Systems biology of lactic acid bacteria: a critical review.

PubWeight™: 0.91‹?›

🔗 View Article (PMC 3231918)

Published in Microb Cell Fact on August 30, 2011

Authors

Bas Teusink1, Herwig Bachmann, Douwe Molenaar

Author Affiliations

1: Systems Bioinformatics/NISB, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands. b.teusink@vu.nl

Articles cited by this

(truncated to the top 100)

Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (1997) 60.15

Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A (2006) 10.24

Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature (2002) 9.07

What is flux balance analysis? Nat Biotechnol (2010) 9.01

The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res (2001) 8.63

Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A (2003) 8.40

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature (2002) 7.38

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng (2003) 6.81

A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc (2010) 6.64

How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev (2006) 6.39

Bacteriocins of lactic acid bacteria. Biochimie (1988) 6.25

Optimality and evolutionary tuning of the expression level of a protein. Nature (2005) 5.94

Bacteriocins: developing innate immunity for food. Nat Rev Microbiol (2005) 5.77

Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A (2003) 5.64

Applications of genome-scale metabolic reconstructions. Mol Syst Biol (2009) 5.54

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng (2003) 5.53

Plasmid distribution and evidence for a proteinase plasmid in Streptococcus lactis C2-1. Appl Microbiol (1975) 5.34

Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol (2008) 4.74

Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A (2005) 4.40

Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol (2006) 4.24

Structured habitats and the evolution of anticompetitor toxins in bacteria. Proc Natl Acad Sci U S A (1981) 4.08

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics (2010) 3.87

Explaining microbial population genomics through phage predation. Nat Rev Microbiol (2009) 3.87

Snowdrift game dynamics and facultative cheating in yeast. Nature (2009) 3.66

The proteolytic systems of lactic acid bacteria. Antonie Van Leeuwenhoek (1996) 3.50

Change from homo- to heterolactic fermentation by Streptococcus lactis resulting from glucose limitation in anaerobic chemostat cultures. J Bacteriol (1979) 3.50

Galactose fermentation by Streptococcus lactis and Streptococcus cremoris: pathways, products, and regulation. J Bacteriol (1980) 3.45

Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol (2007) 3.43

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem (2000) 3.33

Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet (2006) 3.25

Allelopathy in Spatially Distributed Populations J Theor Biol (1997) 2.89

Plasmid DNA in Streptococcus cremoris Wg2: Influence of pH on Selection in Chemostats of a Variant Lacking a Protease Plasmid. Appl Environ Microbiol (1982) 2.86

Control of key metabolic intersections in Bacillus subtilis. Nat Rev Microbiol (2007) 2.81

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res (2004) 2.71

Cloning and expression of the Lactococcus lactis subsp. cremoris SK11 gene encoding an extracellular serine proteinase. Gene (1989) 2.53

Chance and necessity in the evolution of minimal metabolic networks. Nature (2006) 2.48

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 2.43

Cloning and expression of a Streptococcus cremoris proteinase in Bacillus subtilis and Streptococcus lactis. Appl Environ Microbiol (1985) 2.43

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc Natl Acad Sci U S A (2007) 2.42

Metabolic modeling of a mutualistic microbial community. Mol Syst Biol (2007) 2.40

Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci U S A (2007) 2.40

Control of the shift from homolactic acid to mixed-acid fermentation in Lactococcus lactis: predominant role of the NADH/NAD+ ratio. J Bacteriol (1997) 2.39

The biomass objective function. Curr Opin Microbiol (2010) 2.32

How did Saccharomyces evolve to become a good brewer? Trends Genet (2006) 2.29

Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol (2009) 2.26

Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J Theor Biol (1992) 2.21

Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo. Nature (2004) 2.20

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem (2006) 2.17

Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol (2005) 2.14

Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol (2003) 2.09

The importance of inorganic phosphate in regulation of energy metabolism of Streptococcus lactis. J Biol Chem (1981) 2.05

In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl Environ Microbiol (2005) 2.04

Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol (2005) 2.03

Exploring Lactobacillus plantarum genome diversity by using microarrays. J Bacteriol (2005) 2.02

