Endy:Translation demand/Demand.bib

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@article{Gadgil2005lu, Abstract = {Temperature shift is often practiced in the cultivation of Escherichia coli to reduce undesired metabolite formation and to maximize synthesis of correctly folded heterologous protein. As the culture temperature is decreased below the optimal 37 degrees C, growth rate decreases and many physiological changes occur. In this study, we investigated the gene expression dynamics of E. coli on switching its cultivation temperature from 37 to 33 and 28 degrees C using whole genome DNA microarrays. Approximately 9% of the genome altered expression level on temperature shift. Overall, the alteration of transcription upon the downshift of temperature is rapid and globally distributed over a wide range of gene classes. The general trends of transcriptional changes at 28 and 33 degrees C were similar. The largest functional class among the differentially expressed genes was energy metabolism. About 12% of genes in energy metabolism show a decrease in their level of expression, and approximately 6% show an increase. Consistent with the decrease in the glucose uptake rate, many genes involved in glycolysis and the PTS sugar transport systems show decreased expression. Genes encoding enzymes related to amino acid biosynthesis and transport also have reduced expression levels. Such decrease in expression probably reflects the reduced growth rate and the accompanying reduction in energy and amino acid demand at lower temperatures. However, nearly all genes encoding enzymes in the TCA cycle have increased expression levels, which may well be compensating the reduction of the activity of TCA cycle enzymes at lower temperatures. Temperature shift also results in shift of the cytochromes from the high affinity cytochrome o system to the low affinity cytochrome d system. There is no evidence that protein processing genes are selectively altered to create favorable conditions for heterologous protein synthesis. Our results indicate that the beneficial effect of temperature shift in many biotechnological processes is likely to be attributed to the general effect of reduced growth and metabolism.}, Affiliation = {Department of Chemical Engineering and Materials Science, Biomedical Genomics Center, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455-0132, USA.}, Aid = {10.1021/bp049630l [doi]}, Au = {Gadgil M and Kapur V and Hu WS}, Author = {Gadgil, Mugdha and Kapur, Vivek and Hu, Wei-Shou}, Da = {20050603}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20050921}, Edat = {2005/06/04 09:00}, Ip = {3}, Jid = {8506292}, Journal = {Biotechnol Prog}, Keywords = {Demand, Demand Response, Environmental Changes}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Gadgil/Gadgil2005vd.pdf}, Mhda = {2005/09/22 09:00}, Number = {8756-7938}, Own = {NLM}, Pages = {689-99}, Pl = {United States}, Pmid = {15932244}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (Transcription Factors)}, Sb = {IM}, So = {Biotechnol Prog 2005 May-Jun;21(3):689-99.}, Stat = {MEDLINE}, Title = {Transcriptional response of Escherichia coli to temperature shift.}, Volume = {21}, Year = {2005}}

@article{Weber2005aq, Abstract = {The sigmaS (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, sigmaS is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of sigmaS and that sigmaS should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a sigmaS consensus promoter in silico. Moreover, our results suggest that sigmaS-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect sigmaS and/or sigma70 selectivity of many promoters. These observations indicate that certain modules of the sigmaS-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with sigma70 RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.}, Affiliation = {Institut fur Biologie, Mikrobiologie, Freie Universitat Berlin, Konigin-Luise-Str. 12-16a, 14195 Berlin, Germany.}, Aid = {10.1128/JB.187.5.1591-1603.2005 [doi]}, Au = {Weber H and Polen T and Heuveling J and Wendisch VF and Hengge R}, Author = {Weber, Harald and Polen, Tino and Heuveling, Johanna and Wendisch, Volker F and Hengge, Regine}, Da = {20050217}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20050322}, Edat = {2005/02/18 09:00}, Ip = {5}, Jid = {2985120R}, Journal = {J Bacteriol}, Keywords = {Demand, Demand Response, Environmental Changes}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Weber/Weber2005oj.pdf}, Mhda = {2005/03/23 09:00}, Number = {0021-9193}, Own = {NLM}, Pages = {1591-603}, Pl = {United States}, Pmid = {15716429}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (sigma factor KatF protein, Bacteria)}, Sb = {IM}, So = {J Bacteriol 2005 Mar;187(5):1591-603.}, Stat = {MEDLINE}, Title = {Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity.}, Volume = {187}, Year = {2005}}

@misc{Y2005js, Abstract = {The osmotic tolerance of microbial cells of different microorganisms was investigated as a function of glycerol concentration and temperatures. Cells displayed specific sensitivity to dehydration in glycerol solutions. The viability of Gram-negative strains (Escherichia coli, Bradyrhizobium japonicum), Gram-positive strains (Lactobacillus plantarum, L. bulgaricus), and yeasts (Saccharomyces cerevisiae, Candida utilis) decreased with increasing osmotic pressure. For each strain, a characteristic osmotic pressure threshold causing a loss of 40% of the population at the growth temperature was determined: 26-40 MPa for E. coli, 15-25 MPa for B. japonicum, 7-15 MPa for L. bulgaricus, 40-133 MPa for L. plantarum, 50-100 MPa for S. cerevisiae, and 15-26 MPa for C. utilis. Because this threshold varies with temperature, it was possible to construct a diagram that could be helpful to the determination of the sensitivity of each strain to osmotic stress as a function of osmotic pressure and temperature. (c) 2005 Wiley Periodicals, Inc.}, Affiliation = {Laboratoire de Genie des Procedes Alimentaires et Biotechnologiques, Ecole Nationale Superieure de Biologie Appliquee a la Nutrition et a l'Alimentation, 1 Esplanade Erasme, 21000 Dijon, France.}, Aid = {10.1002/bit.20631 [doi]}, Author = {Mille Y and Beney L and Gervais P}, Da = {20050823}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dep = {20050822}, Edat = {2005/08/24 09:00}, Jid = {7502021}, Journal = {Biotechnol Bioeng}, Keywords = {Demand Response}, Language = {ENG}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Y/Y2005nt.pdf}, Mhda = {2005/08/24 09:00}, Number = {0006-3592}, Own = {NLM}, Pmid = {16116658}, Pst = {aheadofprint}, Pt = {JOURNAL ARTICLE}, Pubm = {Print-Electronic}, So = {Biotechnol Bioeng 2005 Aug 22;.}, Stat = {Publisher}, Title = {Compared tolerance to osmotic stress in various microorganisms: Towards a survival prediction test.}, Year = {2005}}

