Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07

Ji, Kaihua; Wang, Wei; Zeng, Bing; Si-bin, Chen; Zhao, Qianqian; Chen, Yueqing; Li, Guoqiang; Ma, Ting

doi:10.1038/srep21863

Cited by 39 publications

(28 citation statements)

References 62 publications

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“…Additional sequence database searches revealed that the non-core loci associated with operon clades B2 and B3 share functionally homologous loci to the cellulose accessory protein D (AxcesD), which has been characterized as increasing the efficiency of cellulose production in the Acetobacter xylinus cellulose synthase complex(34); GalU an uridine triphosphate (UTP)-glucose-1-phosphate uridylyltransferase involved in cellulose precursor biosynthesis; and an additional uncharacterized locus predicted to possess both PAS_9 and GGDEF signalling domains, indicating the potential adaptation in Proteus and Enterobacter spp. to produce varied forms of cellulose upon different environmental stimuli(35).…”

Section: Resultsmentioning

confidence: 99%

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

Bundalovic-Torma

Whitfield

Marmont

et al. 2019

Preprint

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19In bacterial functionally related genes comprising metabolic pathways and protein complexes are 20 frequently encoded in operons and are widely conserved across phylogenetically diverse species. The 21 evolution of these operon-encoded processes is affected by diverse mechanisms such gene duplication, 22 loss, rearrangement, and horizontal transfer. These mechanisms can result in functional diversification 23 of gene-families, increasing the potential evolution of novel biological pathways, and serves to adapt 24 evolutionary relationships of operon encoded genes and the evolution of operon organization as a 49 whole. To address this challenge, we present a novel method to study operon evolution by integrating 50 phylogenetic tree based clustering and genomic-context networks. We apply this approach to perform 51 the first systematic survey of all known synthase dependent bacterial biofilm machineries, 52 demonstrating the generalizability of our approach for operons of diverse size, protein family 53 composition, and species distribution. Our approach is able to identify distinct biofilm operon clades 54 across phylogenetically diverse bacteria, resulting from gene rearrangement, duplication, loss, fusion, 55 and horizontal gene transfer. We also elucidate different evolutionary trajectories of Gram-negative and 56Gram-positive biofilm production machineries, and in a companion paper (BIORXIV/2019/768473) 57 present the experimental validation of a novel mode of biofilm production in a subset of Gram-positive 58 bacteria. 59 60

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Section: Resultsmentioning

confidence: 99%

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

Bundalovic-Torma

Whitfield

Marmont

et al. 2019

Preprint

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“…1b), and sucrose [21,22]. The biosynthesis pathway of BC from glucose in FY-07 has been described in our previous study [21]; briefly, glucose is consecutively catalyzed by glucokinase (GK), phosphoglucomutase (PM), UDP-glucose pyrophosphorylase, and BC synthase complex, resulting in BC biosynthesis [21]. Inactivation of any enzyme involved in this pathway restricts the ability of FY-07 to produce BC.…”

Section: Determination Of Target Genes For Constructing Conditional Bmentioning

confidence: 98%

“…Enterobacter sp. FY-07 is a Gram-negative bacterium with a fast growth rate and high salt tolerance; it can produce BC at 24-39 °C under different oxygen conditions using economic sources of carbon such as molasses and crude glycerol [21][22][23]. Hence, FY-07 shows great potential for selective plugging and profile control in order to enhance oil recovery.…”

mentioning

confidence: 99%

Microbial enhanced oil recovery through deep profile control using a conditional bacterial cellulose-producing strain derived from Enterobacter sp. FY-07

Gao

Zhang

et al. 2020

Microb Cell Fact

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Background: Heterogeneity of oil-bearing formations is one of major contributors to low oil recovery efficiency globally. Long-term water flooding will aggravate this heterogeneity by resulting in many large channels during the exploitation process. Thus, injected water quickly flows through these large channels rather than oil-bearing areas, which ultimately leads to low oil recovery. This problem can be solved by profile control using polymer plugging. However, non-deep profile control caused by premature plugging is the main challenge. Here, a conditional bacterial cellulose-producing strain, namely Enterobacter sp. FY-0701, was constructed for deep profile control to solve the problem of premature plugging. Its deep profile control and oil displacement capabilities were subsequently identified and assessed. Results: The conditional bacterial cellulose-producing strain Enterobacter sp. FY-0701 was constructed by knocking out a copy of fructose-1, 6-bisphosphatase (FBP) encoding gene in Enterobacter sp. FY-07. Scanning electron microscope observation showed this strain produced bacterial cellulose using glucose rather than glycerol as the sole carbon source. Bacterial concentration and cellulose production at different locations in core experiments indicated that the plugging position of FY-0701 was deeper than that of FY-07. Moreover, enhanced oil recovery by FY-0701 was 12.09%, being 3.86% higher than that by FY-07 in the subsequent water flooding process. Conclusions: To our knowledge, this is the first report of conditional biopolymer-producing strains used in microbial enhance oil recovery (MEOR). Our results demonstrated that the conditional bacterial cellulose-producing strain can in situ produce biopolymer far from injection wells and plugs large channels, which increased the sweep volume of injection water and enhance oil recovery. The construction of this strain provides an alternative strategy for using biopolymers in MEOR.

