scholarly journals Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Francisco Díaz-Pascual ◽  
Martin Lempp ◽  
Kazuki Nosho ◽  
Hannah Jeckel ◽  
Jeanyoung K Jo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Spatial Organization ◽  
Interaction Strength ◽  
Growth Dynamics ◽  
Nitrogen Sources ◽  
Spatial Arrangement ◽  
Model Systems ◽  
Biofilm Growth ◽  
Carbon And Nitrogen ◽  
And Function

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.

scholarly journals Alanine cross-feeding determines Escherichia coli colony growth dynamics

2021 ◽  
Author(s):  
Francisco Diaz-Pascual ◽  
Martin Lempp ◽  
Kazuki Nosho ◽  
Hannah Jeckel ◽  
Jeanyoung K. Jo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Interaction Strength ◽  
Growth Dynamics ◽  
Spatial Arrangement ◽  
Colony Growth ◽  
Model Systems ◽  
Biofilm Growth ◽  
E Coli ◽  
Carbon And Nitrogen ◽  
Metabolic Interactions

Bacteria commonly live in spatially structured assemblages encased by an extracellular matrix, termed biofilms. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of subpopulations with different metabolism. Basic information about the spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like biofilms of Escherichia coli grown as colonies on agar-solidified media. Here, we use an unbiased approach based on temporal and spatial transcriptome and metabolome data during E. coli colony biofilm growth to identify many potential cross-feeding interactions. The strongest signature for cross-feeding in these data was displayed by alanine metabolism, and we discovered that alanine is indeed a cross-fed metabolite between two spatially segregated subpopulations: Alanine is secreted primarily via the transporter AlaE by anaerobically growing cells that are saturated with carbon and nitrogen, whereas alanine is utilized as a carbon and nitrogen source via DadA and DadX in the aerobic nutrient-deprived region at mid-height of the colony. We demonstrate that alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our methodology enables an unbiased path to the identification and characterization of spatially organized metabolic interactions in microbial communities, which are essential for understanding community structure and stability.

scholarly journals Novel Partial Reductive Pathway for 4-Chloronitrobenzene and Nitrobenzene Degradation in Comamonas sp. Strain CNB-1

2006 ◽  
Vol 72 (3) ◽  
pp. 1759-1765 ◽  
Author(s):  
Jian-feng Wu ◽  
Cheng-ying Jiang ◽  
Bao-jun Wang ◽  
Ying-fei Ma ◽  
Zhi-pei Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Nitrogen Sources ◽  
Cloning And Expression ◽  
Nitroaromatic Compound ◽  
Carbon And Nitrogen Sources ◽  
Subunit A ◽  
Carbon And Nitrogen ◽  
Semialdehyde Dehydrogenase ◽  
Reductive Pathway ◽  
Sequence Identities

ABSTRACT Comamonas sp. strain CNB-1 grows on 4-chloronitrobenzene (4-CNB) and nitrobenzene as sole carbon and nitrogen sources. In this study, two genetic segments, cnbB-orf2-cnbA and cnbR-orf1-cnbCaCbDEFGHI, located on a newly isolated plasmid, pCNB1 (ca. 89 kb), and involved in 4-CNB/nitrobenzene degradation, were characterized. Seven genes (cnbA, cnbB, cnbCa, cnbCb, cnbD, cnbG, and cnbH) were cloned and functionally expressed in recombinant Escherichia coli, and they were identified as encoding 4-CNB nitroreductase (CnbA), 1-hydroxylaminobenzene mutase (CnbB), 2-aminophenol 1,6-dioxygenase (CnbCab), 2-amino-5-chloromuconic semialdehyde dehydrogenase (CnbD), 2-hydroxy-5-chloromuconic acid (2H5CM) tautomerase, and 2-amino-5-chloromuconic acid (2A5CM) deaminase (CnbH). In particular, the 2A5CM deaminase showed significant identities (31 to 38%) to subunit A of Asp-tRNAAsn/Glu-tRNAGln amidotransferase and not to the previously identified deaminases for nitroaromatic compound degradation. Genetic cloning and expression of cnbH in Escherichia coli revealed that CnbH catalyzed the conversion of 2A5CM into 2H5CM and ammonium. Four other genes (cnbR, cnbE, cnbF, and cnbI) were tentatively identified according to their high sequence identities to other functionally identified genes. It was proposed that CnbH might represent a novel type of deaminase and be involved in a novel partial reductive pathway for chloronitrobenzene or nitrobenzene degradation.

scholarly journals STORM imaging reveals the spatial arrangement of transition zone components and IFT particles at the ciliary base in Tetrahymena