@article{Sorensen2005fs, Abstract = {Preparations enriched by a specific protein are rarely easily obtained from natural host cells. Hence, recombinant protein production is frequently the sole applicable procedure. The ribosomal machinery, located in the cytoplasm is an outstanding catalyst of recombinant protein biosynthesis. Escherichia coli facilitates protein expression by its relative simplicity, its inexpensive and fast high-density cultivation, the well-known genetics and the large number of compatible tools available for biotechnology. Especially the variety of available plasmids, recombinant fusion partners and mutant strains have advanced the possibilities with E. coli. Although often simple for soluble proteins, major obstacles are encountered in the expression of many heterologous proteins and proteins lacking relevant interaction partners in the E. coli cytoplasm. Here we review the current most important strategies for recombinant expression in E. coli. Issues addressed include expression systems in general, selection of host strain, mRNA stability, codon bias, inclusion body formation and prevention, fusion protein technology and site-specific proteolysis, compartment directed secretion and finally co-overexpression technology. The macromolecular background for a variety of obstacles and genetic state-of-the-art solutions are presented.}, Affiliation = {Laboratory of BioDesign, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark.}, Aid = {10.1016/j.jbiotec.2004.08.004 {$[$}doi{$]$}}, Au = {Mortensen KK}, Author = {Sorensen, Hans Peter and Mortensen, Kim Kusk}, Da = {20041220}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20050526}, Edat = {2004/12/21 09:00}, Jid = {8411927}, Journal = {J Biotechnol}, Keywords = {Gene Expression and Demand Response and Chassis and Chassis Characterization}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Sorensen/Sorensen2005rm.pdf}, Mhda = {2005/05/27 09:00}, Number = {2}, Own = {NLM}, Pages = {113-28}, Phst = {2004/08/30 {$[$}accepted{$]$}}, Pl = {Netherlands}, Pmid = {15607230}, Pst = {ppublish}, Pt = {Review, Tutorial}, Pubm = {Print}, Rf = {127}, Rn = {0 (Recombinant Proteins)}, Sb = {IM}, Stat = {MEDLINE}, Title = {Advanced genetic strategies for recombinant protein expression in Escherichia coli.}, Volume = {115}, Year = {2005}}

@article{Studier2005po, Abstract = {Inducible expression systems in which T7 RNA polymerase transcribes coding sequences cloned under control of a T7lac promoter efficiently produce a wide variety of proteins in Escherichia coli. Investigation of factors that affect stability, growth, and induction of T7 expression strains in shaking vessels led to the recognition that sporadic, unintended induction of expression in complex media, previously reported by others, is almost certainly caused by small amounts of lactose. Glucose prevents induction by lactose by well-studied mechanisms. Amino acids also inhibit induction by lactose during log-phase growth, and high rates of aeration inhibit induction at low lactose concentrations. These observations, and metabolic balancing of pH, allowed development of reliable non-inducing and auto-inducing media in which batch cultures grow to high densities. Expression strains grown to saturation in non-inducing media retain plasmid and remain fully viable for weeks in the refrigerator, making it easy to prepare many freezer stocks in parallel and use working stocks for an extended period. Auto-induction allows efficient screening of many clones in parallel for expression and solubility, as cultures have only to be inoculated and grown to saturation, and yields of target protein are typically several-fold higher than obtained by conventional IPTG induction. Auto-inducing media have been developed for labeling proteins with selenomethionine, 15N or 13C, and for production of target proteins by arabinose induction of T7 RNA polymerase from the pBAD promoter in BL21-AI. Selenomethionine labeling was equally efficient in the commonly used methionine auxotroph B834(DE3) (found to be metE) or the prototroph BL21(DE3).}, Affiliation = {Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA. studier@bnl.gov}, Au = {Studier FW}, Author = {Studier, F William}, Da = {20050524}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Edat = {2005/05/26 09:00}, Jid = {9101496}, Journal = {Protein Expr Purif}, Keywords = {Demand, Environmental Changes, Gene Expression}, Language = {eng}, Mhda = {2005/05/26 09:00}, Number = {1}, Own = {NLM}, Pages = {207-34}, Pl = {United States}, Pmid = {15915565}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, Stat = {In-Process}, Title = {Protein production by auto-induction in high density shaking cultures.}, Volume = {41}, Year = {2005}}

@article{Bonomo2005xj, Abstract = {Recombinant protein production in Escherichia coli often results in a dramatic cellular stress response best characterized by a decrease in overall cell fitness. We determined that the primary sequence (the amino acid sequence) of the recombinant protein alone plays an important role in mitigating this response. To do so, we created two polypeptides, modeled after the 39-40 amino acid Defensin class of proteins, which contained exclusively the five least (PepAA; His, Trp, Tyr, Phe, Met), or most (PepCO: Ala, Glu, Gln, Asp, Asn) abundant amino acids in E. coli. We determined that overexpression of PepAA resulted in a drastic decrease in growth rate compared to overexpression of PepCO, our model Defensin protein MGD-1, or the 26 amino acid polypeptide contained within the pET-3d vector backbone. We further determined, using Affymetrix E. coli gene chips, that differences among the whole-genome transcriptional responses of these model systems were best characterized by altered expression of genes whose products are involved in translation, transport, or metabolic functions as opposed to stress response genes. Based on these results, we confirmed that translation efficiency was significantly reduced in cells overexpressing PepAA compared with the other model polypeptides evaluated.}, Affiliation = {Department of Chemical and Biological Engineering, Campus Box 424, University of Colorado, Boulder, Colorado 80309, USA.}, Aid = {10.1002/bit.20436 {$[$}doi{$]$}}, Au = {Gill RT}, Author = {Bonomo, Jeanne and Gill, Ryan T}, Ci = {Copyright (c) 2005 Wiley Periodicals, Inc.}, Da = {20050321}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Edat = {2005/03/01 09:00}, Jid = {7502021}, Journal = {Biotechnol Bioeng}, Keywords = {Demand and Demand Response}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Bonomo/Bonomo2005dy.pdf}, Mhda = {2005/03/01 09:00}, Number = {1}, Own = {NLM}, Pages = {116-26}, Pl = {United States}, Pmid = {15736162}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, Stat = {In-Process}, Title = {Amino acid content of recombinant proteins influences the metabolic burden response.}, Volume = {90}, Year = {2005}}

@article{Kayser2005jy, Abstract = {The Escherichia coli K-12 strain TG1 was grown at 28 degrees C in aerobic glucose-limited continuous cultures at dilution rates ranging from 0.044 to 0.415 h(-1). The rates of biomass formation, the specific rates of glucose, ammonium and oxygen uptake and the specific carbon dioxide evolution rate increased linearly with the dilution rate up to 0.3 h(-1). At dilution rates between 0.3 h(-1) and 0.4 h(-1), a strong deviation from the linear increase to lower specific oxygen uptake and carbon dioxide evolution rates occurred. The biomass formation rate and the specific glucose and ammonium uptake rates did not deviate that strongly from the linear increase up to dilution rates of 0.4 h(-1). An increasing percentage of glucose carbon flow towards biomass determined by a reactor mass balance and a decreasing specific ATP production rate concomitant with a decreasing adenylate energy charge indicated higher energetic efficiency of carbon substrate utilization at higher dilution rates. Estimation of metabolic fluxes by a stoichiometric model revealed an increasing activity of the pentose phosphate pathway and a decreasing tricarboxylic acid cycle activity with increasing dilution rates, indicative of the increased NADPH and precursor demand for anabolic purposes at the expense of ATP formation through catabolic activities. Thus, increasing growth rates first result in a more energy-efficient use of the carbon substrate for biomass production, i.e. a lower portion of the carbon substrate is channelled into the respiratory, energy-generating pathway. At dilution rates above 0.4 h(-1), close to the wash-out point, respiration rates dropped sharply and accumulation of glucose and acetic acid was observed. Energy generation through acetate formation yields less ATP compared with complete oxidation of the sugar carbon substrate, but is the result of maximized energy generation under conditions of restrictions in the tricarboxylic acid cycle or in respiratory NADH turnover. Thus, the data strongly support the conclusion that, in aerobic glucose-limited continuous cultures of E. coli TG1, two different carbon limitations occur: at low dilution rates, cell growth is limited by cell-carbon supply and, at high dilution rates, by energy-carbon supply.}, Affiliation = {Biochemical Engineering Division, GBF-National Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany.}, Aid = {10.1099/mic.0.27481-0 {$[$}doi{$]$}}, Au = {Rinas U}, Author = {Kayser, Anke and Weber, Jan and Hecht, Volker and Rinas, Ursula}, Da = {20050310}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Edat = {2005/03/11 09:00}, Jid = {9430468}, Journal = {Microbiology}, Keywords = {Demand Response}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Kayser/Kayser2005nl.pdf}, Mhda = {2005/03/11 09:00}, Number = {Pt 3}, Own = {NLM}, Pages = {693-706}, Pl = {England}, Pmid = {15758216}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, Stat = {In-Process}, Title = {Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state.}, Volume = {151}, Year = {2005}}

