but as MRPS28p is larger, includes only the portion of the MRPS28p sequence from amino acids 150 to 238. Based on this homology, we predict that MRPS28p, like E. coli S15, interacts directly with small subunit rRNA and functions as an early protein in ribosome assembly. Cells carrying a disrupted chromosomal copy of MRPS28 are unable to respire and spontaneously lose portions of their mitochondrial genomes at a high frequency. These phenotypes are consistent with an essential role for MRPS28p in the assembly and/or function of the mitochondrial ribosome.     

Isolation of cloned ribosomal protein genes from the yeast Saccharomyces carlsbergensis

A colony bank of yeast dna obtained by cloning HindIII-generated fragments of total yeast nuclear DNA in Escherichia coli K-12 with the vector pBR322, was screened with a radioactive RNA probe enriched for a subset of ribosomal protein mRNAs. The selected recombinant DNA molecules were hybridized with poly(A)-containing mRNA under R-loop conditions. From the DNA-RNA hybrids the respective mRNAs were melted off and translated in vitro in a rabbit reticulocyte cell-free system. The translational products were analyzed by immunoprecipitation with antibodies raised against ribosomal proteins. The identity of the ribosomal protein gene products was further established by electrophoresis on two-dimensional gels. At least 15 recombinant DNA molecules were shown to contain ribosomal protein genes. Four of them, i.e. Y65, Y89, Y113 and Y138, have been characterized preliminarily.     

Characterization of two types of yeast ribosomal DNA genes.

The intragenic organization of ribosomal DNA from a diploid strain of Saccharomyces cerevisiae was analyzed by using recombinant DNA molecules constructed in vitro. Restriction analysis of the yeast ribosomal DNA with the EcoRI restriction enzyme indicated that eight restriction fragments were present in the ribosomal DNA of this strain: X' (1.87 X 10(6) daltons), A (1.77 X 10(6) daltons), B (1.48 X 10(6) daltons), C (1.22 X 10(6) daltons), D (0.39 X 10(6) daltons), E (0.36 X 10(6) daltons), F (0.22 X 10(6) daltons), and G (0.17 X 10(6) daltons). These fragments were distributed between two different types of ribosomal DNA genes, which had the restriction maps: (formula: see text) in which the underlined region shows the repeating unit. The diploid yeast strain contained approximately equal amounts of each of these two types of genes. The analysis of the recombinant DNA molecules also indicated that the yeast ribosomal genes are homogeneous and extensively clustered.     

酵母核糖体蛋白基因组合转录调控位点统计分析

真核基因的转录调控是后基因组时代研究的主要问题之一,其基础是认识DNA上转录因子结合位点(模体)及分布状况。基于马尔可夫链模型对酵母核糖体蛋白基因上游启动子序列中模体出现次数进行统计,利用Z-score统计量抽提出过表达和低表达的模体,其中95%的模体与实验得到的转录因子结合位点相符合。然后将抽提出的模体两两配对,通过与背景序列比较,找出酵母核糖体蛋白基因中出现概率及距离分布均具有统计显著性的模体对,这些非随机出现的模体对具有潜在的组合转录调控功能,其中一些模体对的组合调控作用已有实验支持。对提取出的模体对在序列中的位置分布进行分析,发现近94%的模体对位于转录起始位点上游,超过半数的模体对两模体之间的最短距离在0～100bp之间,距离小于30bp的模体对接近30%,这样的短距离间隔有利于两模体的相同作用。这些结果将有助于对酵母核糖体蛋白基因转录调控机制的深入认识。     

Introns within ribosomal protein genes regulate the production and function of yeast ribosomes

In budding yeast, the most abundantly spliced pre-mRNAs encode ribosomal proteins (RPs). To investigate the contribution of splicing to ribosome production and function, we systematically eliminated introns from all RP genes to evaluate their impact on RNA expression, pre-rRNA processing, cell growth, and response to stress. The majority of introns were required for optimal cell fitness or growth under stress. Most introns are found in duplicated RP genes, and surprisingly, in the majority of cases, deleting the intron from one gene copy affected the expression of the other in a nonreciprocal manner. Consistently, 70% of all duplicated genes were asymmetrically expressed, and both introns and gene deletions displayed copy-specific phenotypic effects. Together, our results indicate that splicing in yeast RP genes mediates intergene regulation and implicate the expression ratio of duplicated RP genes in modulating ribosome function.     

A pair of Bacillus subtilis ribosomal protein genes mapping outside the principal ribosomal protein cluster.

Before now, the only ribosomal protein gene loci to be identified in Bacillus subtilis map within the principal ribosomal protein gene cluster at about 10 degrees on the linkage map. Using mutants with alterations in large subunit ribosomal proteins L20 or L24, I mapped the corresponding genes near leuA at approximately 240 degrees. The data were fully consistent with the fact that the genes for the two proteins were close together but not near any other ribosomal protein genes, as is also the case with the genes for the corresponding proteins of Escherichia coli.     

Restriction analysis of tandemly repeated yeast ribosomal RNA genes

Summary Ribosomal RNA (rRNA) genes of Saccharomyces cerevisiae are clustered in a DNA repeat unit of 5.9 megadaltons with the gene order 5S-18S-5.8S-25S rRNA (Nath and Bollon, 1977). By using two restriction endonucleases, EcoRII and HindII, which generate DNA fragments that span contiguous portions of two repeat units, we report that the rRNA gene clusters are tandemly repeated without the intervention of additional spacer DNA.The treatment of yeast DNA with the restriction endonucleases EcoRII and HindII result in the generation of 4 different DNA fragments that are of varying sizes and which hybridize with rRNA. The largest DNA fragments, 3.30 megadaltons in the case of HindII and 3.67 megadaltons in the case of EcoRII, encompass regions that code for the two opposite end regions of the 35S precuursor-rRNA. These two end regions are joined by a constant DNA segment of about 0.9 megadaltons in size of which a 0.08 megadalton segment codes for 5S rRNA. Since the 35S precursor-rRNA includes the 5.8S, 18S and 25S rRNA most of the repeat units containing the 4 rRNA coding genes in yeast are linked to each other contiguously without any intervening spacer DNA.A composite map of the DNA restriction fragments obtained by the action of the restriction endonucleases EcoRI, EcoRII, HindII and HindIII on the 5.9 megadalton repeat unit is presented. Some striking features concerning the location of the restriction sites are noted. Of the total 17 DNA restriction sites present on each repeat unit, 9 are located at or near the 3 transcribed spacer regions contained in the 5 megadalton DNA segment that codes for the 35S precursor-rRNA. The 3 transcribed spacer regions in the 35S precursor-rRNA include the two external transcribed spacer regions and an internal transcribed spacer region, the latter representing the 5.8S rRNA.