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E B Keller

Publications and source records attributed to E B Keller.

At least 19 recordsLinked to original sources
PubMed1994

Start site selection by Sp1 in the TATA-less human Ha-ras promoter.

The promoter of the human Ha-ras gene is very GC-rich, has four Sp1-binding sites and no TATA element. Transcription initiates at multiple start sites spread over a 90-base pair region, with a major cluster between +1 and +11. We detected the binding of a HeLa nuclear protein to the region from +6 to +20, a region which overlaps the major cluster and includes nine start sites within its boundaries. When part of this region was mutated, the nine start sites were abolished, so the region may be an initiator. The regulatory elements of the promoter have no differential effect on start site usage. But Sp1 bound to GCIV located at -38 acts as a start site selector, increasing the activity of the start sites from +1 downstream but not the upstream sites at -31, -21, and -10. When spacers of increasing length were inserted 3' to GCIV, the major cluster dwindled, and the upstream sites became strong sites, first the one at -10 and then the one at -21. Thus start sites were strongest when put into an Sp1-selected locus 36 to 53 base pairs downstream from GCIV and weak when outside this locus. The start sites with these properties may be due to initiators.

Animals↗
PubMed1991

The TATA-dependent and TATA-independent promoters of the Drosophila melanogaster actin 5C-encoding gene.

The major cytoskeletal actin of Drosophila melanogaster, actin 5C, is encoded by a gene (act5C) that has two promoters which are differentially controlled and possess distinct sets of regulatory elements. The distal basal promoter has a TATA motif, but the proximal does not. The distal strong positive domain, centered at nucleotide -290, can be shifted and fused directly to the distal basal promoter without losing its activity. It can also activate heterologous basal promoters containing either TATAAAT or TATTTAA signal when directly fused to them, but cannot activate the basal proximal promoter, which is TATA-less. When the entire distal regulatory region, which includes a remote enhancer-like region, is fused to the proximal promoter, it does not increase the proximal promoter activity. Fusion of the distal strong negative domain to the proximal promoter does not inhibit activity. Thus, all the three major strong regulatory domains of the distal promoter are unable to act on the proximal promoter.

Actins↗
PubMed1991

Regulatory elements mediating transcription of the human Ha-ras gene.

In order to identify transcriptional regulatory elements controlling the expression of the human Ha-ras gene and to quantitatively assess the role of each element, we made mutations of the transcriptional regulatory region, including 5' and internal deletions, linker scanning and replacement mutations, and combinations of these mutations all fused to the bacterial chloramphenicol acetyltransferase gene. The promoter activity of each of these mutants was determined by measuring the transient expression of chloramphenicol acetyltransferase activity after transfection into human epithelial HeLa cells. We found that the most important regulatory region consists of two closely linked but functionally independent elements, the non-consensus GC-II element, CGGGCGGGC, centered at position -153 from the major transcription start site cluster and a new element, CCGGAA, centered at position -161 directly upstream from GC-II. In addition, there are two functional regulatory elements which make minor contributions to the full promoter activity; a double CCAAT NF-I binding site at position -88 and an unidentified upstream element between positions -199 and -252. Aside from GC-II, the GC boxes, of which there are a total of six between positions -185 and +85, make little or no contribution to Ha-ras promoter activity when individual mutations are tested in growing HeLa cells. The three potential AP2 sites and a weak single NF-I binding site make no contribution. The basal promoter region extending to position -75 from the major start site cluster has no independent activity in this TATA-less gene.

Base Sequence↗
PubMed1990

Regulatory elements mediating transcription from the Drosophila melanogaster actin 5C proximal promoter.