@book{Schweder2004kx, Author = {Schweder, Thomas AND Hecker, Michael}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Ep = {71}, Journal = {Advances in Biochemical Engineering/Biotechnology}, Keywords = {Demand Response}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Egli/Egli2004ww.pdf}, Pages = {47--71}, Sp = {47}, Title = {Monitoring of Stress Responses}, Ty = {BOOK}, Url = {http://www.springerlink.com/openurl.asp?genre=article\& id=doi:10.1007/b93993}, Volume = {89}, Year = {2004}}

@article{Wick2004gx, Author = {Wick, Lukas M. AND Egli, Thomas}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Ep = {45}, Journal = {Advances in Biochemical Engineering/Biotechnology}, Keywords = {Demand Response and Chassis Characterization}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Wick/Wick2004tz.pdf}, Pages = {1--45}, Sp = {1}, Title = {Molecular Components of Physiological Stress Responses in Escherichia coli}, Ty = {BOOK}, Url = {http://www.springerlink.com/openurl.asp?genre=article\& id=doi:10.1007/b93957}, Volume = {89}, Year = {2004}}

@article{Hoffmann2004lj, Author = {Hoffmann, Frank}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Ep = {92}, Journal = {Advances in Biochemical Engineering/Biotechnology}, Keywords = {Demand Response and Chassis and Chassis Characterization}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Hoffmann/Hoffmann2004oc.pdf}, Pages = {73--92}, Sp = {73}, Title = {Stress Induced by Recombinant Protein Production in Escherichia coli}, Ty = {BOOK}, Url = {http://www.springerlink.com/openurl.asp?genre=article\& id=doi:10.1007/b93994}, Volume = {89}, Year = {2004}}

@article{Valesova2004rn, Abstract = {Segregational stability of the recombinant plasmid pKA18 bearing the pga gene encoding penicillin G acylase (PGA) and the production stability for PGA was studied in Escherichia coli strain W and its descendants. The hosts differ in the number of indigenous plasmids (pRK1-3) and the specific activity of PGA. The production of PGA by the recombinant strain RE3(pKA18) is the highest among the hosts and the increase of activity is proportional to the increase of copy number (CN) of the plasmid pKA18. The plasmid is segregationally stable in spite of the presence of the indigenous plasmid pRK2 that belong to the same ColE1 plasmid family. Both plasmids (total sum of CN equals 271) are maintained without selection pressure during 102 generations. Subculture-based selection experiments taking advantage of a very high segregational and production stability of plasmid pKA18 in the host RE3 were used to study the optimization of the host-plasmid interaction. The clones with increased synthesis of the enzyme average value of 833 U/g DM were isolated: the expression of PGA per plasmid molecule increased in these strains from 3 to 4 U. Once this expression is reached, the population of segregationally stable, high-producing strains becomes heterogeneous: segregationally stable, low-producing clones and segregationally unstable, high-producing clones appear in population.}, Author = {Valesova, Renata and Hollerova-Sobotkova, Lenka and Stepanek, Vaclav and Kyslik, Pavel}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Ep = {80}, Journal = {Enzyme and Microbial Technology}, Keywords = {Demand Response}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Valesova/Valesova2004nh.pdf}, Number = {1}, Pages = {74--80}, Sp = {74}, Title = {Optimization of the host-plasmid interaction in the recombinant Escherichia coli strains overproducing penicillin G acylase}, Ty = {JOUR}, Url = {http://www.sciencedirect.com/science/article/B6TG1-4CF5H0S-3/2/b84bd7640a5eec722cb589d48b2daa1f}, Volume = {35}, Year = {2004}}

@article{Lee:2002aa, Abstract = {The influence of growth rate on Escherichia coli plasmid content and expression of a cloned-gene product has been described by a mathematical model based upon the molecular mechanism of lambdadv plasmid replication and known relationships between growth rate and transcription and translation activities of the host cell. The model simulates correctly decreases in plasmid content with increasing growth rate as observed experimentally for pBR322, NR1, R1, and Col E1 plasmids. A maximum with respect to growth rate in intracellular product accumulation is indicated by the model, as is a transient overshoot in product concentration following a shift from smaller to larger growth rate. Available data, although very limited, show the same trends. These results, obtained without parameter or kinetic form adjustments or manipulation, clearly illustrate the advantages of kinetic descriptions of recombinant systems based upon the pertinent molecular mechanisms.}, Affiliation = {Department of Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.}, Aid = {10.1002/bit.10439 {$[$}doi{$]$}}, Au = {Lee SB and Bailey JE}, Author = {Lee, Sun Bok and Bailey, James E}, Ci = {Copyright 2002 Wiley Periodicals, Inc.}, Da = {20020904}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20030319}, Edat = {2002/09/05 10:00}, Ip = {5}, Jid = {7502021}, Journal = {Biotechnol Bioeng}, Jt = {Biotechnology and bioengineering.}, Keywords = {Chassis Characterization and Demand}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Lee/Lee2002jt.pdf}, Lr = {20041117}, Mhda = {2003/03/20 04:00}, Number = {0006-3592 (Print)}, Own = {NLM}, Pages = {550-7}, Pl = {United States}, Pmid = {12209826}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (Plasmids)}, Sb = {IM}, So = {Biotechnol Bioeng. 2002 Sep 5;79(5):550-7.}, Stat = {MEDLINE}, Title = {Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models.}, Volume = {79}, Year = {2002}}

