Deletion of 76 genes relevant to flagella and pili formation to facilitate polyhydroxyalkanoate production in Pseudomonas putida

Environment signal dependent biocontainment systems for engineered organisms: Leveraging triggered responses and combinatorial systems

As synthetic biology advances, the necessity for robust biocontainment strategies for genetically engineered organisms (GEOs) grows increasingly critical to mitigate biosafety risks related to their potential environmental release. This paper aims to evaluate environment signal-dependent biocontainment systems for engineered organisms, focusing specifically on leveraging triggered responses and combinatorial systems. There are different types of triggers-chemical, light, temperature, and pH-this review illustrates how these systems can be designed to respond to environmental signals, ensuring a higher safety profile. It also focuses on combinatorial biocontainment to avoid consequences of unintended GEO release into an external environment. Case studies are discussed to demonstrate the practical applications of these systems in real-world scenarios.

Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum

Purple photosynthetic bacteria (PPB) are versatile microorganisms capable of producing various value-added chemicals, e.g., biopolymers and biofuels. They employ diverse metabolic pathways, allowing them to adapt to various growth conditions and even extreme environments. Thus, they are ideal organisms for the Next Generation Industrial Biotechnology concept of reducing the risk of contamination by using naturally robust extremophiles. Unfortunately, the potential of PPB for use in biotechnology is hampered by missing knowledge on regulations of their metabolism. Although Rhodospirillum rubrum represents a model purple bacterium studied for polyhydroxyalkanoate and hydrogen production, light/chemical energy conversion, and nitrogen fixation, little is known regarding the regulation of its metabolism at the transcriptomic level. Using RNA sequencing, we compared gene expression during the cultivation utilizing fructose and acetate as substrates in case of the wild-type strain R. rubrum DSM 467T and its knock-out mutant strain that is missing two polyhydroxyalkanoate synthases PhaC1 and PhaC2. During this first genome-wide expression study of R. rubrum, we were able to characterize cultivation-driven transcriptomic changes and to annotate non-coding elements as small RNAs.

Effect of folA gene in human breast milk-derived Limosilactobacillus reuteri on its folate biosynthesis

Introduction

Folate supplementation is crucial for the human body, and the chemically synthesized folic acid might have undesirable side effects. The use of molecular breeding methods to modify the genes related to the biosynthesis of folate by probiotics to increase folate production is currently a focus of research.

Methods

In this study, the folate-producing strain of Limosilactobacillus reuteri B1-28 was isolated from human breast milk, and the difference between B1-28 and folA gene deletion strain ΔFolA was investigated by phenotyping, in vitro probiotic evaluation, metabolism and transcriptome analysis.

Results

The results showed that the folate producted by the ΔFolA was 2-3 folds that of the B1-28. Scanning electron microscope showed that ΔFolA had rougher surface, and the acid-producing capacity (p = 0.0008) and adhesion properties (p = 0.0096) were significantly enhanced than B1-28. Transcriptomic analysis revealed that differentially expressed genes were mainly involved in three pathways, among which the biosynthesis of ribosome and aminoacyl-tRNA occurred in the key metabolic pathways. Metabolomics analysis showed that folA affected 5 metabolic pathways, involving 89 different metabolites.

Discussion

In conclusion, the editing of a key gene of folA in folate biosynthesis pathway provides a feasible pathway to improve folate biosynthesis in breast milk-derived probiotics.

Becoming settlers: Elements and mechanisms for surface colonization by Pseudomonas putida

Pseudomonads are considered to be among the most widespread culturable bacteria in mesophilic environments. The evolutive success of Pseudomonas species can be attributed to their metabolic versatility, in combination with a set of additional functions that enhance their ability to colonize different niches. These include the production of secondary metabolites involved in iron acquisition or having a detrimental effect on potential competitors, different types of motility, and the capacity to establish and persist within biofilms. Although biofilm formation has been extensively studied using the opportunistic pathogen Pseudomonas aeruginosa as a model organism, a significant body of knowledge is also becoming available for non-pathogenic Pseudomonas. In this review, we focus on the mechanisms that allow Pseudomonas putida to colonize biotic and abiotic surfaces and adapt to sessile life, as a relevant persistence strategy in the environment. This species is of particular interest because it includes plant-beneficial strains, in which colonization of plant surfaces may be relevant, and strains used for environmental and biotechnological applications, where the design and functionality of biofilm-based bioreactors, for example, also have to take into account the efficiency of bacterial colonization of solid surfaces. This work reviews the current knowledge of mechanistic and regulatory aspects of biofilm formation by P. putida and pinpoints the prospects in this field.