The major cytoskeletal actin gene of Drosophila melanogaster, the actin 5C gene, has two promoters, the proximal one of which controls constitutive synthesis of actin in all growing tissues. To locate regulatory elements required for constitutive activity of the proximal promoter, mutants of this promoter were fused to the bacterial chloramphenicol acetyltransferase gene and assayed for transient expression activity in cultured Drosophila embryonic Schneider line 2 cells. An essential regulatory element has been located 313 base pairs upstream from the cap site. Deletion of this element lowered expression to one-third of the wild-type level. The element has the sequence AAGTTGTAGTTG, as shown by protein-binding footprinting with the reagent methidiumpropyl-EDTA-Fe(II). This element is probably not a general one, since it was not detected in a search of the published 5'-flanking sequences of 27 Drosophila genes. In addition to this regulatory element, there are five GAGA elements in the actin 5C proximal promoter, some or all of which are essential for the promoter activity as shown by an in vivo competition assay. Although this promoter has no classical TATA element, there is an essential promoter region about 35 base pairs upstream from the cap site that could be a TATA surrogate. The promoter also shows sequences homologous to the alcohol dehydrogenase factor 1-binding site and to the core of the vertebrate serum response element, but mutations of these sites did not affect promoter activity in transient expression assays.

Actins↗
PubMed1990

Positive and negative regulatory elements mediating transcription from the Drosophila melanogaster actin 5C distal promoter.

The major cytoskeletal actin gene of Drosophila melanogaster, the actin 5C gene, has two promoters, the distal one of which controls synthesis of actin in a tissue- and developmental stage-specific manner. This very strong promoter has widely been used for expression of heterologous genes in cultured cells. To locate functional regulatory elements in this distal promoter, mutants of the promoter were fused to the bacterial chloramphenicol acetyltransferase gene and assayed for transient expression activity in cultured Drosophila embryonic Schneider line 2 cells. The results showed that the upstream end of the promoter extends to 522 bp from the transcription start site. In addition, there are two remote activating regions about 2 kb upstream. Between -522 and -379 are two regions that exert a strong negative effect. Downstream from these negative regions are at least six positive regions and a TATA element. The strongest positive determinant of the promoter was identified at -320 as AAAATGTG by footprinting and by a replacement experiment. When the relevant region was replaced by a synthetic sequence containing this element in a random context, the transient expression activity was restored. The sequence TGTATG located at -355 was also identified as a positive element by a similar replacement approach. Apparently the very high activity of this promoter is the result of the combined activities of multiple factors.

Actins↗
PubMed1985

Intron splicing: a conserved internal signal in introns of Drosophila pre-mRNAs.

The introns of Drosophila pre-mRNAs have been analysed for conserved internal sequence elements near the 3' intron boundary similar to the T-A-C-T-A-A-C in yeast introns and the C/T-T-A/G-A-C/T in introns of other organisms. Such conserved internal elements are the 3' splice signals recognized in intron splicing. In the lariat splicing mechanism, the G at the 5' end of an intron joins covalently to the last A of a 3' splice signal to form a branch point in a splicing intermediate. Analysis of 39 published sequences of Drosophila introns reveals that potential 3' splice signals with the consensus C/T-T-A/G-A-C/T are present in 18 cases. In 17 of the remaining cases signals are present which vary from this consensus just in the middle or last position. In Drosophila introns the 3' splice signal is usually located in a discrete region between 18 and 35 nucleotides upstream from the 3' splice point. We note that the Drosophila small nuclear U2-RNA has sequences complementary to C-T-G-A-T, one variant of the signal, and to C-A-G, one variant of the 3' terminus of an intron. We also note that the absence of any A-G between -3 and -19 from the 3' splice point may be an essential feature of a strong 3' boundary.

Animals↗
PubMed1984

Intron splicing: a conserved internal signal in introns of animal pre-mRNAs.

Splicing of introns of yeast pre-mRNAs requires an internal conserved sequence T-A-C-T-A-A-C that is located 20-55 nucleotides from the 3' intron boundary. Sequences differing only in certain positions from this yeast signal have now been identified in the corresponding internal region of pre-mRNA introns of a variety of animal genes. A computer program that searches for homologues to a consensus structure and calculates the accuracy of match of each homologue is used to locate these sequences. We list here the signals found by this search in introns of sea urchin, mouse, rat, and human genes and give the consensus for each species. We also give the consensus found for Drosophila and chicken and duck signals. We then discuss the accumulating evidence that these internal signals are required for splicing in animals. It is also noted that a single-stranded region of small nuclear RNA U2 contains sequences complementary both to the proposed mammalian internal signal and to the neighboring CT-A-G at the 3' intron boundary. A role for U2 ribonucleoprotein in intron splicing is thus suggested.