@article{Lee2000yq, Abstract = {The influence of growth rate on Escherichia coli plasmid content and expression of a cloned-gene product has been described by a mathematical model based upon the molecular mechanism of lambdadv plasmid replication and known relationships between growth rate and transcription and translation activities of the host cell. The model simulates correctly decreases in plasmid content with increasing growth rate as observed experimentally for pBR322, NR1, R1, and Col E1 plasmids. A maximum with respect to growth rate in intracellular product accumulation is indicated by the model, as is a transient overshoot in product concentration following a shift from smaller to larger growth rate. Available data, although very limited, show the same trends. These results, obtained without parameter or kinetic form adjustments or manipulation, clearly illustrate the advantages of kinetic descriptions of recombinant systems based upon the pertinent molecular mechanisms.}, Aid = {10.1002/(SICI)1097-0290(20000320)67:6<805::AID-BIT16>3.0.CO;2-0 [pii]}, Au = {Lee SB and Bailey JE}, Author = {Lee, S B and Bailey, J E}, Da = {20000324}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20000324}, Edat = {2000/03/04 09:00}, Fps = {Bailey, J E}, Ip = {6}, Jid = {7502021}, Journal = {Biotechnol Bioeng}, Keywords = {Demand Modeling and Demand Response and Chassis}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Lee/Lee2000pk.pdf}, Lr = {20050714}, Mhda = {2000/04/01 09:00}, Number = {0006-3592}, Own = {NLM}, Pages = {805-12}, Pl = {UNITED STATES}, Pmid = {10699859}, Ps = {Bailey JE}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (Plasmids)}, Sb = {IM}, So = {Biotechnol Bioeng 2000 Mar 20;67(6):805-12.}, Stat = {MEDLINE}, Title = {Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Reprinted from Biotechnology and Bioengineering, Vol. 26, Issue 1, Pages 66-73 (1984).}, Volume = {67}, Year = {2000}}

@article{Gill2000lw, Abstract = {Global gene regulation throughout the Escherichia coli stress response to overexpression of each of five recombinant proteins was evaluated. Reverse-transcriptase polymerase chain reaction-amplified mRNA from induced and control cells were hybridized with a DNA array of Kohara clones representing 16% (700 genes) of the E. coli genome. Subsequently, Northern analysis was performed for quantification of specific gene dynamics and statistically significant overlap in the regulation of 11 stress-related genes was found using correlation analysis. The results reported here establish that there are dramatic changes in the transcription rates of a broad range of stress genes (representing multiple regulons) after induction of recombinant protein. Specifically, the responses included significantly increased upregulation of heat shock (ftsH, clpP, lon, ompT, degP, groEL, aceA, ibpA), SOS/DNA damage (recA, lon, IS5 transposase), stationary phase (rpoS, aceA), and bacteriophage life cycle (ftsH, recA) genes. Importantly, similarities at the microscopic (gene) level were not clearly reflected at the macroscopic (growth rate, lysis) level. The use of such dynamic data is critical to the design of gene-based sensors, the engineering of metabolic pathways, and the determination of parameters (harvest and induction times) needed for successful recombinant E. coli fermentations.}, Affiliation = {Department of Chemical Engineering, University of Maryland, College Park, Maryland 20742, USA.}, Aid = {S1096717600901484 {$[$}pii{$]$}}, Au = {Bentley WE}, Author = {Gill, R T and Valdes, J J and Bentley, W E}, Ci = {Copyright 2000 Academic Press.}, Da = {20001201}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20010111}, Edat = {2000/11/01 11:00}, Jid = {9815657}, Journal = {Metab Eng}, Keywords = {Demand Response}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Gill/Gill2000ch.pdf}, Lr = {20041118}, Mhda = {2001/02/28 10:01}, Number = {3}, Own = {NLM}, Pages = {178-89}, Pl = {UNITED STATES}, Pmid = {11056060}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (Recombinant Proteins)}, Sb = {IM}, Stat = {MEDLINE}, Title = {A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli.}, Volume = {2}, Year = {2000}}

@article{Liang2000mb, Abstract = {The expression of any given bacterial protein is predicted to depend on (i) the transcriptional regulation of the promoter and the translational regulation of its mRNA and (ii) the synthesis and translation of total (bulk) mRNA. This is because total mRNA acts as a competitor to the specific mRNA for the binding of initiation-ready free ribosomes. To characterize the effects of mRNA competition on gene expression, the specific activity of beta-galactosidase expressed from three different promoter-lacZ fusions (P(spc)-lacZ, P(RNAI)-lacZ, and P(RNAII)-lacZ) was measured (i) in a relA(+) background during exponential growth at different rates and (ii) in relA(+) and DeltarelA derivatives of Escherichia coli B/r after induction of a mild stringent or a relaxed response to raise or lower, respectively, the level of ppGpp. Expression from all three promoters was stimulated during slow exponential growth or at elevated levels of ppGpp and was reduced during fast exponential growth or at lower levels of ppGpp. From these observations and from other considerations, we propose (i) that the concentration of free, initiation-ready ribosomes is approximately constant and independent of the growth rate and (ii) that bulk mRNA made during slow growth and at elevated levels of ppGpp is less efficiently translated than bulk mRNA made during fast growth and at reduced levels of ppGpp. These features lead to an indirect enhancement in the expression of LacZ (or of any other protein) during growth in media of poor nutritional quality and at increased levels of ppGpp.}, Affiliation = {Program in Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083-0688, USA.}, Au = {Bremer H}, Author = {Liang, S T and Xu, Y C and Dennis, P and Bremer, H}, Da = {20000605}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20000605}, Edat = {2000/05/16 09:00}, Jid = {2985120R}, Journal = {J Bacteriol}, Keywords = {Demand Response and Demand Modeling and Chassis}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Liang/Liang2000fl.pdf}, Lr = {20041117}, Mhda = {2000/06/10 09:00}, Number = {11}, Own = {NLM}, Pages = {3037-44}, Pl = {UNITED STATES}, Pmid = {10809680}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {EC 2.7.7.6 (DNA-Directed RNA Polymerases)}, Sb = {IM}, Stat = {MEDLINE}, Title = {mRNA composition and control of bacterial gene expression.}, Volume = {182}, Year = {2000}}

@article{Baneyx1999yf, Abstract = {Escherichia coli is one of the most widely used hosts for the production of heterologous proteins and its genetics are far better characterized than those of any other microorganism. Recent progress in the fundamental understanding of transcription, translation, and protein folding in E. coli, together with serendipitous discoveries and the availability of improved genetic tools are making this bacterium more valuable than ever for the expression of complex eukaryotic proteins.}, Affiliation = {Department of Chemical Engineering University of Washington Box 351750, Seattle, WA 98195, USA. baneyx@cheme.washington.edu}, Aid = {bta504 {$[$}pii{$]$}}, Au = {Baneyx F}, Author = {Baneyx, F}, Da = {19991207}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19991207}, Edat = {1999/10/06}, Jid = {9100492}, Journal = {Curr Opin Biotechnol}, Keywords = {Demand Response}, Language = {eng}, Lr = {20041117}, Mhda = {1999/10/06 00:01}, Number = {5}, Own = {NLM}, Pages = {411-21}, Pl = {ENGLAND}, Pmid = {10508629}, Pst = {ppublish}, Pt = {Review, Tutorial}, Pubm = {Print}, Rf = {69}, Rn = {0 (Recombinant Proteins)}, Sb = {IM}, Stat = {MEDLINE}, Title = {Recombinant protein expression in Escherichia coli.}, Volume = {10}, Year = {1999}}

