scholarly journals Mutations Enhancing Amino Acid Catabolism Confer a Growth Advantage in Stationary Phase

1999 ◽  
Vol 181 (18) ◽  
pp. 5800-5807 ◽  
Author(s):  
Erik R. Zinser ◽  
Roberto Kolter
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Stationary Phase ◽  
Carbon Starvation ◽  
Amino Acid Catabolism ◽  
Rich Media ◽  
Dying Cells

ABSTRACT Starved cultures of Escherichia coli undergo successive rounds of population takeovers by mutants of increasing fitness. These mutants express the growth advantage in stationary phase (GASP) phenotype. Previous work identified the rpoS819 allele as a GASP mutation allowing cells to take over stationary-phase cultures after growth in rich media (M. M. Zambrano, D. A. Siegele, M. A. Almirón, A. Tormo, and R. Kolter, Science 259:1757–1760, 1993). Here we have identified three new GASP loci from an aged rpoS819 strain: sgaA, sgaB, and sgaC. Each locus is capable of conferring GASP on therpoS819 parent, and they can provide successively higher fitnesses for the bacteria in the starved cultures. All four GASP mutations isolated thus far allow for faster growth on both individual and mixtures of amino acids. Each mutation confers a growth advantage on a different subset of amino acids, and these mutations act in concert to increase the overall catabolic capacity of the cell. We present a model whereby this enhanced ability to catabolize amino acids is responsible for the fitness gain during carbon starvation, as it may allow GASP mutants to outcompete the parental cells when growing on the amino acids released by dying cells.

scholarly journals Prolonged Stationary-Phase Incubation Selects forlrp Mutations in Escherichia coliK-12

2000 ◽  
Vol 182 (15) ◽  
pp. 4361-4365 ◽  
Author(s):  
Erik R. Zinser ◽  
Roberto Kolter
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Stationary Phase ◽  
Carbon Starvation ◽  
Dominant Negative ◽  
Mutant Protein ◽  
Amino Acid Catabolism ◽  
Loss Of Function ◽  
Global Regulator ◽  
Majority Population

ABSTRACT Evolution by natural selection occurs in cultures ofEscherichia coli maintained under carbon starvation stress. Mutants of increased fitness express a growth advantage in stationary phase (GASP) phenotype, enabling them to grow and displace the parent as the majority population. The first GASP mutation was identified as a loss-of-function allele of rpoS, encoding the stationary-phase global regulator, ςS (M. M. Zambrano, D. A. Siegele, M. A. Almirón, A. Tormo, and R. Kolter, Science 259:1757–1760, 1993). We now report that a second global regulator, Lrp, can also play a role in stationary-phase competition. We found that a mutant that took over an aged culture of an rpoS strain had acquired a GASP mutation inlrp. This GASP allele, lrp-1141, encodes a mutant protein lacking the critical glycine in the turn of the helix-turn-helix DNA-binding domain. The lrp-1141 allele behaves as a null mutation when in single copy and is dominant negative when overexpressed. Hence, the mutant protein appears to retain stability and the ability to dimerize but lacks DNA-binding activity. We also demonstrated that a lrp null allele generated by a transposon insertion has a fitness gain identical to that of thelrp-1141 allele, verifying that cells lacking Lrp activity have a competitive advantage during prolonged starvation. Finally, we tested by genetic analysis the hypothesis that the lrp-1141GASP mutation confers a fitness gain by enhancing amino acid catabolism during carbon starvation. We found that while amino acid catabolism may play a role, it is not necessary for the lrp GASP phenotype, and hence the lrp GASP phenotype is due to more global physiological changes.

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

Physiologische Bedeutung der „Stringent Control“ bei Escherichia coli unter extremen Hungerbedingungen / Stringent Control and Starvation Survival in Escherichia coli

1989 ◽  
Vol 44 (9-10) ◽  
pp. 838-844 ◽  
Author(s):  
H. Mach ◽  
M. Hecker ◽  
I. Hill ◽  
A. Schroeter ◽  
F. Mach
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Protein Turnover ◽  
Stringent Response ◽  
Phosphate Starvation ◽  
Pleiotropic Effects ◽  
Prolonged Starvation ◽  
Stringent Control ◽  
Starvation Survival

The viability of three isogenic relA+/relA strain pairs of Escherichia coli (CP78/CP79; NF 161/ NF162; CP 107/CP 143) was studied during prolonged starvation for amino acids, glucose or phosphate. After amino acid limitation we found a prolonged viability of all relA+ strains which synthesized ppGpp. We suggest that some ppGpp-mediated pleiotropic effects of the stringent response (e.g. glykogen accumulation, enhanced protein turnover) might be involved in this prolongation of survival. After glucose or phosphate starvation there was no difference in the relA+/relA strains either in the ppGpp content or in the survival.

scholarly journals Characterization of the 6'-N-aminoglycoside acetyltransferase gene aac(6')-Im [corrected] associated with a sulI-type integron.

