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Frontiers in Bioengineering and... 2021is an important industrial platform capable of producing a variety of biofuels and bulk chemicals. Biofilm of renders many production advantages and has been long and... (Review)
Review
is an important industrial platform capable of producing a variety of biofuels and bulk chemicals. Biofilm of renders many production advantages and has been long and extensively applied in fermentation. However, molecular and genetic mechanisms underlying the biofilm have been much less studied and remain largely unknown. Here, we review studies to date focusing on biofilms, especially on its physiological and molecular aspects, summarizing the production advantages, cell physiological changes, extracellular matrix components and regulatory genes of the biofilm. This represents the first review dedicated to the biofilm of . Hopefully, it will deepen our understanding toward biofilm and inspire more research to learn and develop more efficient biofilm processes in this industrially important bacterium.
PubMed: 34150727
DOI: 10.3389/fbioe.2021.658568 -
ACS Omega Sep 2023This paper considers the total synthesis of a cellular differentiation regulator of , clostrienose, which is a unique fatty-acid glycosyl ester consisting of...
This paper considers the total synthesis of a cellular differentiation regulator of , clostrienose, which is a unique fatty-acid glycosyl ester consisting of clostrienoic acid, (3,5,8,10)-3-hydroxy-tetradeca-5,8,10-trienoic acid and α-d-galactofuranosyl-(1 → 2)-α-l-rhamnose. The key features of our synthesis include stereoselective construction of a skipped-triene system in clostrienoic acid and its esterification with a disaccharide residue. The partially protected clostrienoic acid employed for the coupling also served for the preparation of l-rhamnosyl clostrienoate, thus leading to confirmation of the proposed structure unambiguously.
PubMed: 37779990
DOI: 10.1021/acsomega.3c05277 -
Journal of Microbiology and... Oct 2021Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase...
Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the host for ABE fermentation, , (PTB) at a 2.9 Å resolution. The overall structure of the PTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of PTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of PTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of PTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.
Topics: Acetone; Acyl Coenzyme A; Amino Acid Sequence; Bacterial Proteins; Butanols; Catalytic Domain; Clostridium acetobutylicum; Ethanol; Fermentation; Phosphate Acetyltransferase; Protein Structure, Quaternary
PubMed: 34584034
DOI: 10.4014/jmb.2109.09036 -
Microbiology and Molecular Biology... Mar 2015Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade... (Review)
Review
Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of a Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σ(F), σ(E), σ(G), and σ(K)) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σ(K), the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level.
Topics: Bacillus; Bacillus subtilis; Clostridium; Clostridium acetobutylicum; Clostridium botulinum; Clostridium perfringens; Gene Expression Regulation, Bacterial; Histidine Kinase; Phenotype; Protein Kinases; Sigma Factor; Spores, Bacterial; Transcription Factors
PubMed: 25631287
DOI: 10.1128/MMBR.00025-14 -
Applied Microbiology and Biotechnology Jun 2019Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide...
Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine. Analysis of the genome sequences revealed that three genes were missing from pantothenate and thiamine biosynthetic pathways, and five genes were absent from the pathway for biotin biosynthesis. Prototrophy in C. autoethanogenum and C. ljungdahlii for pantothenate was obtained by the introduction of plasmids carrying the heterologous gene clusters panBCD from Clostridium acetobutylicum, and for thiamine by the introduction of the thiC-purF operon from Clostridium ragsdalei. Integration of panBCD into the chromosome through allele-coupled exchange also conveyed prototrophy. C. autoethanogenum was converted to biotin prototrophy with gene sets bioBDF and bioHCA from Desulfotomaculum nigrificans strain CO-1-SRB, on plasmid and integrated in the chromosome. The genes could be used as auxotrophic selection markers in recombinant DNA technology. Additionally, transformation with a subset of the genes for pantothenate biosynthesis extended selection options with the pantothenate precursors pantolactone and/or beta-alanine. Similarly, growth was obtained with the biotin precursor pimelate combined with genes bioYDA from C. acetobutylicum. The work raises questions whether alternative steps exist in biotin and thiamine biosynthesis pathways in these acetogens.
Topics: Clostridium; Culture Media; Desulfotomaculum; Gene Expression; Genes, Bacterial; Metabolic Engineering; Metabolic Networks and Pathways; Recombinant Proteins; Vitamins
PubMed: 30972463
DOI: 10.1007/s00253-019-09763-6 -
Biotechnology For Biofuels 2018Biofilms are cell communities wherein cells are embedded in a self-produced extracellular polymeric substances (EPS). The biofilm of confers the cells superior...
BACKGROUND
Biofilms are cell communities wherein cells are embedded in a self-produced extracellular polymeric substances (EPS). The biofilm of confers the cells superior phenotypes and has been extensively exploited to produce a variety of liquid biofuels and bulk chemicals. However, little has been known about the physiology of in biofilm as well as the composition and biosynthesis of the EPS. Thus, this study is focused on revealing the cell physiology and EPS composition of biofilm.
RESULTS
Here, we revealed a novel lifestyle of in biofilm: elimination of sporulation and vegetative growth. Extracellular polymeric substances and wire-like structures were also observed in the biofilm. Furthermore, for the first time, the biofilm polysaccharides and proteins were isolated and characterized. The biofilm contained three heteropolysaccharides. The major fraction consisted of predominantly glucose, mannose and aminoglucose. Also, a great variety of proteins including many non-classically secreted proteins moonlighting as adhesins were found considerably present in the biofilm, with GroEL, a S-layer protein and rubrerythrin being the most abundant ones.