@misc{Kurland:1996aa, Abstract = {Multicopy plasmids that have been engineered to produce large quantities of a single gratuitous (non-functional, non-toxic) protein are often problematic. When fully induced, these engineered constructions produce very sick bacteria. The reasons for this may be found in the physiology of wild-type laboratory strains that have been selected to grow at maximum rates with optimal quantities of their proteins. Such bacteria apparently experience the accumulation of gratuitous proteins as an internal shift down and they respond to this with a starvation response. Unlike the shift down associated with a change of growth media, the production of large quantities of gratuitous protein is not associated with a new pre-programmed steady-state of balanced growth. Consequently, the starvation response continues until the bacteria commit suicide by, among other things, destroying their ribosomes.}, Affiliation = {Uppsala University, Department of Molecular Biology, Biomedical Centre, Sweden. chuck@xray. bmc.uu.se}, Au = {Kurland CG and Dong H}, Author = {Kurland, C G and Dong, H}, Da = {19970108}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19970108}, Edat = {1996/07/01}, Ip = {1}, Jid = {8712028}, Journal = {Mol Microbiol}, Jt = {Molecular microbiology.}, Keywords = {Demand, Chassis}, Language = {eng}, Lr = {20051116}, Mhda = {1996/07/01 00:01}, Number = {0950-382X (Print)}, Own = {NLM}, Pages = {1-4}, Pl = {ENGLAND}, Pmid = {8843428}, Pst = {ppublish}, Pt = {Review}, Pubm = {Print}, Rf = {25}, Rn = {0 (Recombinant Proteins)}, Sb = {IM}, So = {Mol Microbiol. 1996 Jul;21(1):1-4.}, Stat = {MEDLINE}, Title = {Bacterial growth inhibition by overproduction of protein.}, Volume = {21}, Year = {1996}}

@article{Herman1995mx, Abstract = {The plasmids harbouring the relA gene under an inducible promoter allowed us to increase the guanosine 5'-diphosphate-3'-diphosphate (ppGpp) concentration in Escherichia coli cells without any starvation and thus, to directly investigate the effect of ppGpp on DNA replication. We studied all types of replicons which were investigated previously in amino acid-starved bacteria and found that ColE1, oriC, lambda plasmid and pSC101 but not RK2 replicons are sensitive to high ppGpp level. To our knowledge, this paper presents the first direct evidence that replication of most, but not all, replicons is dependent on ppGpp concentration and thus, is under stringent control.}, Affiliation = {Department of Molecular Biology, University of Gdansk, Poland.}, Au = {Wegrzyn G}, Author = {Herman, A and Wegrzyn, G}, Da = {19950607}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19950607}, Edat = {1995/01/01}, Gs = {relA}, Jid = {8503885}, Journal = {J Basic Microbiol}, Keywords = {Demand Response and Demand Modeling}, Language = {eng}, Lr = {20041117}, Mhda = {1995/01/01 00:01}, Number = {1}, Own = {NLM}, Pages = {33-9}, Pl = {GERMANY}, Pmid = {7738786}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {33503-72-9 (Guanosine Tetraphosphate)}, Sb = {IM}, Stat = {MEDLINE}, Title = {Effect of increased ppGpp concentration on DNA replication of different replicons in Escherichia coli.}, Volume = {35}, Year = {1995}}

@article{Glick1995ew, Abstract = {The expression of a foreign protein(s) in a recombinant host cell or organism often utilizes a significant amount of the host cell's resources, removing those resources away from host cell metabolism and placing a metabolic load (metabolic drain, metabolic burden) on the host. As a consequence of the imposed metabolic load, the biochemistry and physiology of the host may be dramatically altered. The numerous physiological changes that may occur often lowers the amount of the target foreign protein that is produced and eventually recovered from the recombinant organism. In this review the physiological changes to host cells, the causes of the phenomenon of metabolic load, and several strategies to avoid some of the problems associated with metabolic load are elaborated and discussed.}, Affiliation = {Department of Biology, University of Waterloo, Ontario, Canada.}, Aid = {073497509500004A {$[$}pii{$]$}}, Au = {Glick BR}, Author = {Glick, B R}, Da = {20031010}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {20031223}, Edat = {2003/10/11 05:00}, Jid = {8403708}, Journal = {Biotechnol Adv}, Keywords = {Demand Response and Demand Modeling}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Glick/Glick1995kz.pdf}, Mhda = {2003/10/11 05:01}, Number = {2}, Own = {NLM}, Pages = {247-61}, Pl = {England}, Pmid = {14537822}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Stat = {PubMed-not-MEDLINE}, Title = {Metabolic load and heterologous gene expression.}, Volume = {13}, Year = {1995}}

@article{Bailey:1993aa, Abstract = {Introduction of a DNA vector into E. coli for the purposes of cloned gene expression can perturb native cell functions at many levels. The presence of foreign DNA can alter regulation of chromosomal DNA replication, regulation of transcription of chromosomal genes, ribosome functions and RNA turnover, activities of regulatory proteins, chaperone and protease levels, membrane energetics and protein post-translational processing, as well as energy and intermediary metabolism of the cell. The combined effects of these interactions on the metabolic characteristics of the host-vector system have major implications for yields of cloned biotechnological products and interactions of genetically engineered organisms with their environment.}, Affiliation = {Department of Chemical Engineering, California Institute of Technology, Pasadena 91125.}, Au = {Bailey JE}, Author = {Bailey, J E}, Da = {19930423}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19930423}, Edat = {1993/01/01}, Issn = {0724-6145 (Print)}, Jid = {8307733}, Journal = {Adv Biochem Eng Biotechnol}, Jt = {Advances in biochemical engineering/biotechnology.}, Keywords = {Demand and Demand Response}, Language = {eng}, Lr = {20060501}, Mhda = {1993/01/01 00:01}, Own = {NLM}, Pages = {29-52}, Pl = {GERMANY}, Pmid = {8460576}, Pst = {ppublish}, Pt = {Review}, Pubm = {Print}, Rf = {40}, Rn = {0 (DNA, Bacterial)}, Sb = {IM}, So = {Adv Biochem Eng Biotechnol. 1993;48:29-52.},	Stat = {MEDLINE}, Title = {Host-vector interactions in Escherichia coli.}, Volume = {48}, Year = {1993}}

@article{Yee:1992aa, Abstract = {Whereas cell concentrations of 5-10 grams dry cell weight per liter (gDCW/l) are typical of batch cultures, fed-batch techniques can be used to achieve concentrations greater than 50 gDCW/l. Feeding strategies for fed-batch cultures include feed-back control as well as pre-determined feeding profiles. The volumetric yield of recombinant products can be improved by controlling the specific growth rate and the substrate concentration. Furthermore, inhibitory by-product formation can be minimized in fed-batch cultures. This review focuses on the use of fed-batch techniques to produce recombinant products in Escherichia coli. The modes of nutrient feeding that have been employed are discussed, and the factors important in attaining high cell concentrations as well as high specific yields of recombinant product are described.}, Affiliation = {Department of Chemical Engineering, University of California, Berkeley 94702.}, Au = {Yee L and Blanch HW}, Author = {Yee, L and Blanch, H W}, Da = {19930325}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19930325}, Edat = {1992/12/01}, Issn = {0733-222X (Print)}, Jid = {8309273}, Journal = {Biotechnology (N Y)}, Jt = {Bio/technology (Nature Publishing Company)}, Keywords = {Demand}, Language = {eng}, Lr = {20051116}, Mhda = {1992/12/01 00:01}, Number = {12}, Own = {NLM}, Pages = {1550-6}, Pl = {UNITED STATES}, Pmid = {1369204}, Pst = {ppublish}, Pt = {Review}, Pubm = {Print}, Rf = {60}, Rn = {0 (Culture Media)}, Sb = {B}, So = {Biotechnology (N Y). 1992 Dec;10(12):1550-6.}, Stat = {MEDLINE}, Title = {Recombinant protein expression in high cell density fed-batch cultures of Escherichia coli.}, Volume = {10}, Year = {1992}}