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Khodor S. Hazime ◽  
Zhu Zhou ◽  
Ewa Joachimiak ◽  
Natalia A. Bulgakova ◽  
Dorota Wloga ◽  
...  
Keyword(s):  
Transition Zone ◽  
Spatial Organization ◽  
Intraflagellar Transport ◽  
Spatial Arrangement ◽  
Interaction Sites ◽  
Narrow Region ◽  
Cilia Formation ◽  
Axial Dimension ◽  
Optical Reconstruction ◽  
And Function

AbstractThe base of the cilium comprising the transition zone (TZ) and transition fibers (TF) acts as a selecting gate to regulate the intraflagellar transport (IFT)-dependent trafficking of proteins to and from cilia. Before entering the ciliary compartment, IFT complexes and transported cargoes accumulate at or near the base of the cilium. The spatial organization of IFT proteins at the cilia base is key for understanding cilia formation and function. Using stochastic optical reconstruction microscopy (STORM) and computational averaging, we show that seven TZ, nine IFT, three Bardet–Biedl syndrome (BBS), and one centrosomal protein, form 9-clustered rings at the cilium base of a ciliate Tetrahymena thermophila. In the axial dimension, analyzed TZ proteins localize to a narrow region of about 30 nm while IFT proteins dock approximately 80 nm proximal to TZ. Moreover, the IFT-A subcomplex is positioned peripheral to the IFT-B subcomplex and the investigated BBS proteins localize near the ciliary membrane. The positioning of the HA-tagged N- and C-termini of the selected proteins enabled the prediction of the spatial orientation of protein particles and likely cargo interaction sites. Based on the obtained data, we built a comprehensive 3D-model showing the arrangement of the investigated ciliary proteins.

scholarly journals Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli

2019 ◽  
Vol 116 (40) ◽  
pp. 20115-20123 ◽  
Author(s):  
Xiaoli Weng ◽  
Christopher H. Bohrer ◽  
Kelsey Bettridge ◽  
Arvin Cesar Lagda ◽  
Cedric Cagliero ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Growth Condition ◽  
Spatial Organization ◽  
Large Fraction ◽  
Spatial Arrangement ◽  
Rrna Synthesis ◽  
Rich Medium ◽  
Transcription Activity ◽  
Rrna Transcription

Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in E. coli cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ70 was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.

Study of acetate metabolism using different carbon and nitrogen sources in Escherichia coli

2018 ◽  
Vol 44 ◽  
pp. S87-S88
Author(s):  
G. Lozano Terol ◽  
J. Gallego Jara ◽  
A. Écija Conesa ◽  
T. De Diego Puente ◽  
M. Cánovas Díaz
Keyword(s):  
Escherichia Coli ◽  
Nitrogen Sources ◽  
Acetate Metabolism ◽  
Carbon And Nitrogen Sources ◽  
Carbon And Nitrogen

Improvement of cyclodextrin glycosyltransferase (CGTase) production by recombinant Escherichia coli pAD26 immobilized on the cotton

Biologia ◽  
2012 ◽  
Vol 67 (6) ◽  
Author(s):  
Mouna Kriaa ◽  
Dorra Zouari Ayadi ◽  
Sonia Jemli ◽  
Mouna Sahnoun ◽  
Samir Bejar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Initial Conditions ◽  
Nitrogen Sources ◽  
Wheat Starch ◽  
Casamino Acid ◽  
Cyclodextrin Glycosyltransferase ◽  
Carbon And Nitrogen ◽  
Burman Design ◽  
Optimized Conditions ◽  
Plackett Burman Design

AbstractThe cyclodextrin glycosyltransferase (CGTase) of the recombinants Escherichia coli pAD26 cells immobilized on cotton was optimally produced by statistical methodology. Primarily, carbon and nitrogen sources were selected by one-factor-at-a-time method. Wheat starch, Casamino acid, Edamin and Hy-soy were identified as the best nutrients. These sources were secondly confirmed by Plackett-Burman design (fifteen variables were studied with sixteen experiments), as the most significant components with respect to CGTase production. In the third step, concentration of most significant factors and their interaction were optimized with a Box-Behnken experimental design. Under the optimized conditions (agitation 200 rpm, yeast extract concentration 20 g/L, wheat starch concentration 10 g/L and Hy-soy concentration 2.5 g/L), CGTase yield 145.11 U/mL was 3.6 and 23 folds higher than those obtained by the use of the initial conditions (39.77 U/mL) and free cells (6.37 U/mL), respectively.

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