Evaluation of hydrogen metabolism by Escherichia coli strains possessing only a single hydrogenase in the genome

Shekhar, Chandra; Kai, Tomonori; García‐Contreras, Rodolfo; Sánchez-Torres, Viviana; Maeda, Takeyasu

doi:10.1016/j.ijhydene.2020.10.070

Cited by 8 publications

(11 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1A and 1B). Comparable lower viabilities of operon mutants than the single gene mutants pointed a more deleterious nature of operon deletion, as suggested by our previous studies on hydrogen metabolism (Shekhar et al 2021). Hyd-2 and Hyd-3 found a relatively signi cant in bacterial survival against the antibiotic.…”

Section: Discussionsupporting

confidence: 64%

“…However, no signi cant change was observed in the number of viable cells before antibiotic treatment from all the mutants, the cell viability was found comparatively more in the case of large subunit gene deletion mutants, indicating operon deletions are more deleterious than single-gene deletions, as shown by our previous study (Shekhar et al 2021). From both types of deletions, hyb and hyc were noted vital for bacterial survival since the viabilities were 20-and 18-fold increased respectively from the PS.…”

Section: Hydrogenase Operon Deletion Enhanced Cell Viabilitysupporting

confidence: 51%

“…Bacterial strains, media, and growth conditions E. coli K-12 BW25113 was used as the parent strain (abbreviated as PS) in the study. Each hydrogenase operon mutant investigated in this study was constructed in our previous study (Shekhar et al 2021) by the one-step inactivation method explained by Datsenko and Wanner (Datsenko et al 2000). All the strains including operon mutants employed in this study are listed in Table 1.…”

Section: Methodsmentioning

confidence: 99%

“…Hydrogenases are enzymes known for their roles in hydrogen metabolism by catalyzing the reversible reaction of hydrogen to protons and electrons (Maeda et al 2018, Shekhar et al 2021). The four hydrogenases of Escherichia coli (E. coli), abbreviated as, Hyd-1, Hyd-2, Hyd-3, and Hyd-4, are encoded by hyaABCDEF, hybOABCDEFG, hycABCDEFGHI, hyfABCDEFGHI operons respectively (Maeda et al 2018).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Evaluation of Escherichia coli hydrogenases in persistence

Shekhar

Kai

Wood

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Persistence enables a subpopulation of tolerant bacteria to survive in the presence of a bactericidal antibiotic. Reports indicate the non-inherited nature of persistence; however, it also seems to be a genetically influenced phenomenon that has evolved to allow the organisms to survive in sudden environmental insults. In contrary to some reports, lowered available pool of ATP, NAD, and ROS leads to increased survival via slowing down the metabolism and resulting in an increased persister fraction. In this study, the hydrogenases of Escherichia coli were analyzed for their role in persistence, where four hydrogenase operon deletion mutants were evaluated before and after antibiotic treatment. As result, the expressions of hydrogenases and cellular viability (specifically hyd-1, 2, 3) were found elevated in antibiotic-treated cells, indicating their influential roles in persistence. Further work elucidated the affected ATP, NAD, and metabolism in the antibiotic-treated mutant cells. The transcriptomic analysis further revealed a wide genomic connectivity of hydrogenases to influence persistence in E. coli. Hydrogenases were mainly reported for their essential roles in bacterial hydrogen metabolism, this study further demonstrates their probable role in bacterial survival against antibiotic stress.

show abstract

Section: Discussionsupporting

confidence: 64%

Section: Hydrogenase Operon Deletion Enhanced Cell Viabilitysupporting

confidence: 51%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evaluation of Escherichia coli hydrogenases in persistence

Shekhar

Kai

Wood

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The glycerol bioconversion pathways to H 2 are based on a simple redox reaction: 2H + + 2e − ↔H 2 [23]. This reaction is catalyzed by hydrogen-producing enzymes, namely [NiFe]-hydrogenases and [FeFe]-hydrogenases, which are mostly present in anaerobic bacteria [23][24][25][26][27]. This process takes place after glycerol enters the glycolysis pathways to produce pyruvate.…”

