Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments

Perrin, Elena; Ghini, Veronica; Giovannini, Michele; Patti, Francesca Di; Cardazzo, Barbara; Carraro, Lisa; Fagorzi, Camilla; Turano, Paola; Fani, Renato; Fondi, Marco

doi:10.1038/s41467-020-16872-8

Cited by 64 publications

(55 citation statements)

References 75 publications

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“…Many substrates belonging to the first cluster were depleted to their maximum potential before subsequent depletion of the second cluster began ( as a metabolic strategy is more common than previously thought when investigating the growth of heterotrophs in diverse, low concentration media (48,49). We observed that acetate, alanine, and glutamate likely provided the majority of carbon from SESOM for Paraburkholderia sp.…”

Section: Discussionmentioning

confidence: 65%

“…1N's biomass production in the first phase, lactate in the second, and reducing sugars coupled with valine in the final phase ( (10). Other observations of the co-existence of multiauxic and simultaneous substrate use tend to reinforce the idea that substrate selection is still based on affording the highest growth rate possible (31,49). Bacillus cereus is one other example of a fast-growing, r-selected organism that has been observed to selectively uptake substrates based on a mechanism outside of maximizing growth rate (31).…”

Section: Discussionmentioning

confidence: 94%

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Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency

Cyle

Klein

Aristilde

et al. 2020

Appl Environ Microbiol

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We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, Paraburkholderia sp. 1N. The growth of Paraburkholderia sp. 1N was monitored under aerobic conditions in a soil-extracted, solubilized organic matter media, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the media and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the media and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as Paraburkholderia sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of Paraburkholderia sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression. Importance Exometabolomic footprinting methods have the capability to provide time-resolved observations of the uptake and release of hundreds of compounds during microbial growth. Of particular interest is microbial phenotyping under environmentally relevant soil conditions, consisting of relatively low concentrations and modeling pulse input events. Here we show that growth of a bacterial soil isolate, Paraburkholderia sp. 1N, on a dilute soil extract resulted in a multiauxic metabolic response, characterized by discrete temporal clusters of substrate depletion and metabolite production. Our data did not support the hypothesis that compounds with lower energy content were used preferentially, as each cluster contained compounds with a range of nominal oxidation states of carbon. These new findings with Paraburkholderia sp. 1N, which belongs to a metabolically diverse genera, provide insights on ecological strategies employed by aerobic heterotrophs competing for low-molecular-weight substrates in soil solution.

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Section: Discussionmentioning

confidence: 65%

Section: Discussionmentioning

confidence: 94%

Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency

Cyle

Klein

Aristilde

et al. 2020

Appl Environ Microbiol

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“…We performed all our expression trials in GG, a defined medium whose only carbon sources are D-gluconate and L-glutamate [ 3 ]. The uptake of substrates is hierarchical in Ph TAC125 [ 7 , 28 ] and specific amino acid combinations had to be formulated in the past to guarantee the optimal induction of another psychrophilic expression plasmid in this bacterium [ 5 ]. To understand if this kind of interference could be experienced also using pP79, we measured the achievable levels of β-galactosidase production when KrPL pP79- lacZ was grown in TYP, a complex medium containing yeast extract and bacto-tryptone.…”

Section: Resultsmentioning

confidence: 99%

Improvement of Pseudoalteromonas haloplanktis TAC125 as a Cell Factory: IPTG-Inducible Plasmid Construction and Strain Engineering

et al. 2020

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Our group has used the marine bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) as a platform for the successful recombinant production of “difficult” proteins, including eukaryotic proteins, at low temperatures. However, there is still room for improvement both in the refinement of PhTAC125 expression plasmids and in the bacterium’s intrinsic ability to accumulate and handle heterologous products. Here, we present an integrated approach of plasmid design and strain engineering finalized to increment the recombinant expression and optimize the inducer uptake in PhTAC125. To this aim, we developed the IPTG-inducible plasmid pP79 and an engineered PhTAC125 strain called KrPL LacY+. This mutant was designed to express the E. coli lactose permease and to produce only a truncated version of the endogenous Lon protease through an integration-deletion strategy. In the wild-type strain, pP79 assured a significantly better production of two reporters in comparison to the most recent expression vector employed in PhTAC125. Nevertheless, the use of KrPL LacY+ was crucial to achieving satisfying production levels using reasonable IPTG concentrations, even at 0 °C. Both the wild-type and the mutant recombinant strains are characterized by an average graded response upon IPTG induction and they will find different future applications depending on the desired levels of expression.

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“…Research on the depletion of PRC1 proteins EED or RING1B was followed by increased expression of differentiation markers in mouse ESCs [ 49 ]. Considering that ESCs have higher methylation rates than differentiated cells [ 50 ], such a global demethylation effect of CXCR4 inhibition would impose a critical defect on early embryonic development, including gastrulation, possibly contributing to prenatal death of CXCR4 knockout embryos. In addition, DNA methylation is a major spatiotemporal modulator of both pluripotency and differentiation during organogenesis [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

CXCR4 Regulates Temporal Differentiation via PRC1 Complex in Organogenesis of Epithelial Glands

Kim¹,

Lee²,

Park³

2021

IJMS

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CXC-chemokine receptor type 4 (CXCR4), a 7-transmembrane receptor family member, displays multifaceted roles, participating in immune cell migration, angiogenesis, and even adipocyte metabolism. However, the activity of such a ubiquitously expressed receptor in epithelial gland organogenesis has not yet been fully explored. To investigate the relationship between CXCL12/CXCR4 signaling and embryonic glandular organogenesis, we used an ex vivo culture system with live imaging and RNA sequencing to elucidate the transcriptome and protein-level signatures of AMD3100, a potent abrogating reagent of the CXCR4-CXCL12 axis, imprinted on the developing organs. Immunostaining results showed that CXCR4 was highly expressed in embryonic submandibular gland, lung, and pancreas, especially at the periphery of end buds containing numerous embryonic stem/progenitor cells. Despite no significant increase in apoptosis, AMD3100-treated epithelial organs showed a retarded growth with significantly slower branching and expansion. Further analyses with submandibular glands revealed that such responses resulted from the AMD3100-induced precocious differentiation of embryonic epithelial cells, losing mitotic activity. RNA sequencing analysis revealed that inhibition of CXCR4 significantly down-regulated polycomb repressive complex (PRC) components, known as regulators of DNA methylation. Treatment with PRC inhibitor recapitulated the AMD3100-induced precocious differentiation. Our results indicate that the epigenetic modulation by the PRC-CXCR12/CXCR4 signaling axis is crucial for the spatiotemporal regulation of proliferation and differentiation of embryonic epithelial cells during embryonic glandular organogenesis.

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Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments

Cited by 64 publications

References 75 publications

Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency

Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency

Improvement of Pseudoalteromonas haloplanktis TAC125 as a Cell Factory: IPTG-Inducible Plasmid Construction and Strain Engineering

CXCR4 Regulates Temporal Differentiation via PRC1 Complex in Organogenesis of Epithelial Glands

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