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“…Additional sequence database searches revealed that the non-core loci associated with operon clades B2 and B3 share functionally homologous loci to the cellulose accessory protein D (AxcesD), which has been characterized as increasing the efficiency of cellulose production in the Acetobacter xylinus cellulose synthase complex [44]; GalU an uridine triphosphate (UTP)-glucose-1-phosphate uridylyltransferase involved in cellulose precursor biosynthesis; and an additional uncharacterized locus predicted to possess both PAS_9 and GGDEF signaling domains, indicating the potential adaptation in Proteus and Enterobacter spp. to produce varied forms of cellulose upon different environmental stimuli [45].…”

Section: Phylogenetic Clustering and Genomic Proximity Network Reveamentioning

confidence: 99%

“…The translocated cellulose polymer is indicated in green. BcsA domains identified using PFAM predictions for the R. sphaeroides reference sequence, BcsB domains were assigned according to [45]. Multiple sequence alignment was visualized generated using Geneious 10.2.2 (http:// www.geneious.com), protein structure was visualized using Chimera 1.11.2 [106].…”

Section: Construction Of Eps Operon Genomic-proximity Networkmentioning

confidence: 99%

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

et al. 2020

View full text Add to dashboard Cite

In bacteria functionally related genes comprising metabolic pathways and protein complexes are frequently encoded in operons and are widely conserved across phylogenetically diverse species. The evolution of these operon-encoded processes is affected by diverse mechanisms such as gene duplication, loss, rearrangement, and horizontal transfer. These mechanisms can result in functional diversification, increasing the potential evolution of novel biological pathways, and enabling pre-existing pathways to adapt to the requirements of particular environments. Despite the fundamental importance that these mechanisms play in bacterial environmental adaptation, a systematic approach for studying the evolution of operon organization is lacking. Herein, we present a novel method to study the evolution of operons based on phylogenetic clustering of operon-encoded protein families and genomic-proximity network visualizations of operon architectures. We applied this approach to study the evolution of the synthase dependent exopolysaccharide (EPS) biosynthetic systems: cellulose, acetylated cellulose, poly-β-1,6-N-acetyl-D-glucosamine (PNAG), Pel, and alginate. These polymers have important roles in biofilm formation, antibiotic tolerance, and as virulence factors in opportunistic pathogens. Our approach revealed the complex evolutionary landscape of EPS machineries, and enabled operons to be classified into evolutionarily distinct lineages. Cellulose operons show phyla-specific operon lineages resulting from gene loss, rearrangement, and the acquisition of accessory loci, and the occurrence of whole-operon duplications arising through horizonal gene transfer. Our evolution-based classification also distinguishes between PNAG production from Gram-negative and Grampositive bacteria on the basis of structural and functional evolution of the acetylation modification domains shared by PgaB and IcaB loci, respectively. We also predict several pel-like operon lineages in Gram-positive bacteria and demonstrate in our companion paper PLOS COMPUTATIONAL BIOLOGY PLOS Computational Biology | https://doi.A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PLoS Comput Biol 16(4): e1007721. https://doi.org/10.(Whitfield et al PLoS Pathogens, in press) that Bacillus cereus produces a Pel-dependent biofilm that is regulated by cyclic-3',5'-dimeric guanosine monophosphate (c-di-GMP). Author summaryIn bacterial genomes, biological processes are frequently encoded by neighbouring cotranscribed genes, termed operons. In addition, operon-associated genes often belong to distinct evolutionary families with diverse biological functions. Studying the evolution of bacterial operons provides valuable insight into understanding the biological significance of genes involved in environmental adaptation. To date, no systematic approach has been devised to examine both the complex evolutionary relationships of operon encoded genes and the evolution of operon organization as a whole. To address t...

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Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07

Cited by 39 publications

References 62 publications

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

Microbial enhanced oil recovery through deep profile control using a conditional bacterial cellulose-producing strain derived from Enterobacter sp. FY-07

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

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