Processed pseudogenes for rat cytochrome c are preferentially derived from one of three alternate mRNAs.

Scarpulla, Richard C.

doi:10.1128/mcb.4.11.2279

Cited by 74 publications

(40 citation statements)

References 33 publications

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“…The coding potential for other processed pseudogenes that lack deleterious mutations in the coding region has been examined. They are the human metallothionein II pseudogene (11,29), the rat RC9 cytochrome c pseudogene (25), the human DHFR 1 pseudogene (1,6), and the mouse L32 ribosomal protein pseudogene rpL32-4A (8). They all appeared to be transcriptionally inactive, but expression at a very low level has not been disproved.…”

Section: Resultsmentioning

confidence: 99%

Multiple calmodulin mRNA species are derived from two distinct genes.

Nishimura¹,

Kishi²,

Sokabe³

1987

Mol. Cell. Biol.

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We have observed three calmodulin mRNA species in rat tissues. In order to know from how many expressed genes they are derived, we have investigated the genomic organization of calmodulin genes in the rat genome. From a rat brain cDNA library, we obtained two kinds of cDNAs (pRCM1 and pRCM3) encoding authentic calmodulin. DNA sequence analysis of these cDNA clones revealed substitutions of nucleotides at 73 positions of 450 nucleotides in the coding region, although the amino acid sequences of these calmodulins are exactly the same. DNA sequences in the 5' and 3' noncoding regions are quite different between these two cDNAs. From these results, we conclude that they are derived from two distinct bona fide calmodulin genes, CaMI (pRCM1) and CaMII (pRCM3). Total genomic Southern hybridization suggested four distinct calmodulin-related genes in the rat genome. By cloning and sequencing the calmodulin-related genes from rat genomic libraries, we demonstrated that the other two genes are processed pseudogenes generated from the CaMI (XSC9) and CaMII (ASC8) genes, respectively, through an mRNA-mediated process of insertions. Northern blotting showed that the CaMI gene is transcribed in liver, muscle, and brain in similar amounts, whereas the CaMU gene is transcribed mainly in brain. Si nuclease mapping indicated that the CaMI gene produced two mRNA species (1.7 and 4 kilobases), whereas the CaMII gene expressed a single mRNA species (1.4 kilobases).Calmodulin, a monomeric Ca2l-binding protein, mediates intracellular calcium interactions by regulating a variety of important enzyme systems through a calcium-calmodulin complex (12,17). It is reported that increases in the intracellular calmodulin concentration are coupled to the G1-S transition of the cell cycle (3) and that calmodulin may play a regulatory role in the reentry of quiescent (Go) cells into the cell cycle (5). The anticalmodulin drug (W13) specifically and reversibly inhibited the progression of cells into the S phase and DNA synthesis (4). These results suggest an important role for calmodulin in the regulation of cell cycle progression and DNA synthesis.The multifunctional roles of calmodulins in the cell through the regulation of calcium interactions with a variety of fundamental enzymes poses a question of how many expressed calmodulin genes exist in the cell. To answer this question, we have investigated the number of expressed calmodulin genes in the rat genome. Here, we report the existence of two kinds of bona fide calmodulin genes in the rat genome which generate at least three kinds of mRNAs species of different sizes. MATERIALS AND METHODSCloning and sequencing of cDNA (pRCM3) and a processed gene (XSC8). Construction of a rat (spontaneously hypertensive rat) genomic library and screening of a processed gene (XSC8) were described before (20). The rat (SpragueDawley) brain cDNA library, a generous gift from Hiroto Okayama (21), was screened with two kinds of probes according to the method of Hanahan and Meselson (10). One probe consisted of the S...

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Section: Resultsmentioning

confidence: 99%

Multiple calmodulin mRNA species are derived from two distinct genes.

Nishimura¹,

Kishi²,

Sokabe³

1987

Mol. Cell. Biol.

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“…Alternatively, promiscuous transcription in the germ line, leading to the generation of Fig. 1 (55). We note that an analogous retroposon is the mouse a-globin processed pseudogene (45,69).…”

Section: Jailacna--a------c-----------------------a6lciiaemjalibmentioning

confidence: 99%

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon.

Soares¹,

Schon²,

Henderson³

et al. 1985

Mol. Cell. Biol.

