The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter mutations. Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence.

/pdf/compilation-and-analysis-of-escherichia-coli-promoter-dna-3laukojglx.pdf

Compilation and analysis of Escherichia coli promoter DNA sequences.

Fluctuations in rates of gene expression can produce highly erratic time patterns of protein production in individual cells and wide diversity in instantaneous protein concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular concentrations competitively control a switch point in a pathway, stochastic variations in their concentrations can produce probabilistic pathway selection, so that an initially homogeneous cell population partitions into distinct phenotypic subpopula- tions. Many pathogenic organisms, for example, use this mechanism to randomly switch surface features to evade host responses. This coupling between molecular-level fluctuations and macroscopic phenotype selection is analyzed using the phage l lysis-lysogeny decision circuit as a model system. The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular- level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations. The kinetic model of the decision circuit uses the stochastic formulation of chemical kinetics, stochastic mechanisms of gene expression, and a statistical-thermodynamic model of promoter regulation. Conven- tional deterministic kinetics cannot be used to predict statistics of regulatory systems that produce probabilis- tic outcomes. Rather, a stochastic kinetic analysis must be used to predict statistics of regulatory outcomes for such stochastically regulated systems.

/pdf/stochastic-kinetic-analysis-of-developmental-pathway-545z0j2lmj.pdf

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda -infected escherichia coli cells

African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including ∼900 pseudogenes and ∼1700 T. brucei–specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.

https://science.sciencemag.org/content/sci/309/5733/416.full.pdf

The Genome of the African Trypanosome Trypanosoma brucei

An abundant chloroplast protein is implicated in the assembly of the oligomeric enzyme ribulose bisphosphate carboxylase-oxygenase, which catalyses photosynthetic CO2-fixation in higher plants. The product of the Escherichia coli groEL gene is essential for cell viability and is required for the assembly of bacteriophage capsids. Sequencing of the groEL gene and the complementary cDNA encoding the chloroplast protein has revealed that these proteins are evolutionary homologues which we term 'chaperonins'. Chaperonins comprise a class of molecular chaperones that are found in chloroplasts, mitochondria and prokaryotes. Assisted post-translational assembly of oligomeric protein structures is emerging as a general cellular phenomenon.

Homologous plant and bacterial proteins chaperone oligomeric protein assembly

http://compbio.korea.ac.kr/wiki/images/8/83/Mmbr.1996.expression.pdf

Strategies for achieving high-level expression of genes in Escherichia coli.

A new gene in bacteriophage λ is described. The product of this gene cro prevents expression of immunity and regulates the expression of those genes to the left of the immunity region. cro- mutants have been isolated and characterized.

https://www.pnas.org/content/pnas/66/3/855.full.pdf

Regulation of Repressor Expression in λ

Acute infection of mice with Trypanosoma cruzi results in severe immunodepression and the appearance of autoimmune symptoms. In vitro, concanavalin A-stimulated T cells from spleens of infected animals could neither produce nor respond to interleukin 2. Interleukin 2 production was not restored by addition of exogenous interleukin 1, and proliferative response to concanavalin A was not restored by exogenous interleukin 2. A population of Thy-1-negative cells in the spleen of infected animals was shown to suppress the concanavalin A proliferative response and, to a lesser extent, the production of interleukin 2. These and other symptoms of T. cruzi-infected mice are similar to the immune dysfunction of autoimmune lpr/lpr mice. These findings are discussed in relationship to the pathology of Chagas disease.

Modification of T-cell proliferation and interleukin 2 production in mice infected with Trypanosoma cruzi.

https://www.cell.com/cell/pdf/0092-8674(77)90102-7.pdf

Surface changes in differentiating Friend erythroleukemic cells in culture

There are two promoters for transcription of gene cI in phage λ, the gene that codes for phage repressor. The promoters, called pre and prm, are located on the distal (pre) and proximal (prm) sides of gene cro, which itself is adjacent to cI. Since cI and cro are transcribed in opposite directions, cI transcription initiating at pre gives rise to an antisense transcript of cro, while cI transcription initiating at prm does not. Pre, active after infection of a sensitive cell, is stimulated by products of phage genes cII and cIII, and may be located at the site defined by the mutant cY. Prm is active in an established lysogen. These conclusions are based on measurements of the rates of synthesis of antisense cro RNA, cI RNA, and repressor protein in infected and lysogenic cells. To measure antisense RNA, an assay based on the formation of nuclease-resistant, double-stranded RNA, specific to the cro region, was developed. These results raise the possibility that bidirectional transcription of cro has a regulatory function in phage λ.

https://www.pnas.org/content/pnas/69/11/3156.full.pdf

Bidirectional Transcription and the Regulation of Phage λ Repressor Synthesis

The expression of genes coding for variable surface glycoproteins (VSGs) in Trypanosoma equiperdum is linked to duplicative transpositions of silent, basic copy sequences into telomere-linked expression sites. Examination of three independently derived late-appearing trypanosome clones expressing VSG-78 revealed that the expressed gene in all cases is composed of sequences derived from three or four individual silent genes. The 182 base pairs at the 3' end of the coding sequence are derived from one silent gene, the 3' donor. The remaining 5' segment is a mosaic structure containing variable-length segments derived from two, or perhaps three, related silent genes. All of the silent genes that participate in the construction of the VSG-78 expression-linked copy (ELC) genes contain multiple stop codons and are unable to code for VSGs. Individual silent pseudogenes complement one another in the mosaic structure of the 5' portions of the ELC genes and create functional VSG genes. The joining of the 3' and 5' portions of the composite genes occurs in short regions of homology and suggests a mechanism by which the ordered expression of the VSG genes is generated.

https://www.pnas.org/content/pnas/86/23/9375.full.pdf

Harvey Eisen

Papers

Regulation of Repressor Expression in λ

Modification of T-cell proliferation and interleukin 2 production in mice infected with Trypanosoma cruzi.

Surface changes in differentiating Friend erythroleukemic cells in culture

Bidirectional Transcription and the Regulation of Phage λ Repressor Synthesis

Active late-appearing variable surface antigen genes in Trypanosoma equiperdum are constructed entirely from pseudogenes.