https://www.cell.com/cell/pdf/0092-8674(87)90503-4.pdf

The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library.

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

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

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate

Ecological stoichiometry is the study of the balance of multiple chemical elements in ecological interactions. This paper reviews recent findings in this area and seeks to broaden the stoichiometric concept for use in evolutionary studies, in integrating ecological dynamics with cellular and genetic mechanisms, and in developing a unified means for studying diverse organisms in diverse habitats. This broader approach would then be considered “biological stoichiometry”. Evidence supporting a hypothesised connection between the C:N:P stoichiometry of an organism and its growth rate (the “growth rate hypothesis”) is reviewed. Various data indicate that rapidly growing organisms commonly have low biomass C:P and N:P ratios. Evidence is then discussed suggesting that low C:P and N:P ratios in rapidly growing organisms reflect increased allocation to P-rich ribosomal RNA (rRNA), as rapid protein synthesis by ribosomes is required to support fast growth. Indeed, diverse organisms (bacteria, copepods, fishes, others) exhibit increased RNA levels when growing actively. This implies that evolutionary processes that generate, directly or indirectly, variation in a major life history trait (specific growth rate) have consequences for ecological dynamics due to their effects on organismal elemental composition. Genetic mechanisms by which organisms generate high RNA, high growth rate phenotypes are discussed next, focusing on the structure and organisation of the ribosomal RNA genes (the “rDNA”). In particular, published studies of a variety of taxa suggest an association between growth rate and variation in the length and content of the intergenic spacer (IGS) region of the rDNA tandem repeat unit. In particular, under conditions favouring increased growth or yield, the number of repeat units (“enhancers”) increases (and the IGS increases in length), and transcription rates of rRNA increase. In addition, there is evidence in the literature that increased numbers of copies of rDNA genes are associated with increased growth and production. Thus, a combination of genetic mechanisms may be responsible for establishing the growth potential, and thus the RNA allocation and C:N:P composition, of an organism. Furthermore, various processes, during both sexual and asexual reproduction, can generate variation in the rDNA to provide the raw material for selection and to generate ecologically significant variation in C:N:P stoichiometry. This leads us to hypothesize that the continuous generation of such variation may also play a role in how species interactions develop in ecosystems under different conditions of energy input and nutrient supply.

Biological stoichiometry from genes to ecosystems.

CONTENTS PERSPECTIVES AND SUMMARY 75 REGULATION OF RIBOSOMAL PROTEIN SyNTHESIS 77 Organization of Ribosomal Protein Genes ...... 78 Translational Feedback Regulation 78 Transcription of Ribosomal Protein Genes and I ts Regulation 91 REGULATION OF rRNA AND RIBOSOME SyNTHESIS 9S Organization ofrRNA Genes and Their Transcription 96' Stringent Control 99 Growth Rate-Dependent Control 101 O ther Possible Modes of R egulation 109

Gail Baughman

Papers

Regulation of the Synthesis of Ribosomes and Ribosomal Components