229

145

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Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome 1 but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes.DNA sequence comparisons of the gene-flanking regions in rats and nmice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.Rats (as well as mice and three fish species) have two insulins instead of one, in contrast to other organisms (13,23). These rat hormones are the products of two nonallelic preproinsulin genes (57) that are almost equally expressed (11). Characterization of the duplicated genes (36), isolated from a rat chromosomal DNA library, indicated a significant structural difference between them. The gene for preproinsulin I has a single 119-base-pair (bp) intron interrupting the segment corresponding to the 5' noncoding region of the mRNA, whereas the other gene, encoding preproinsulin II, contains in addition to this small intron a second 499-bp intron interrupting the segment encoding the C-peptide. Since the structures of the unique chicken (46) and human (2, 62) genes are similar to that of the rat gene II (two introns at corresponding positions) we concluded that the two-intron organization corresponds to that of the common ancestor and that introns can be lost during evolution (46). This conclusion was strengthened by the subsequent determination of the structures of the unique dog (30) and guinea pig (7) preproinsulin genes, which are of the twointron type.Intron loss was subsequently documented in a mouse ot-globin pseudogene (45, 69) and later in other pseudogenes that exhibit clearly the features of processed genes (22; see references 34, 56, and 68 for reviews). These observations raised the possibility that the rat preproinsulin I gene was a * Corresponding author. retroposon (51) that had been generated by an RNAmediated duplication-transposition event but which for some reason remained functional. To examine this possibility we mapped the chromosomal location of the two genes and characterized their flanking regions by DNA sequencing to define the break po...

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“…Sl-mapping of Transcripts Total RNA was isolated from strain W3110 wild-type, which was growing exponentially in LB + cysteine medium at 37°C, by variations of the "hot phenol" (12) or "hot SDS" methods (13). Labeling 5' ends of restriction fragments, DNA strand separations, RNA-DNA hybridizations, and nuclease Sl treatment were performed as described by Scarpulla (14). Hybridization reactions in different experiments contained 50-250 ig of total bacterial RNA or purified tRNA control and 100,000-400,000 cpm (Cerenkov) of 5' end-labeled, single-strand DNA.…”

Section: Imterials and Iethods Materials Smentioning

confidence: 99%

Structural features of thehisT operon ofEscherichia coliK-12

Arps¹,

Marvel

Rubin³

et al. 1985

Nucl Acids Res

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The DNA sequence of a 2.3-kilobase segment of the E. coli hisT operon was determined. Analysis of the sequence indicated that the upstream gene in the operon encodes a 36,364-dalton polypeptide, which runs aberrantly on SDS-polyacryl ami de gel s. The distal hisT gene encodes the tRNA modification enzyme, pseudouridine synthase I, whichwias shown to have a polypeptide molecular mass of 30,399 daltons. The DNA sequence was consistent with the phenotypes and hisT expression of mutant operons. Analysis of the sequence and genetic complementation experiments demonstrated that the upstream and hisT genes are evolutionarily, structurally, and functionally unrelated; however, translation signals for the two genes overlap, which is consistent with genetic evidence suggesting translational coupling. Codon usage in the upstream gene is radically different from the hisT gene and may underlie the differential expression observed from the operon. Gene-inactivation experiments and Sl-mapping of in vivo transcripts indicated that the operon contains an additional upstream gene. S1-mapping experiments al so confirmed the presence of an internal promoter, which might be stringently controlled. Taken together, these results show that the structure of the hisT operon is complex and suggest that the operon might be regulated at sever levels.INTRODUCTI ON Maturation of stable RNA molecules occurs by multistep processing and modification of primary transcripts. A considerable number of biochemical and genetic studies have outlined the organization of genes that specify stable RNA molecules and the enzymatic cleavage steps involved in processing (reviewed in 1). In contrast, comparatively little is known about modification, even though this process is a dynamic, integral part of stable RNA biosynthesis in both prokaryotes and eukaryotes. In Escherichia coli, greater than 1% of the chromosome encodes the enzymes that modify tRNA and rRNA molecules (2). With the exception of the work of Bjork and his associates on tRNA-methyl transferase genes (sumimarized in 2), the structure and regulation of these genes are largely unknown. In addition, there is currently inadequate knowledge of the functions played by RNA modifications. Modifications undoubtedly play structural roles in stable RNA molecules, and they may influence the interac-© I R L Press Limited, Oxford, England.

show abstract

Processed pseudogenes for rat cytochrome c are preferentially derived from one of three alternate mRNAs.

Cited by 74 publications

References 33 publications

Multiple calmodulin mRNA species are derived from two distinct genes.

Multiple calmodulin mRNA species are derived from two distinct genes.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon.

Structural features of thehisT operon ofEscherichia coliK-12

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