@article{Birnbaum:1991aa, Author = {S. Birnbaum and J. E. Bailey}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Journal = {Biotechnology and Bioengineering}, Keywords = {Demand and Demand Response}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Birnbaum/Birnbaum1991qy.pdf}, Number = {8}, Pages = {736-745}, Title = {Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli}, Volume = {37}, Year = {1991}}

@article{Studier1991ch, Abstract = {Bacteriophage T7 lysozyme, a natural inhibitor of T7 RNA polymerase, can reduce basal activity from an inducible gene for T7 RNA polymerase and allow relatively toxic genes to be established in the same cell under control of a T7 promoter. Low levels of T7 lysozyme supplied by plasmids pLysS or pLysL, which are compatible with the pET vectors for expressing genes from a T7 promoter, are sufficient to stabilize many target plasmids and yet allow high levels of target protein to be produced upon induction of T7 RNA polymerase. Higher levels of lysozyme supplied by plasmids pLysE or pLysH reduce the fully induced activity of T7 RNA polymerase such that induced cells can continue to grow and produce innocuous target proteins indefinitely. Different configurations of the expression system can maintain several different steady-state levels of target gene expression. The presence of T7 lysozyme has the further advantage of facilitating the lysis of cells in preparing extracts for purification of target gene products.}, Affiliation = {Biology Department, Brookhaven National Laboratory Upton, NY 11973.}, Au = {Studier FW}, Author = {Studier, F W}, Da = {19910606}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19910606}, Edat = {1991/05/05}, Jid = {2985088R}, Journal = {J Mol Biol}, Keywords = {Demand Response}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Studier/Studier1991qy.pdf}, Lr = {20041117}, Mhda = {1991/05/05 00:01}, Number = {1}, Own = {NLM}, Pages = {37-44}, Pl = {ENGLAND}, Pmid = {2023259}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {EC 3.2.1.17 (Muramidase)}, Sb = {IM}, Stat = {MEDLINE}, Title = {Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system.}, Volume = {219}, Year = {1991}}

@article{Baracchini1991qm, Abstract = {The effects of extra, plasmid-borne rRNA genes on the synthesis rate of rRNA in Escherichia coli were examined by measuring the fraction of total RNA synthesis that is rRNA and tRNA (rs/rt), the cytoplasmic concentration of guanosine tetraphosphate (ppGpp), and the absolute rates of RNA and protein synthesis. Experiments were carried out in different growth media and with two different strains of E. coli, B/r and K-12. The results indicated: 1) increased rrn gene dosage from either intact or defective rrn genes reduced bacterial growth rates and ribosome activity (protein synthesis rate/average ribosome), and increased rs/rt. 2) Extra intact, but not extra defective, plasmid-borne rrn genes caused the level of ppGpp to be increased in comparison to the pBR322-carrying control strain. 3) As a function of ppGpp, rs/rt was increased with either intact or defective rrn genes. 4) The rRNA synthesis rate/rrn gene was reduced in the presence of extra rrn genes; this reduction in gene activity was greater with intact than with defective rrn genes. An analysis of these results showed that they are consistent with the ppGpp hypothesis of rRNA control but not with a feedback effector role of translating ribosomes.}, Affiliation = {Molecular Program, University of Texas, Richardson 75083-0688.}, Au = {Bremer H}, Author = {Baracchini, E and Bremer, H}, Da = {19910724}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19910724}, Edat = {1991/06/25}, Gs = {rrn}, Jid = {2985121R}, Journal = {J Biol Chem}, Keywords = {Demand Modeling and Demand Response and Chassis}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Baracchini/Baracchini1991rg.pdf}, Lr = {20001218}, Mhda = {1991/06/25 00:01}, Number = {18}, Own = {NLM}, Pages = {11753-60}, Pl = {UNITED STATES}, Pmid = {1711040}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {33503-72-9 (Guanosine Tetraphosphate)}, Sb = {IM}, Stat = {MEDLINE}, Title = {Control of rRNA synthesis in Escherichia coli at increased rrn gene dosage. Role of guanosine tetraphosphate and ribosome feedback.}, Volume = {266}, Year = {1991}}

@article{Hernandez1991ct, Abstract = {Escherichia coli has two enzymes catalyzing the synthesis of guanosine tetraphosphate (ppGpp), designated ppGpp synthetase I (PSI = RelA) and II (PSII), whose activities are regulated differently. Until now, the gene for PSII had not been identified. Here, an E. coli relA1 strain that expresses lacZ from an rrnB P1 promoter was used to screen mutants with increased beta-galactosidase activity on 5-bromo-4-chloro-3-indoyl beta-D-galactoside indicator plates at 30 degrees C. About 15% of the mutants obtained in this manner had reduced levels of ppGpp at 30 degrees C and no detectable ppGpp at 43 degrees C. These mutants did not form colonies at 42 degrees C on minimal medium plates and had elevated ribosome concentrations and higher growth rates at 30 degrees C. Genetic mapping by phage P1 transduction and complementation analyses showed that the mutations were located in spoT and that they were recessive. Specific inhibition of SpoT-dependent ppGpp degradation activity with picolinic acid showed that two of the mutants tested were deficient in ppGpp synthesis activity. These results indicate that spoT is required for PSII activity, suggesting that spoT encodes both ppGpp degradation and synthesis activities and that these two functions can be affected independently by mutation.}, Affiliation = {Molecular Program, University of Texas, Dallas, Richardson 75083-0688.}, Au = {Bremer H}, Author = {Hernandez, V J and Bremer, H}, Da = {19910423}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19910423}, Edat = {1991/03/25}, Gs = {spoT}, Jid = {2985121R}, Journal = {J Biol Chem}, Keywords = {Demand Response and Chassis and Chassis Characterization}, Language = {eng}, Lr = {20001218}, Mhda = {1991/03/25 00:01}, Number = {9}, Own = {NLM}, Pages = {5991-9}, Pl = {UNITED STATES}, Pmid = {2005135}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {33503-72-9 (Guanosine Tetraphosphate)}, Sb = {IM}, So = {J Biol Chem 1992 Feb 5;267(4):2337-44.}, Stat = {MEDLINE}, Title = {Escherichia coli ppGpp synthetase II activity requires spoT.}, Volume = {266}, Year = {1991}}

@article{Bentley:1990aa, Author = {William E. Bentley and Noushin Mirjalili and Dana C. Andersen and Robert H. Davis and Dhinakar S. Kompala}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Journal = {Biotechnology and Bioengineering}, Keywords = {Demand and Demand Response}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Bentley/Bentley1990lr.pdf}, Number = {7}, Pages = {668-681}, Read = {No}, Title = {Plasmid-encoded protein: The principal factor in the ?metabolic burden? associated with recombinant bacteria}, Volume = {35}, Year = {1990}}