1997 ◽  
Vol 41 (2) ◽  
pp. 314-318 ◽  
Author(s):  
E Hannecart-Pokorni ◽  
F Depuydt ◽  
L de wit ◽  
E van Bossuyt ◽  
J Content ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Resistance Gene ◽  
Citrobacter Freundii ◽  
Gram Negative ◽  
Gene Environment ◽  
Insert Region ◽  
Klebsiella Spp

The amikacin resistance gene aac(6')-Im [corrected] from Citrobacter freundii Cf155 encoding an aminoglycoside 6'-N-acetyltransferase was characterized. The gene was identified as a coding sequence of 521 bp located down-stream from the 5' conserved segment of an integron. The sequence of this aac(6')-Im [corrected] gene corresponded to a protein of 173 amino acids which possessed 64.2% identity in a 165-amino-acid overlap with the aac(6')-Ia gene product (F.C. Tenover, D. Filpula, K.L. Phillips, and J. J. Plorde, J. Bacteriol. 170:471-473, 1988). By using PCR, the aac(6')-Im [corrected] gene could be detected in 8 of 86 gram-negative clinical isolates from two Belgian hospitals, including isolates of Citrobacter, Klebsiella spp., and Escherichia coli. PCR mapping of the aac(6')-Im [corrected] gene environment in these isolates indicated that the gene was located within a sulI-type integron; the insert region is 1,700 bases long and includes two genes cassettes, the second being ant (3")-Ib.

Changes in metabolic rate and N excretion in the marine invertebrateSipunculus nudusunder conditions of environmental hypercapnia

2002 ◽  
Vol 205 (8) ◽  
pp. 1153-1160 ◽  
Author(s):  
M. Langenbuch ◽  
H. O. Pörtner
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Metabolic Rate ◽  
Intracellular Ph ◽  
Energy Demand ◽  
Control Level ◽  
Ammonia Excretion ◽  
Amino Acid Catabolism ◽  
Acid Base ◽  
Selection Of

SUMMARYIncreased CO2 partial pressures (hypercapnia) as well as hypoxia are natural features of marine environments like the intertidal zone. Nevertheless little is known about the specific effects of CO2 on metabolism, except for the well-described effects on acid—base variables and regulation. Accordingly, the sediment-dwelling worm Sipunculus nudus was used as an experimental model to investigate the correlation of acid—base-induced metabolic depression and protein/amino acid catabolism, by determining the rates of oxygen consumption, ammonia excretion and O/N ratios in non-perfused preparations of body wall musculature at various levels of extra- and intracellular pH, PCO2 and [HCO3-]. A decrease in extracellular pH from control level (7.9) to 6.7 caused a reduction in aerobic metabolic rate of both normocapnic and hypercapnic tissues by 40-45 %. O/N ratios of 4.0-4.5 under control conditions indicate that amino acid catabolism meets the largest fraction of aerobic energy demand. A significant 10-15 % drop in ammonia excretion, a simultaneous reduction of O/N ratios and a transient accumulation of intracellular bicarbonate during transition to extreme acidosis suggest a reduction in net amino acid catabolism and a shift in the selection of amino acids used,favouring monoamino dicarboxylic acids and their amines (asparagine,glutamine, aspartic and glutamic acids). A drop in intracellular pH was identified as mediating this effect. In conclusion, the present data provide evidence for a regulatory role of intracellular pH in the selection of amino acids used by catabolism.

scholarly journals Amino Acid Toxicities of Escherichia coli That Are Prevented by Leucyl-tRNA Synthetase Amino Acid Editing

2007 ◽  
Vol 189 (23) ◽  
pp. 8765-8768 ◽  
Author(s):  
Vrajesh A. Karkhanis ◽  
Anjali P. Mascarenhas ◽  
Susan A. Martinis
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Trna Synthetase ◽  
Amino Acid Editing

ABSTRACT Leucyl-tRNA synthetase (LeuRS) has evolved an editing function to clear misactivated amino acids. An Escherichia coli-based assay was established to identify amino acids that compromise the fidelity of LeuRS and translation. Multiple nonstandard as well as standard amino acids were toxic to the cell when LeuRS editing was inactivated.

scholarly journals Mutation in the DNA Gyrase A Gene ofEscherichia coli That Expands the Quinolone Resistance-Determining Region

2001 ◽  
Vol 45 (8) ◽  
pp. 2378-2380 ◽  
Author(s):  
S. Marvin Friedman ◽  
Tao Lu ◽  
Karl Drlica
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Dna Gyrase ◽  
Ofescherichia Coli ◽  
Quinolone Resistance ◽  
Gyrase A