Animals↗
PubMed1983

DNA sequence of two linked actin genes of sea urchin.

DNA sequences have been determined for two actin genes which are closely linked in the genome of the sea urchin Strongylocentrotus purpuratus. The two genes have the same 5'-3' orientation; they were apparently formed originally by tandem gene duplication. The amino acids encoded by the two genes closely resemble those of cytoplasmic actins of mammals and slime molds and differ somewhat from those of mammalian muscle actin. Actin gene 1 had been tentatively identified earlier as the gene for an embryonic cytoplasmic actin by the homology of the 3' noncoding region with that of the cDNA of an embryonic actin mRNA from S. purpuratus. The DNA sequence of gene 1 shows presumptive signals for the initiation and termination of transcription which would govern the formation of a mature mRNA of 1.9 kilobases. Both actin genes 1 and 2 have introns in their coding regions at codons 121/122 and 204. These positions for actin introns have been reported so far only in the rat, not in lower organisms. The divergence of the sequences of these coding-region introns in the two actin genes is 66%, suggesting that the genes diverged about 90 million years ago. By contrast to the introns, the coding regions have been highly conserved; the amino acids of the two genes differ by only 1.3%, and the silent sites of the codons differ by only 12%.

Actins↗
PubMed1981

The chromosomal arrangement of two linked actin genes in the sea urchin S. purpuratus.

Four distinct actin genes of the sea urchin Strongylocentrotus purpuratus have been isolated from a recombinant Charon 4 phage library of genomic DNA. The four genes differ considerably from each other in many of their restriction sites. Two of the four genes are closely linked; they are present in the same fragment of cloned DNA. This fragment has been extensively mapped, and some parts of the DNA have been sequenced. The two linked genes are oriented in the same direction, separated by 7.5 kb of DNA. One has an intron following the CAG that codes for the glutamine residue at position 121 in the amino acid sequence of actin. This represents the fifth distinct site at which introns have been found in actin genes, suggesting that the primordial actin gene had at least 6 exons and 5 introns. The actin genes from a distinctive family in which most introns have apparently been precisely excised from the genes.

Actins↗
PubMed1979

leu operon of Salmonella typhimurium is controlled by an attenuation mechanism.

The nucleotide sequence of the control region of the leu operon of Salmonella typhimurium was determined. A prominent feature of this region is a signal for termination of transcription. In vitro, transcription does terminate at this site, yielding a leader RNA of about 160 nucleotides as a major product. This leader RNA is potentially translatable into a peptide containing 28 amino acids, 4 of which are adjacent leucine residues. Several regions of base complementarity exist within the leader, positioned such that pairing of one region precludes pairing of another. The position of the four leucine codons relative to two regions of base complementarity suggest a model for the regulation of the leu operon similar to that proposed by Yanofsky and coworkers for the trp operon. In addition, a third region of base complementarity was identified which, when incorporated into the model, explains why premature termination is the usual outcome when transcription is initiated in vitro by purified RNA polymerase.

Base Sequence↗
PubMed1979

Alternative secondary structures of leader RNAs and the regulation of the trp, phe, his, thr, and leu operons.