@article{Nguyen1989jn, Abstract = {We have been examining the consequences of alternative modes of regulation of plasmid-borne, Tn10-encoded tetracycline resistance for the fitness of Escherichia coli. In a tetracycline-free environment, we measured the effects on fitness that were caused by (1) maximally induced expression of the resistance operon, (2) low-level constitutive expression of the resistance protein, (3) residual expression of the repressed resistance operon, (4) carriage of the resistance operon, (5) the remainder of the plasmid genome, and (6) hyperexpression of the repressor protein. We observed large reductions in fitness that were associated with induction and with constitutive expression of the tetracycline-resistance protein, but there was no discernible effect of hyperexpression of the repressor protein. We also observed a small reduction in fitness associated with the remainder of the plasmid genome. However, any reductions in fitness that were caused by residual expression and by carriage of the repressed operon were not more than 0.3%. We conclude that tight gene regulation has eliminated antagonistic pleiotropic effects of the resistance gene on fitness, so that possession of an inducible Tn10-encoded tetracycline-resistance operon imposes essentially no burden in the absence of antibiotic.}, Affiliation = {Department of Ecology and Evolutionary Biology, University of California, Irvine 92717.}, Au = {Lenski RE}, Author = {Nguyen, T N and Phan, Q G and Duong, L P and Bertrand, K P and Lenski, R E}, Da = {19900319}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19900319}, Edat = {1989/05/01}, Gr = {GM-37105/GM/NIGMS}, Jid = {8501455}, Journal = {Mol Biol Evol}, Keywords = {Demand}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Nguyen/Nguyen1989rg.pdf}, Lr = {20041117}, Mhda = {1989/05/01 00:01}, Number = {3}, Own = {NLM}, Pages = {213-25}, Pl = {UNITED STATES}, Pmid = {2560115}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {1665-56-1 (5a,6-anhydrotetracycline)}, Sb = {IM}, Stat = {MEDLINE}, Title = {Effects of carriage and expression of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli K12.}, Volume = {6}, Year = {1989}}

@article{Knaus1988in, Abstract = {Promoter PL of coliphage lambda is highly active in vivo although it is recognized 15-30 times less efficiently by RNA polymerase when compared with promoters of similar strength. Moreover, it differs significantly from the consensus sequence for Escherichia coli promoters. Sequence variants of PL which are more homologous to consensus promoters bind RNA polymerase with increased efficiency. They are nevertheless significantly reduced in their in vivo strength. High activity can be restored by a downstream sequence of a typical consensus-like promoter. Evidently, such elements are required for the efficient release of a stably bound RNA polymerase into a transcriptional elongation complex. We propose that the functional programme encoded in a promoter sequence can be optimized in alternative ways.}, Affiliation = {Zentrum fur Molekulare Biologie, University of Heidelberg, FRG.}, Au = {Knaus R and Bujard H}, Author = {Knaus, R and Bujard, H}, Da = {19881221}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19881221}, Edat = {1988/09/01}, Ip = {9}, Jid = {8208664}, Journal = {EMBO J}, Keywords = {Demand}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Knaus/Knaus1988mo.pdf}, Lr = {20041117}, Mhda = {1988/09/01 00:01}, Number = {0261-4189}, Own = {NLM}, Pages = {2919-23}, Pl = {ENGLAND}, Pmid = {2972539}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {EC 2.7.7.6 (DNA-Directed RNA Polymerases)}, Sb = {IM}, So = {EMBO J 1988 Sep;7(9):2919-23.}, Stat = {MEDLINE}, Title = {PL of coliphage lambda: an alternative solution for an efficient promoter.}, Volume = {7}, Year = {1988}}

@article{Baracchini1988ic, Abstract = {Weak stringent or relaxed responses were induced in Escherichia coli (relA+), using mild amino acid starvation or treatment with chloramphenicol at low concentrations, respectively, such that the growth rate was barely reduced. In this manner, the intracellular concentration of the nucleotide guanosine tetraphosphate, ppGpp, could be varied in any desired range between 0 and 1000 pmol of ppGpp per OD460 unit of culture mass. At the same time, the rate of synthesis of stable RNA (rs; rRNA and tRNA) was measured, relative to the total instantaneous rate of RNA synthesis (rt). The correlation between the cytoplasmic concentration of ppGpp and stable RNA gene activity (rs/rt) was the same as that observed previously with relA+ and relA strains growing exponentially at different rates in different media. This suggests that the distinction between growth control and stringent control of stable RNA synthesis is arbitrary, and that both kinds of control reflect the same ppGpp-dependent phenomenon. By increasing the stable RNA gene dosage, using high copy number plasmids carrying an rrn gene, we have tested the idea that ppGpp partitions the bacterial RNA polymerase into two forms with different probabilities to initiate at stable RNA and mRNA promoters. The relaxed response was not significantly altered, but the extent of the stringent response was reduced by the presence of extra rrn genes. The results agree with quantitative predictions derived from the RNA polymerase partitioning hypothesis.}, Affiliation = {Biology Programs, University of Texas at Dallas, Richardson 75080.}, Au = {Bremer H}, Author = {Baracchini, E and Bremer, H}, Da = {19880325}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19880325}, Edat = {1988/02/25}, Jid = {2985121R}, Journal = {J Biol Chem}, Keywords = {Demand Response and Chassis}, Language = {eng}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Baracchini/Baracchini1988yd.pdf}, Lr = {20001218}, Mhda = {1988/02/25 00:01}, Number = {6}, Own = {NLM}, Pages = {2597-602}, Pl = {UNITED STATES}, Pmid = {2449428}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {56-75-7 (Chloramphenicol)}, Sb = {IM}, So = {Mol Gen Genet 1988 Aug;213(2-3):379-87.}, Stat = {MEDLINE}, Title = {Stringent and growth control of rRNA synthesis in Escherichia coli are both mediated by ppGpp.}, Volume = {263}, Year = {1988}}

@article{Baracchini1988ct, Abstract = {Previous studies on two Escherichia coli rpoB mutants, carrying single amino acid substitutions at approximate amino acid positions 736 and 906 in the beta subunit, showed that these alterations in the RNA polymerase resulted in an apparent reduced response to valine-induced amino acid starvation in vivo and prevented ppGpp-mediated inhibition of transcriptional initiation at stable RNA promoters in vitro. These observations suggested that the mutations had altered either the ppGpp binding site or the promoter selectivity of the enzyme. The in vivo analysis presented here indicates that these mutants encode an RNA polymerase that responds normally to changes in the level of ppGpp; their apparent relaxedness is due to a reduced accumulation of ppGpp during isoleucine starvation. Thus, there is no indication that the mutations have altered ppGpp binding sites. These observations and the difference between in vitro and in vivo results can be explained by the assumption that the mutations produce an extended ppGpp-dependent pausing of RNA polymerase during the transcription of unstable RNA. Comparison of the vivo and in vitro effects of ppGpp on rrn transcription further suggests that these reflect different phenomena, although in both cases ppGpp inhibits rrn transcription.}, Affiliation = {Biology Programs, University of Texas at Dallas, Richardson 75083-0688.}, Au = {Bremer H}, Author = {Baracchini, E and Glass, R and Bremer, H}, Da = {19881221}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19881221}, Edat = {1988/08/01}, Jid = {0125036}, Journal = {Mol Gen Genet}, Keywords = {Demand Response and Demand Modeling}, Language = {eng}, Lr = {20021101}, Mhda = {1988/08/01 00:01}, Number = {2-3}, Own = {NLM}, Pages = {379-87}, Pl = {GERMANY, WEST}, Pmid = {2460732}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {EC 2.7.7.6 (DNA-Directed RNA Polymerases)}, Sb = {IM}, So = {J Biol Chem 1990 Jul 15;265(20):11605-14.}, Stat = {MEDLINE}, Title = {Studies in vivo on Escherichia coli RNA polymerase mutants altered in the stringent response.}, Volume = {213}, Year = {1988}}