Online Omics Platform Expedites Industrial Application of Halomonas bluephagenesis TD1.0

Multi-omic data mining has the potential to revolutionize synthetic biology especially in non-model organisms that have not been extensively studied. However, tangible engineering direction from computational analysis remains elusive due to the interpretability of large datasets and the difficulty in analysis for non-experts. New omics data are generated faster than our ability to use and analyse results effectively, resulting in strain development that proceeds through classic methods of trial-and-error without insight into complex cell dynamics. Here we introduce a user-friendly, interactive website hosting multi-omics data. Importantly, this new platform allows non-experts to explore questions in an industrially important chassis whose cellular dynamics are still largely unknown. The web platform contains a complete KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis derived from principal components analysis, an interactive bio-cluster heatmap analysis of genes, and the Halomonas TD1.0 genome-scale metabolic (GEM) model. As a case study of the effectiveness of this platform, we applied unsupervised machine learning to determine key differences between Halomonas bluephagenesis TD1.0 cultivated under varied conditions. Specifically, cell motility and flagella apparatus are identified to drive energy expenditure usage at different osmolarities, and predictions were verified experimentally using microscopy and fluorescence labelled flagella staining. As more omics projects are completed, this landing page will facilitate exploration and targeted engineering efforts of the robust, industrial chassis H bluephagenesis for researchers without extensive bioinformatics background.

The Influence of Outer Membrane Protein on Ampicillin Resistance of Vibrio parahaemolyticus

The antibiotic resistance of the food-borne pathogen Vibrio parahaemolyticus has attracted researchers' attention in recent years, but its molecular mechanism remains poorly understood. In this study, 7 genes encoding outer membrane proteins (OMPs) were individually deleted in V. parahaemolyticus ATCC33846, and the resistance of these 7 mutants to 14 antibiotics was investigated. The results revealed that the resistance of the 7 mutants to ampicillin was significantly increased. Further exploration of 20-gene transcription changes by real time-qPCR (RT-qPCR) demonstrated that the higher ampicillin resistance might be attributed to the expression of β-lactamase and reduced peptidoglycan (PG) synthesis activity through reduced transcription of penicillin-binding proteins (PBPs), increased transcription of l,d-transpeptidases, downregulated d,d-carboxypeptidase, and alanine deficiency. This study provides a new perspective on ampicillin resistance in OMP mutants with respect to PG synthesis.

Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering

Conversion of CO₂ to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO₂, has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. The metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ΔphcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.

Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO2

Background

A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO₂) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO₂ is still too low for commercialization.

Results

Here, we engineer the carbon fixation metabolism to improve CO₂ utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO₂—fixing metabolism and PHB production were investigated.

Conclusions

The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01962-7.

Random genome reduction coupled with polyhydroxybutyrate biosynthesis to facilitate its accumulation in Escherichia coli

Genome reduction has been emerged as a powerful tool to construct ideal chassis for synthetic biology. Random genome reduction couple genomic deletion with growth and has the potential to construct optimum genome for a given environment. Recently, we developed a transposon-mediated random deletion (TMRD) method that allows the random and continuous reduction of Escherichia coli genome. Here, to prove its ability in constructing optimal cell factories, we coupled polyhydroxybutyrate (PHB) accumulation with random genome reduction and proceeded to reduce the E. coli genome. Five mutants showed high biomass and PHB yields were selected from 18 candidates after ten rounds of genome reduction. And eight or nine genomic fragments (totally 230.1–270.0 Kb) were deleted in their genomes, encompassing 4.95%–5.82% of the parental MG1655 genome. Most mutants displayed better growth, glucose utilization, protein expression, and significant increase of electroporation efficiency compared with MG1655. The PHB content and concentration enhanced up to 13.3%–37.2% and 60.2%–102.9% when batch fermentation was performed in M9-glucose medium using the five mutants. Particularly, in mutant H16, lacking 5.28% of its genome, the increase of biomass and PHB concentration were more than 50% and 100% compared with MG1655, respectively. This work expands the strategy for creating streamlined chassis to improve the production of high value-added products.