CONCLUSIONS
This study evidenced that vegetative cells rather than commonly assumed spore-forming cells were essentially the solvent-forming cells. The abundant non-classically secreted moonlighting proteins might be important for the biofilm formation. This study provides the first physiological and molecular insights into biofilm which should be valuable for understanding and development of the biofilm-based processes.
PubMed: 30479660
DOI: 10.1186/s13068-018-1316-4 -
Microbiology (Reading, England) Jun 2020The strictly anaerobic bacterium is well known for its ability to convert sugars into organic acids and solvents, most notably the potential biofuel butanol. However,...
The strictly anaerobic bacterium is well known for its ability to convert sugars into organic acids and solvents, most notably the potential biofuel butanol. However, the regulation of its fermentation metabolism, in particular the shift from acid to solvent production, remains poorly understood. The aim of this study was to investigate whether cell-cell communication plays a role in controlling the timing of this shift or the extent of solvent formation. Analysis of the available genome sequences revealed the presence of eight putative RRNPP-type quorum-sensing systems, here designated to , each consisting of an RRNPP-type regulator gene followed by a small open reading frame encoding a putative signalling peptide precursor. The identified regulator and signal peptide precursor genes were designated to and to , respectively. Triplicate regulator mutants were generated in strain ATCC 824 for each of the eight systems and screened for phenotypic changes. The mutants showed increased solvent formation during early solventogenesis and hence the QssB system was selected for further characterization. Overexpression of severely reduced solvent and endospore formation and this effect could be overcome by adding short synthetic peptides to the culture medium representing a specific region of the QspB signalling peptide precursor. In addition, overexpression of increased the production of acetone and butanol and the initial (48 h) titre of heat-resistant endospores. Together, these findings establish a role for QssB quorum sensing in the regulation of early solventogenesis and sporulation in .
Topics: Bacterial Proteins; Base Composition; Base Sequence; Clostridium acetobutylicum; Gene Expression Regulation, Bacterial; Multigene Family; Quorum Sensing; Sequence Analysis, DNA; Spores, Bacterial
PubMed: 32375981
DOI: 10.1099/mic.0.000916 -
MSystems Feb 2021and grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene...
and grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate persists in the coculture through proteome exchange during fusing events, which endow cells with expanded substrate utilization, and access to additional reducing equivalents from -evolved H and through acquisition of -native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community. Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic / culture is a novel observation that has not been explored The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.
PubMed: 33622858
DOI: 10.1128/mSystems.01325-20 -
Applied Microbiology and Biotechnology Mar 2017Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the... (Review)
Review
Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the production of industrial-relevant solvents, solventogensis. In recent decades, mathematical models have been employed to elucidate the complex interlinked regulation and conditions that determine these two distinct metabolic states and govern the transition between them. In this review, we discuss these models with a focus on the mechanisms controlling intra- and extracellular changes between acidogenesis and solventogenesis. In particular, we critically evaluate underlying model assumptions and predictions in the light of current experimental knowledge. Towards this end, we briefly introduce key ideas and assumptions applied in the discussed modelling approaches, but waive a comprehensive mathematical presentation. We distinguish between structural and dynamical models, which will be discussed in their chronological order to illustrate how new biological information facilitates the 'evolution' of mathematical models. Mathematical models and their analysis have significantly contributed to our knowledge of ABE fermentation and the underlying regulatory network which spans all levels of biological organization. However, the ties between the different levels of cellular regulation are not well understood. Furthermore, contradictory experimental and theoretical results challenge our current notion of ABE metabolic network structure. Thus, clostridial ABE fermentation still poses theoretical as well as experimental challenges which are best approached in close collaboration between modellers and experimentalists.
Topics: 1-Butanol; Acetic Acid; Acetone; Batch Cell Culture Techniques; Butyric Acid; Clostridium acetobutylicum; Computer Simulation; Ethanol; Fermentation; Hydrogen-Ion Concentration; Lactic Acid; Metabolic Networks and Pathways; Models, Theoretical; Solvents
PubMed: 28210797
DOI: 10.1007/s00253-017-8137-4 -
Frontiers in Microbiology 2021In selective RNA processing and stabilization (SRPS) operons, stem-loops (SLs) located at the 3'-UTR region of selected genes can control the stability of the...
In selective RNA processing and stabilization (SRPS) operons, stem-loops (SLs) located at the 3'-UTR region of selected genes can control the stability of the corresponding transcripts and determine the stoichiometry of the operon. Here, for such operons, we developed a computational approach named SLOFE (stem-loop free energy) that identifies the SRPS operons and predicts their transcript- and protein-level stoichiometry at the whole-genome scale using only the genome sequence the minimum free energy (Δ) of specific SLs in the intergenic regions within operons. As validated by the experimental approach of differential RNA-Seq, SLOFE identifies genome-wide SRPS operons in with 80% accuracy and reveals that the SRPS mechanism contributes to diverse cellular activities. Moreover, in the identified SRPS operons, SLOFE predicts the transcript- and protein-level stoichiometry, including those encoding cellulosome complexes, ATP synthases, ABC transporter family proteins, and ribosomal proteins. Its accuracy exceeds those of existing approaches in , , , and . The ability to identify genome-wide SRPS operons and predict their stoichiometry DNA sequence should facilitate studying the function and evolution of SRPS operons in bacteria.
PubMed: 34177856
DOI: 10.3389/fmicb.2021.673349