@article{Seo:1985aa, Author = {Jin-Ho Seo and James E. Bailey}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Journal = {Biotechnology and Bioengineering}, Keywords = {Demand and Demand Response}, Local-Url = {file://localhost/Users/Barry/Desktop/Papers/Seo/Seo1985fk.pdf}, Number = {12}, Pages = {1668-1674}, Title = {Effects of recombinant plasmid content on growth properties and cloned gene product formation in Escherichia coli}, Volume = {27}, Year = {1985}}

@article{Little:1983aa, Abstract = {An isogenic pair of relA+ and relA strains of Escherichia coli B/r with a mutation in the RNA polymerase subunit gene rpoB (Rifr) was isolated in which the relationship between guanosine tetraphosphate (ppGpp) concentration and stable RNA (rRNA, tRNA) gene activity was altered. The RNA polymerase in the rpoB strains was found to be about 20-fold more sensitive to ppGpp with respect to its stable RNA promoter activity than was the wild-type enzyme. The existence of such mutants is consistent with the idea that ppGpp interacts with the RNA polymerase enzyme and thereby alters its promoter selectivity, i.e., reduces its affinity for the stable RNA promoters. Under most conditions, the rpoB mutants had a reduced rate of growth and about a 10-fold-reduced intracellular concentration of ppGpp compared with the rpoB wild-type strains. The reduction of the level of ppGpp in the rpoB mutants during exponential growth was presumably a reflection of an indirect effect of the rpoB mutation on the control of relA-independent ppGpp metabolism.}, Au = {Bremer H}, Author = {Little, R and Ryals, J and Bremer, H}, Da = {19830617}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19830617}, Edat = {1983/05/01}, Jid = {2985120R}, Journal = {J Bacteriol}, Keywords = {Demand Modeling and Demand Response}, Language = {eng}, Lr = {20041117}, Mhda = {1983/05/01 00:01}, Number = {2}, Own = {NLM}, Pages = {787-92}, Pl = {UNITED STATES}, Pmid = {6188747}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {EC 2.7.7.6 (DNA-Directed RNA Polymerases)}, Sb = {IM}, So = {J Bacteriol 1983 Sep;155(3):1162-70.}, Stat = {MEDLINE}, Title = {rpoB mutation in Escherichia coli alters control of ribosome synthesis by guanosine tetraphosphate.}, Volume = {154}, Year = {1983}}

@article{Ryals1982ct, Abstract = {The expression of stable RNA (rRNA and tRNA) genes and the concentration of guanosine tetraphosphate (ppGpp) were measured in an isogenic pair of relA+ and relA derivatives of Escherichia coli B/r. The cells were either growing exponentially at different rates or subject to amino acid starvation when they were measured. The specific stable RNA gene activity (rs/rt, the rate of rRNA and tRNA synthesis relative to the total instantaneous rate of RNA synthesis) was found to decrease from 1.0 at a ppGpp concentration of 0 (extrapolated value) to 0.24 at saturating concentrations of ppGpp (above 100 pmoles per optical density at 460 nm unit of cell mass). The same relationship between the rs/rt ratio and ppGpp concentration was obtained independent of the physiological state of the bacteria (i.e., independent of the growth rate or of amino acid starvation) and independent of the relA allele. It can be concluded that ppGpp is an effector for stable RNA gene control and that stable RNA genes are not controlled by factors other than the ppGpp-mediated system. The results were shown to be qualitatively and quantitatively consistent with data on in vitro rRNA gene control by ppGpp, and they were interpreted in the light of reported ideas derived from those in vitro experiments.}, Au = {Bremer H}, Author = {Ryals, J and Little, R and Bremer, H}, Da = {19821029}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19821029}, Edat = {1982/09/01}, Gr = {GM 15142/GM/NIGMS}, Jid = {2985120R}, Journal = {J Bacteriol}, Keywords = {Demand Response and Chassis}, Language = {eng}, Lr = {20041117}, Mhda = {1982/09/01 00:01}, Number = {3}, Own = {NLM}, Pages = {1261-8}, Pl = {UNITED STATES}, Pmid = {6179924}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {9014-25-9 (RNA, Transfer)}, Sb = {IM}, So = {J Bacteriol 1982 Sep;151(3):1425-32.}, Stat = {MEDLINE}, Title = {Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate.}, Volume = {151}, Year = {1982}}

@article{Churchward1982ct, Abstract = {The effect of changing the DNA concentration on RNA synthesis, protein synthesis, and cell growth rate was studied in Escherichia coli B/r. The DNA concentration was varied by changing the replication velocity or by changing replication initiation in a thymine-requiring strain with a mutation in replication control. The results demonstrate that changes in DNA concentration (per mass) have no effect on the cell growth rate and the rates of synthesis (per mass) of stable RNA (rRNA, tRNA), bulk mRNA, or protein or on the concentration of RNA polymerase (total RNA polymerase per mass). Thus, transcription in E. coli is not limited by the concentration of DNA, but rather by the concentration of functional RNA polymerase in the cytoplasm. Changing the DNA concentration does, however, affect fully induced lac gene activity, here used as a model for constitutive gene expression. The magnitude of the effect of DNA concentration on lac gene activity depends on the distribution of replication forks over the chromosome, which is a function of the replication velocity. Analysis of these date reinforces the conclusion that transcription is limited by the concentration of functional RNA polymerase in the cytoplasm.}, Au = {Young R}, Author = {Churchward, G and Bremer, H and Young, R}, Da = {19820624}, Date-Added = {2006-07-10 11:09:21 -0400}, Date-Modified = {2006-07-10 11:09:21 -0400}, Dcom = {19820624}, Edat = {1982/05/01}, Gr = {GM 15142/GM/NIGMS}, Jid = {2985120R}, Journal = {J Bacteriol}, Keywords = {Demand Response and Demand Modeling}, Language = {eng}, Lr = {20041117}, Mhda = {1982/05/01 00:01}, Number = {2}, Own = {NLM}, Pages = {572-81}, Pl = {UNITED STATES}, Pmid = {6175615}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {EC 2.7.7.6 (DNA-Directed RNA Polymerases)}, Sb = {IM}, So = {J Bacteriol 1982 Sep;151(3):1261-8.}, Stat = {MEDLINE}, Title = {Transcription in bacteria at different DNA concentrations.}, Volume = {150}, Year = {1982}}

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