Deficiency of exopolysaccharides and O-antigen makes Halomonas bluephagenesis self-flocculating and amenable to electrotransformation

Halomonas bluephagenesis, a haloalkaliphilic bacterium and native polyhydroxybutyrate (PHB) producer, is a non-traditional bioproduction chassis for the next generation industrial biotechnology (NGIB). A single-sgRNA CRISPR/Cas9 genome editing tool is optimized using dual-sgRNA strategy to delete large DNA genomic fragments (>50 kb) with efficiency of 12.5% for H. bluephagenesis. The non-essential or redundant gene clusters of H. bluephagenesis, including those encoding flagella, exopolysaccharides (EPSs) and O-antigen, are sequentially deleted using this improved genome editing strategy. Totally, ~3% of the genome is reduced with its rapid growth and high PHB-production ability unaffected. The deletion of EPSs and O-antigen gene clusters shows two excellent properties from industrial perspective. Firstly, the EPSs and O-antigen deleted mutant rapidly self-flocculates and precipitates within 20 min without centrifugation. Secondly, DNA transformation into the mutant using electroporation becomes feasible compared to the wild-type H. bluephagenesis. The genome-reduced H. bluephagenesis mutant reduces energy and carbon source requirement to synthesize PHB comparable to its wild type. The H. bluephagenesis chassis with a reduced genome serves as an improved version of a NGIB chassis for productions of polyhydroxyalkanoates (PHA) or other chemicals.

CRISPR/Cas9 editing of a PHB-producing H. bluephagenesis strain is used to delete the redundant synthesis pathways of flagella and EPSs, allowing for enhanced self-flocculation, less carbon and energy requirement for metabolic processes and feasible electrotransformation.

High-throughput identification of genes influencing the competitive ability to obtain nutrients and performance of biocontrol in Pseudomonas putida JBC17

Elucidating underlying mechanisms of biocontrol agents (BCAs) could aid in selecting potent BCAs and increasing their biocontrol efficacy. Nutrient competition is an important biocontrol mechanism; however, essential nutrient sources, and contributing genes for nutrient competition still remain to be explored. Pseudomonas putida JBC17 (JBC17WT) suppressed green mold in satsuma mandarins by inhibiting conidial germination of Penicillium digitatum via nutrient competition. To analyze genes essential for biocontrol performance of JBC17WT, we generated a transposon (Tn)-mediated mutant library and selected mutants with the ability to suppress conidial germination. Several mutants in the genes of flagella-formation, including fliR, fliH, and flgG, increased biocontrol performance and enhanced inhibition of conidial germination. They lost swimming motility, exhibited increased growth and rapid carbon and nitrogen utilization than the wild type under nutrient-poor conditions. The nutrient competition assay using polytetrafluoroethylene cylinders revealed that conidial germination was inhibited by nutrient absorption under nutrient-poor conditions. In addition, genes, including amidohydrolase (ytcJ), tonB-dependent receptor (cirA), argininosuccinate synthase (argG), D-3-phosphoglycerate dehydrogenase (serA), and chaperone protein (dnaJ), were involved in the inhibition of conidial germination. The results of this study indicate that rapid and continuous absorption of nutrients by JBC17WT restrict nutrient availability for conidial germination on nutrient-limited fruit surfaces, thereby decreasing the chances of fungal spores infecting fruits. The high-throughput analysis of Tn mutants of this study highlighted the importance of nutrient competition and the genes that influence biocontrol ability, which contributes to the development of biocontrol applications.

Microbial cell surface engineering for high-level synthesis of bio-products

Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.

Engineering the Outer Membrane Could Facilitate Better Bacterial Performance and Effectively Enhance Poly-3-Hydroxybutyrate Accumulation

