The Phenomenological Approach

Oppenheim, Loïs

doi:10.2307/461765

Cited by 10 publications

(18 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the trp operon, the stop codon of trpE overlaps the start codon of trpD (23). A similar arrangement of codons exists between trpB and trpA (23). A different type of overlap was found in the pyrB-pyrI operon, in which the stop codon of pyrB overlaps the Shine-Delgarno sequence of pyrI (24).…”

Section: Discussionmentioning

confidence: 97%

See 1 more Smart Citation

Structural features of thehisT operon ofEscherichia coliK-12

Arps¹,

Marvel

Rubin³

et al. 1985

Nucl Acids Res

View full text Add to dashboard Cite

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

Section: Discussionmentioning

confidence: 97%

“…In the trp operon, the stop codon of trpE overlaps the start codon of trpD (23). A similar arrangement of codons exists between trpB and trpA (23).…”

Section: Discussionmentioning

confidence: 99%

Structural features of thehisT operon ofEscherichia coliK-12

Arps¹,

Marvel

Rubin³

et al. 1985

Nucl Acids Res

View full text Add to dashboard Cite

show abstract

“…The nonflowering plant Marchantia polymorpha also has a close positioning of the termination and initiation codons for the 13 and E genes, and although they are 5 bp apart, the ShineBiochemistry: Gatenby et al The mechanism of translational coupling is not clearly understood. Two possibilities have been considered for a tightly coupled system (12,38). (i) Translational initiation of the distal gene is defective because of a weak ribosomebinding site, and only a translating ribosome approaching from the upstream gene can initiate translation.…”

Section: Discussionmentioning

confidence: 99%

“…The close proximity of the termination and initiation codons of two genes, or the overlapping of parts of their sequences, indicates that translation of the genes may be coupled. In E, coli translational coupling has been identified in the trp (12,13), gal (14), ilv (15), and several ribosomal protein (16)(17)(18)(19) operons, where it presumably serves as a mechanism to ensure the appropriate level of synthesis of these proteins. Reports on translational coupling in other organisms are scarce, and no translation coupling in chloroplast genes has been reported, although the existence of coupling was invoked to explain the overlapping P3 and E genes (7,8).…”

mentioning

confidence: 99%

Translational coupling of the maize chloroplast atpB and atpE genes

Gatenby¹,

Rothstein²,

Nomura³

1989

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The genes for the 13 and E subunits of maize chioroplast ATP synthase are encoded by the organelle genome, are cotranscribed, and have overlapping translation initiation and termination codons. To determine whether the atpB and atpE genes are translationally coupled, they were transformed into Escherichia coli on a multicopy plasmid. Synthesis of full-length 13 and E polypeptides demonstrated correct initiation of translation by the bacterial ribosomes. To assay for translational coupling, the promoter-distal alpE gene was fused to lacZ, resulting in the synthesis of an active hybrid B8-galactosidase. A frameshift mutation was introduced into the promoter-proximal atpB gene, and its effect on the transcription and translation of the atpE::lacZ fusion was measured. The mutation resulted in a 1000-to 2000-fold reduction in 13-galactosidase activity, but only a 2-fold decrease in LacZ mRNA synthesis rates or galactoside transacetylase levels. Similar results were obtained when the atpB/atpE::lacZ fusion and the atpB frameshift mutation were introduced into the photosynthetic cyanobacterium Synechocystis sp. PCC6803. We show that >99% of atpE translation depends on successful translation of atpB and, thus, conclude that the two genes are translationally coupled.The energy-transducing ATP synthase (ATPase) has a highly conserved structure that couples proton translocation across membranes with the synthesis of ATP. The complex present in chloroplasts, mitochondria, and prokaryotes consists of an F1, or CF1, extrinsic membrane component composed of five subunits (a-e) that catalyzes the final step in oxidative phosphorylation or photophosphorylation (1, 2). The integral membrane FO, or CFO, sector forms the proton channel. Genes for the a, /3, and 6 subunits of CF1 and subunits I, III, and IV of CFo are present in the chloroplast genome (3-6).The remaining three subunits (y,8, and II) are nuclear encoded and are imported into chloroplasts for assembly into an active enzyme. The chloroplast atp genes are organized into two transcriptional units that have retained a similar positional conservation to the arrangement ofgenes in the atp operon of Escherichia coli (3, 4). One cluster of genes has the order atpl/atpH/atpF/atpA, and there is evidence that they are cotranscribed (3,4). The other chloroplast-encoded atp genes are located many kilobases from the atpIHFA cluster (4-6), have the order atpB/atpE, and encode the /3 and E

show abstract

“…Coexpression of these adjacent genes was examined and it was observed that their translation was coupled, i.e. whenever translation of the trpE or trpB coding region was prematurely terminated by introducing a stop codon, expression of the downstream coding region, trpD or trpA, was markedly reduced (86). This was not due solely to Rho-mediated transcription termination.…”

Section: Translational Couplingmentioning

confidence: 99%

Advancing Our Knowledge in Biochemistry, Genetics, and Microbiology Through Studies on Tryptophan Metabolism

Yanofsky

2001

Annu. Rev. Biochem.

View full text Add to dashboard Cite

I was fortunate to practice science during the last half of the previous century, when many basic biological and biochemical concepts could be experimentally addressed for the first time. My introduction to research involved isolating and identifying intermediates in the niacin biosynthetic pathway. These studies were followed by investigations focused on determining the properties of genes and enzymes essential to metabolism and examining how they were alterable by mutation. The most challenging problem I initially attacked was establishing the colinear relationship between gene and protein. Subsequent research emphasized identification and characterization of regulatory mechanisms that microorganisms use to control gene expression. An elaborate regulatory strategy, transcription attenuation, was discovered that is often based on selection between alternative RNA structures. Throughout my career I enjoyed the excitement of solving basic scientific problems. Most rewarding, however, was the feeling that I was helping young scientists experience the pleasure of performing creative research. CONTENTS

show abstract

The Phenomenological Approach

Cited by 10 publications

References 0 publications

Structural features of thehisT operon ofEscherichia coliK-12

Structural features of thehisT operon ofEscherichia coliK-12

Translational coupling of the maize chloroplast atpB and atpE genes

Advancing Our Knowledge in Biochemistry, Genetics, and Microbiology Through Studies on Tryptophan Metabolism

Contact Info

Product

Resources

About