Gene inactivation in Lactococcus lactis: branched-chain amino acid biosynthesis. J Bacteriol (1993) 1.99

Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol (2003) 1.98

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng (2009) 1.96

Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol (2006) 1.94

Fructose 1,6-diphosphate-activated L-lactate dehydrogenase from Streptococcus lactis: kinetic properties and factors affecting activation. J Bacteriol (1977) 1.85

Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol (2010) 1.83

Selection of Protease-Positive and Protease-Negative Variants of Streptococcus cremoris. Appl Environ Microbiol (1987) 1.83

The nature of systems biology. Trends Microbiol (2006) 1.79

The control of flux. Biochem Soc Trans (1995) 1.78

Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol (2006) 1.77

Effect of specific growth rate on fermentative capacity of baker's yeast. Appl Environ Microbiol (1998) 1.75

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J (2010) 1.63

OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol (2010) 1.61

Identification of a novel operon in Lactococcus lactis encoding three enzymes for lactic acid synthesis: phosphofructokinase, pyruvate kinase, and lactate dehydrogenase. J Bacteriol (1993) 1.60

Transient heterogeneity in extracellular protease production by Bacillus subtilis. Mol Syst Biol (2008) 1.60

Regulation of glycolysis in Lactococcus lactis: an unfinished systems biological case study. Syst Biol (Stevenage) (2006) 1.48

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol (2010) 1.47

Conversion of Lactococcus lactis from homolactic to homoalanine fermentation through metabolic engineering. Nat Biotechnol (1999) 1.46

Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PLoS Comput Biol (2008) 1.46

Overview on sugar metabolism and its control in Lactococcus lactis - the input from in vivo NMR. FEMS Microbiol Rev (2005) 1.44

Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Microbiology (2002) 1.40

Towards genome-scale signalling network reconstructions. Nat Rev Genet (2010) 1.39

Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput Biol (2009) 1.37

The intricate side of systems biology. Proc Natl Acad Sci U S A (2006) 1.37

Gene inactivation in Lactococcus lactis: histidine biosynthesis. J Bacteriol (1993) 1.35

Molecular characterization of a cell wall-associated proteinase gene from Streptococcus lactis NCDO763. Mol Microbiol (1989) 1.33

Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates. Biotechnol Bioeng (1994) 1.31

A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae. Biotechnol Bioeng (2007) 1.23

Competitive interactions in Escherichia coli populations: the role of bacteriocins. ISME J (2010) 1.21

The level of pyruvate-formate lyase controls the shift from homolactic to mixed-acid product formation in Lactococcus lactis. Appl Microbiol Biotechnol (2001) 1.18

Control of glycolysis by glyceraldehyde-3-phosphate dehydrogenase in Streptococcus cremoris and Streptococcus lactis. J Bacteriol (1987) 1.16

Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol (2009) 1.14

The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology (2006) 1.14

Approximative kinetic formats used in metabolic network modeling. Biotechnol Bioeng (2005) 1.13

Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput Biol (2009) 1.10

Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl Environ Microbiol (2009) 1.10

Enzyme kinetics informatics: from instrument to browser. FEBS J (2010) 1.06

Glyceraldehyde-3-phosphate dehydrogenase has no control over glycolytic flux in Lactococcus lactis MG1363. J Bacteriol (2003) 1.04

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J (2010) 1.01

Metabolism of lactic acid bacteria studied by nuclear magnetic resonance. Antonie Van Leeuwenhoek (2002) 1.01

Examination of post-transcriptional regulations in prokaryotes by integrative biology. C R Biol (2009) 1.00

Expression of genes encoding F(1)-ATPase results in uncoupling of glycolysis from biomass production in Lactococcus lactis. Appl Environ Microbiol (2002) 0.99

A critical view of metabolic network adaptations. HFSP J (2008) 0.98

Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates. Microb Cell Fact (2011) 0.97

Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes. Metab Eng (2010) 0.97

Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis. Appl Environ Microbiol (2008) 0.96

Articles by these authors

Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A (2003) 8.40

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol (2009) 3.57

Visualization for genomics: the Microbial Genome Viewer. Bioinformatics (2004) 3.52

Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ Microbiol (2009) 2.18

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem (2006) 2.17

The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Natl Acad Sci U S A (2007) 1.94

Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. J Bacteriol (2010) 1.90

Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum. J Bacteriol (2005) 1.85

Glutathione protects Lactococcus lactis against oxidative stress. Appl Environ Microbiol (2003) 1.68

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics (2006) 1.65

An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence. J Bacteriol (2005) 1.61

Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. Appl Environ Microbiol (2007) 1.55

Natural diversity and adaptive responses of Lactococcus lactis. Curr Opin Biotechnol (2006) 1.54

Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells. BMC Microbiol (2010) 1.51

Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays. Appl Environ Microbiol (2007) 1.48

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res (2011) 1.41

Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice. ISME J (2010) 1.33

Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS One (2011) 1.25

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol (2011) 1.19

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1. Microb Cell Fact (2007) 1.17

Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ Microbiol (2009) 1.15

Heterologous expression of Arabidopsis UDP-glucosyltransferases in Saccharomyces cerevisiae for production of zearalenone-4-O-glucoside. Appl Environ Microbiol (2006) 1.13

PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics (2009) 1.10

Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. Appl Environ Microbiol (2010) 1.03

sigma54-Mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism. Microbiology (2009) 1.02

PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics (2012) 1.02

Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria. J Bacteriol (2007) 1.00

Trehalose degradation and glucose efflux precede cell ejection during germination of heat-resistant ascospores of Talaromyces macrosporus. Arch Microbiol (2002) 0.99

Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A (2013) 0.99

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3. FEBS Lett (2010) 0.98

Regulatory phenotyping reveals important diversity within the species Lactococcus lactis. Appl Environ Microbiol (2009) 0.97

Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis. Appl Environ Microbiol (2008) 0.96

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds. Brief Bioinform (2013) 0.96

The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis. Microbiology (2009) 0.95

Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions. Appl Environ Microbiol (2011) 0.95

Volatile compound fingerprinting of mixed-culture fermentations. Appl Environ Microbiol (2011) 0.94

Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri. Appl Environ Microbiol (2009) 0.92

Using Lactococcus lactis for glutathione overproduction. Appl Microbiol Biotechnol (2004) 0.89

Genome instability in Lactobacillus rhamnosus GG. Appl Environ Microbiol (2013) 0.89

High local substrate availability stabilizes a cooperative trait. ISME J (2010) 0.88

Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1. Microb Cell Fact (2010) 0.87

Two homologous Agr-like quorum-sensing systems cooperatively control adherence, cell morphology, and cell viability properties in Lactobacillus plantarum WCFS1. J Bacteriol (2008) 0.87

A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl Environ Microbiol (2012) 0.87

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis. Microb Cell Fact (2011) 0.86

Unity in organisation and regulation of catabolic operons in Lactobacillus plantarum, Lactococcus lactis and Listeria monocytogenes. Syst Appl Microbiol (2005) 0.86

Functional ingredient production: application of global metabolic models. Curr Opin Biotechnol (2005) 0.86

Expression of plant flavor genes in Lactococcus lactis. Appl Environ Microbiol (2007) 0.86

Introducing glutathione biosynthetic capability into Lactococcus lactis subsp. cremoris NZ9000 improves the oxidative-stress resistance of the host. Metab Eng (2006) 0.83

Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol Lett (2012) 0.83

Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide stress tolerance. Appl Environ Microbiol (2010) 0.83

Gene expression analysis reveals a gene set discriminatory to different metals in soil. Toxicol Sci (2010) 0.82

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism. Genetics (2013) 0.82

Genomics of dairy fermentations. Microb Biotechnol (2008) 0.81

Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis. Microb Biotechnol (2010) 0.79

Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome. J Bacteriol (2009) 0.78

The pivotal regulator GlnB of Escherichia coli is engaged in subtle and context-dependent control. FEBS J (2009) 0.78

Dichotomy in post-genomic microbiology. Nat Biotechnol (2007) 0.78

Vesicle trafficking via the Spitzenkörper during hyphal tip growth in Rhizoctonia solani. Antonie Van Leeuwenhoek (2013) 0.77