Poly-3-hydroxybutyrate (PHB) is an environmentally friendly polymer and can be produced in Escherichia coli cells after overexpression of the heterologous gene cluster phaCAB. The biosynthesis of the outer membrane (OM) consumes many nutrients and influences cell morphology. Here, we engineered the OM by disrupting all gene clusters relevant to the polysaccharide portion of lipopolysaccharide (LPS), colanic acid (CA), flagella, and/or fimbria in E. coli W3110. All these disruptions benefited PHB production. Especially, disrupting all these OM components increased the PHB content to 83.0 wt% (PHB content percentage of dry cell weight), while the wild-type control produced only 1.5 wt% PHB. The increase was mainly due to the LPS truncation to Kdo₂ (3-deoxy-d-manno-octulosonic acid)-lipid A, which resulted in 82.0 wt% PHB with a 25-fold larger cell volume, and disrupting CA resulted in 57.8 wt% PHB. In addition, disrupting LPS facilitated advantageous fermentation features, including 69.1% less acetate, a 550% higher percentage of autoaggregated cells among the total culture cells, 69.1% less biofilm, and a higher broken cell ratio. Further detailed mechanism investigations showed that disrupting LPS caused global changes in envelope and cellular metabolism: (i) a sharp decrease in flagella, fimbria, and secretions; (ii) more elastic cells; (iii) much greater carbon flux toward acetyl coenzyme A (acetyl-CoA) and supply of cofactors, including NADP, NAD, and ATP; and (iv) a decrease in by-product acids but increase in γ-aminobutyric acid by activating σ^E factor. Disrupting CA, flagella, and fimbria also improved the levels of acetyl-CoA and cofactors. The results indicate that engineering the OM is an effective strategy to enhance PHB production and highlight the applicability of OM engineering to increase microbial cell factory performance. IMPORTANCE Understanding the detailed influence of the OM on the cell envelope and cellular metabolism is important for optimizing the E. coli cell factory and many other microorganisms. This study revealed the applicability of remodeling the OM to enhance PHB accumulation as representative inclusion bodies. The results generated in this study give essential information for producing other inclusion bodies or chemicals which need more acetyl-CoA and cofactors but less by-product acids. This study is promising to provide new ideas for the improvement of microbial cell factories.

Engineering microbial metabolic energy homeostasis for improved bioproduction

Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.

Core Oligosaccharide Portion of Lipopolysaccharide Plays Important Roles in Multiple Antibiotic Resistance in Escherichia coli

Gram-negative bacteria are intrinsically resistant to antibiotics due to the presence of the cell envelope, but the mechanisms of this resistance are still not fully understood. In this study, a series of mutants that lack one or more major components associated with the cell envelope were constructed from Escherichia coli K-12 W3110. WJW02 can only synthesize Kdo2-lipid A, which lacks the core oligosaccharide portion of lipopolysaccharide (LPS). WJW04, WJW07, and WJW08 were constructed from WJW02 by deleting the gene clusters relevant to the biosynthesis of exopolysaccharide, flagella, and fimbriae, respectively. WJW09, WJW010, and WJW011 cells cannot synthesize exopolysaccharide (EPS), flagella, and fimbria, respectively. Compared to the wild type (W3110), mutants WJW02, WJW04, WJW07, and WJW08 cells showed decreased resistance to more than 10 different antibacterial drugs, but the mutants WJW09, WJW010, and WJW011 did not. This indicates that the core oligosaccharide portion of lipopolysaccharide plays an important role in multiple antibiotic resistance in E. coli and that the first heptose in the core oligosaccharide portion is critical. Furthermore, the removal of the core oligosaccharide of LPS leads to influences on cell wall morphology, cell phenotypes, porins, efflux systems, and response behaviors to antibiotic stimulation. The results demonstrate the important role of lipopolysaccharide in the antibiotic resistance of Gram-negative bacteria.

Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria

Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for heterologous BGC expression, but its cells undergo early autolysis, hindering further applications. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chitinimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression.

Construction and Application of an Escherichia coli Strain Lacking 62 Genes Responsible for the Biosynthesis of Enterobacterial Common Antigen and Flagella

The biosynthesis of the enterobacterial common antigen and flagella in Escherichia coli consumes lots of substrates and energy. In this study, 12 genes responsible for the biosynthesis of the enterobacterial common antigen were deleted in E. coli MG1655, resulting in WQM021. WQM021 grew better than MG1655 in both rich LB medium and minimum M9 medium. Compared with MG1655, WQM021 showed higher membrane permeability and higher production efficiency for recombinant proteins, polyhydroxyalkanoate, and l-threonine. Transcriptome analysis revealed that genes relevant to glucose consumption, glycolysis, and flagellar synthesis were significantly upregulated in WQM021. Therefore, 50 genes responsible for flagellar biosynthesis were further deleted in WQM021, resulting in WQM022. WQM022 grew better and could synthesize more polyhydroxyalkanoate and l-threonine than WQM021. The results demonstrate that the productivity of E. coli can be efficiently improved when the enterobacterial common antigen and flagella are eliminated. This strategy has guiding significance in the optimization of other industrial products and microorganisms.

Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions

Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness in hypermutator strains of the environmental bacterium Pseudomonas aeruginosa in comparison to the host-niche-adapted Salmonella enterica. We demonstrate that P. aeruginosa, but not S. enterica, hypermutators evolve toward higher fitness under planktonic conditions. Adaptation to increased growth performance was accompanied by a reversible perturbing of the local genetic context of membrane and cell wall biosynthesis genes. Furthermore, we observed a fine-tuning of complex regulatory circuits involving multiple di-guanylate modulating enzymes that regulate the transition between fast growing planktonic and sessile biofilm-associated lifestyles. The redundancy and local specificity of the di-guanylate signaling pathways seem to allow a convergent shift toward increased growth performance across niche-adapted clonal P. aeruginosa lineages, which is accompanied by a pronounced heterogeneity of their motility, virulence, and biofilm phenotypes.

Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories

Escherichia coli is generally used as model bacteria to define microbial cell factories for many products and to investigate regulation mechanisms. E. coli exhibits phospholipids, lipopolysaccharides, colanic acid, flagella and type I fimbriae on the outer membrane which is a self-protective barrier and closely related to cellular morphology, growth, phenotypes and stress adaptation. However, these outer membrane associated molecules could also lead to potential contamination and insecurity for fermentation products and consume lots of nutrients and energy sources. Therefore, understanding critical insights of these membrane associated molecules is necessary for building better microbial producers. Here the biosynthesis, function, influences, and current membrane engineering applications of these outer membrane associated molecules were reviewed from the perspective of synthetic biology, and the potential and effective engineering strategies on the outer membrane to improve fermentation features for microbial cell factories were suggested.

Truncating the Structure of Lipopolysaccharide in Escherichia coli Can Effectively Improve Poly-3-hydroxybutyrate Production

Poly-3-hydroxybutyrate is an environmentally friendly polymer with many promising applications and can be produced in Escherichia coli cells after overexpressing the heterologous gene cluster phaCAB. In this study, we found that truncating the structure of lipopolysaccharide in E. coli can effectively enhance poly-3-hydroxybutyrate production. E. coli mutant strains WJW00, WJD00, and WJJ00 were constructed by deleting rfaD from E. coli strain W3110, DH5α, and JM109, respectively. Compared to the controls W3110/pDXW-8-phaCAB, DH5a/pDXW-8-phaCAB, and JM109/pDXW-8-phaCAB, the yield of poly-3-hydroxybutyrate in WJW00/pDXW-8-phaCAB, WJD00/pDXW-8-phaCAB, and WJJ00/pDXW-8-phaCAB cells increased by 200%, 81.5%, and 75.6%, respectively, and the conversion rate of glucose to poly-3-hydroxybutyrate was increased by ∼250%. Further analysis revealed that LPS truncation in E. coli rebalanced carbon and nitrogen metabolism, increased the levels of acetyl-CoA, γ-aminobutyric acid, NADPH, NADH, and ATP, and decreased the levels of organic acids and flagella, resulting in the high ratio of carbon to nitrogen. These metabolic changes in these E. coli mutants led to the significant increase of poly-3-hydroxybutyrate production.

Trade-offs between gene expression, growth and phenotypic diversity in microbial populations

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Limitations in molecular resources for gene expression influence bacterial physiology.

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Bacteria optimise trade-offs between resource allocation and growth.

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Resource allocation plays a role in the emergence of phenotypic heterogeneity.

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Trade-offs between bet-hedging and growth can be harnessed in biotechnology.

Bacterial cells have a limited number of resources that can be allocated for gene expression. The intracellular competition for these resources has an impact on the cell physiology. Bacteria have evolved mechanisms to optimize resource allocation in a variety of scenarios, showing a trade-off between the resources used to maximise growth (e.g. ribosome synthesis) and the rest of cellular functions. Limitations in gene expression also play a role in generating phenotypic diversity, which is advantageous in fluctuating environments, at the expenses of decreasing growth rates. Our current understanding of these trade-offs can be exploited for biotechnological applications benefiting from the selective manipulation of the allocation of resources.