The trp, phe, his, thr, and leu operons of enteric bacteria are regulated by a transcriptional attenuation mechanism. Under conditions of amino acid sufficiency, transcription terminates at an attenuator site after a leader of about 150 nucleotides has been synthesized. Under conditions of limitation of a controlling amino acid, transcription continues past the attenuator into adjacent structural genes. As demonstrated by others, each of the five leader RNAs contains two regions of potential secondary structure which are partially overlapping. One of these regions occurs at the 3' terminus of the leader and is named the "terminator." The other region, which potentially can preclude the formation of the terminator, is named the "preemptor." Conditions that allow the preemptor to form result in derepression. We report here that the five published leader RNA sequences contain an additional potential region of secondary structure, which we call the "protector." The protector partially overlaps the preemptor in such a way that pairing of the former precludes pairing of the latter. For derepression to occur, a ribosome that is translating the leader must block the protector without blocking the preemptor, a condition that is met when the ribosome is arrested at the 3' end of a set of control codons. Including the protector in the model for attenuation explains why derepression of the operon does not result from the arrest of a ribosome at a codon preceding the control set. It also explains why termination is the outcome when transcription occurs in the absence of ribosomes. Finally, termination is the predicted outcome when unfettered translation of the leader RNA occurs, resulting in release of the ribosome at the translational stop signal.

Amino Acids↗
PubMed1975

The polyadenylate polymerases from yeast.

Poly(A) polymerase activity was first detected in yeast extracts, primarily in association with the ribosomal fraction, by Twu and Bretthauer in 1971 (Twu, J. S., and Bretthauer, RK. (1971) Biochemistry 10, 1576-1582). This activity has now been separated into three distinct enzymes by chromatography on DEAE-cellulose. Each of the three enzymes can catalyze the incorporation of adenylate residues from ATP into a polyadenylate (poly(A)) tract at the 3' terminus of a primer RNA. Enzyme I elutes at 0.07 M ammonium sulfate from the DEAE-cellulose column, utilizes the mixed polynucleotide poly(A,G,C,U) or ribosomal RNA most efficiently in vitro, and may be responsible in vivo for the initiation of the poly(A) tracts found on yeast messenger RNA. Enzyme II elutes from the column at 0.20 M ammonium sulfate, requires poly(A) itself or an RNA primer containing a 3'-oligo(A) tract, and may be responsible in the nucleus for the elongation of tracts initiated by enzyme I. Enzyme III elutes from the column at 0.56 M ammonium sulfate and is present in low amounts in nuclear extracts. It may be involved in adding poly(A) tracts to messenger RNA in mitochondria. These enzymes also have the intrinsic capacity for the incorporation of cytidylate residues from CTP, which correlates with the finding of cytidylate residues in the poly(A) tracts present in the yeast RNA which is rapidly labeled in vivo. About 75% of the total poly(A) polymerase activity of yeast is enzyme I, most of which is present in the soluble protein fraction of the whole yeast extract. About 20% of the total poly(A) polymerase is enzyme II, and 1 to 5% is enzyme III. All three of the yeast poly(A) polymerases require an RNA primer with a free 3'-hydroxyl group, show no requirement for a DNA template, require Mn-2+ for optimal activity, have pH optima of 8.5, and are inhibited by GTP, CTP, UTP, and native yeast DNA. Polymerases I and II have similar molecular weights by gel filtration.

Adenosine Triphosphate↗
PubMed1974

Poly(A) polymerase and poly(g) polymerase in wheat chloroplasts.

Extracts of wheat chloroplasts contain a poly(A) polymerase which can polymerize AMP residues from ATP onto an RNA primer. Whole extracts of wheat leaves also contain another poly(A) polymerase which is present in much larger amount and is probably derived from the nuclei. Both polymerases can utilize as primer poly(A), poly(C), transfer RNA, and ribosomal RNA, but only the chloroplast polymerase can utilize poly(U) and poly(G). Both enzymes have a specific requirement for ATP. Extracts of wheat chloroplasts contain, in addition to the poly(A) polymerase, a poly(G) polymerase which can polymerize GMP residues from GTP onto primers such as poly(G), poly(A), or ribosomal RNA. The poly(G) polymerase cannot utilize ATP but can slowly polymerize CMP from CTP. When the two chloroplast polymerases are present together in an in vitro incubation with ATP plus GTP and poly(A), the polymerization product is a mixed poly(A,G) tract.

Journal Article↗