ABSTRACT In three Escherichia coli mutants, a change (Ala-51 to Val) in the gyrase A protein outside the standard quinolone resistance-determining region (QRDR) lowered the level of quinolone susceptibility more than changes at amino acids 67, 82, 84, and 106 did. Revision of the QRDR to include amino acid 51 is indicated.

scholarly journals Involvement of FtsE ATPase and FtsX Extracellular Loops 1 and 2 in FtsEX-PcsB Complex Function in Cell Division of Streptococcus pneumoniae D39

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Lok-To Sham ◽  
Katelyn R. Jensen ◽  
Kevin E. Bruce ◽  
Malcolm E. Winkler
Keyword(s):  
Signal Transduction ◽  
Amino Acids ◽  
Cell Division ◽  
Streptococcus Pneumoniae ◽  
Amino Acid ◽  
Stationary Phase ◽  
Coiled Coil ◽  
Extracellular Loop ◽  
Coiled Coil Domain ◽  
Loop Domain

ABSTRACT The FtsEX protein complex has recently been proposed to play a major role in coordinating peptidoglycan (PG) remodeling by hydrolases with the division of bacterial cells. According to this model, cytoplasmic FtsE ATPase interacts with the FtsZ divisome and FtsX integral membrane protein and powers allosteric activation of an extracellular hydrolase interacting with FtsX. In the major human respiratory pathogen Streptococcus pneumoniae (pneumococcus), a large extracellular-loop domain of FtsX (ECL1FtsX) is thought to interact with the coiled-coil domain of the PcsB protein, which likely functions as a PG amidase or endopeptidase required for normal cell division. This paper provides evidence for two key tenets of this model. First, we show that FtsE protein is essential, that depletion of FtsE phenocopies cell defects caused by depletion of FtsX or PcsB, and that changes of conserved amino acids in the FtsE ATPase active site are not tolerated. Second, we show that temperature-sensitive (Ts) pcsB mutations resulting in amino acid changes in the PcsB coiled-coil domain (CCPcsB) are suppressed by ftsX mutations resulting in amino acid changes in the distal part of ECL1FtsX or in a second, small extracellular-loop domain (ECL2FtsX). Some FtsX suppressors are allele specific for changes in CCPcsB, and no FtsX suppressors were found for amino acid changes in the catalytic PcsB CHAP domain (CHAPPcsB). These results strongly support roles for both ECL1FtsX and ECL2FtsX in signal transduction to the coiled-coil domain of PcsB. Finally, we found that pcsB CC(Ts) mutants (Ts mutants carrying mutations in the region of pcsB corresponding to the coiled-coil domain) unexpectedly exhibit delayed stationary-phase autolysis at a permissive growth temperature. IMPORTANCE Little is known about how FtsX interacts with cognate PG hydrolases in any bacterium, besides that ECL1FtsX domains somehow interact with coiled-coil domains. This work used powerful genetic approaches to implicate a specific region of pneumococcal ECL1FtsX and the small ECL2FtsX in the interaction with CCPcsB. These findings identify amino acids important for in vivo signal transduction between FtsX and PcsB for the first time. This paper also supports the central hypothesis that signal transduction between pneumococcal FtsX and PcsB is linked to ATP hydrolysis by essential FtsE, which couples PG hydrolysis to cell division. The classical genetic approaches used here can be applied to dissect interactions of other integral membrane proteins involved in PG biosynthesis. Finally, delayed autolysis of the pcsB CC(Ts) mutants suggests that the FtsEX-PcsB PG hydrolase may generate a signal in the PG necessary for activation of the major LytA autolysin as pneumococcal cells enter stationary phase.

scholarly journals Escherichia coli amino acid auxotrophic expression host strains for investigating protein structure-function relationships

2020 ◽  
Author(s):  
Toshio Iwasaki ◽  
Yoshiharu Miyajima-Nakano ◽  
Risako Fukazawa ◽  
Myat T Lin ◽  
Shin-Ichi Matsushita ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Protein Structure ◽  
Amino Acid ◽  
Structure Function ◽  
Growth Medium ◽  
Isotope Labeling ◽  
Water Soluble ◽  
Expression Host ◽  
Host Strains

Abstract A set of C43(DE3) and BL21(DE3) Escherichia coli host strains that are auxotrophic for various amino acids is briefly reviewed. These strains require the addition of a defined set of one or more amino acids in the growth medium, and have been specifically designed for overproduction of membrane or water-soluble proteins selectively labeled with stable isotopes such as 2H, 13C and 15N. The strains described here are available for use and have been deposited into public strain banks. Although they cannot fully eliminate the possibility of isotope dilution and mixing, metabolic scrambling of the different amino acid types can be minimized through a careful consideration of the bacterial metabolic pathways. The use of a suitable auxotrophic expression host strain with an appropriately isotopically labeled growth medium ensures high levels of isotope labeling efficiency as well as selectivity for providing deeper insight into protein structure-function relationships.

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