Section: Introductionmentioning

confidence: 99%

Improvement of Biohydrogen and Usable Chemical Products from Glycerol by Co-Culture of Enterobacter spH1 and Citrobacter freundii H3 Using Different Supports as Surface Immobilization

et al. 2021

View full text Add to dashboard Cite

Glycerol is a by-product of biodiesel production in a yield of about 10% (w/w). The present study aims to improve the dark fermentation of glycerol by surface immobilization of microorganisms on supports. Four different supports were used—maghemite (Fe2O3), activated carbon (AC), silica gel (SiO2), and alumina (γ-Al2O3)—on which a newly isolated co-culture of Enterobacter spH1 and Citrobacter freundii, H3, was immobilized. The effect of iron species on dark fermentation was also studied by impregnation on AC and SiO2. The fermentative metabolites were mainly ethanol, 1,3-propanediol, lactate, H2 and CO2. The production rate (Rmax,i) and product yield (Yi) were elucidated by modeling using the Gompertz equation for the batch dark fermentation kinetics (maximum product formation (Pmax,i): (i) For each of the supports, H2 production (mmol/L) and yield (mol H2/mol glycerol consumed) increased in the following order: FC < γ-Al2O3 < Fe2O3 < SiO2 < Fe/SiO2 < AC < Fe/AC. (ii) Ethanol production (mmol/L) increased in the following order: FC < Fe2O3 < γ-Al2O3 < SiO2 < Fe/SiO2 < Fe/AC < AC, and yield (mol EtOH/mol glycerol consumed) increased in the following order: FC < Fe2O3 < Fe/AC < Fe/SiO2 < SiO2 < AC < γ-Al2O3. (iii) 1,3-propanediol production (mmol/L) and yield (mol 1,3PDO/mol glycerol consumed) increased in the following order: γ-Al2O3 < SiO2 < Fe/SiO2 < AC < Fe2O3 < Fe/AC < FC. (iv) Lactate production(mmol/L) and yield (mol Lactate/mol glycerol consumed) increased in the following order: γ-Al2O3 < SiO2 < AC < Fe/SiO2 < Fe/AC < Fe2O3 < FC. The study shows that in all cases, glycerol conversion was higher when the support assisted culture was used. It is noted that glycerol conversion and H2 production were dependent on the specific surface area of the support. H2 production clearly increased with the Fe2O3, Al2O3, SiO2 and AC supports. H2 production on the iron-impregnated AC and SiO2 supports was higher than on the corresponding bare supports. These results indicate that the support enhances the productivity of H2, perhaps because of specific surface area attachment, biofilm formation of the microorganisms and activation of the hydrogenase enzyme by iron species.

show abstract

A simple approach for random genomic insertion–deletions using ambiguous sequences in Escherichia coli

Shekhar

Maeda

2022

J Basic Microbiol

Self Cite

View full text Add to dashboard Cite

Escherichia coli K-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt.Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletion mutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics. K E Y W O R D Sambiguous sequences, Escherichia coli, random genomic deletion, red recombination | INTRODUCTIONEscherichia coli, the most completely characterized single-cell life form, is a preferred model organism in bacterial genetic engineering research because of the available whole-genome sequence and described molecular genetics [1,2]. There are several methods available for genome-based engineering and to generate large mutant sets through both random and directed approaches [3][4][5]. Among all the reported approaches, homology-dependent, recombination-mediated, genetic engineering is considered as most efficient that allows engineering genes and segments of the bacterial chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides [6,7]. The E. coli KEIO mutant library is the best example of a directed

show abstract

Evaluation of hydrogen metabolism by Escherichia coli strains possessing only a single hydrogenase in the genome

Cited by 8 publications

References 46 publications

Evaluation of Escherichia coli hydrogenases in persistence

Evaluation of Escherichia coli hydrogenases in persistence

Improvement of Biohydrogen and Usable Chemical Products from Glycerol by Co-Culture of Enterobacter spH1 and Citrobacter freundii H3 Using Different Supports as Surface Immobilization

A simple approach for random genomic insertion–deletions using ambiguous sequences in Escherichia coli

Contact Info

Product

Resources

About