{"database":"Cell Collective","file_versions":[],"scores":{"citationCount":896,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Models"],"submitter":["Jana Musilov"],"version_name":["1.1"],"full_dataset_link":["https://cellcollective.org/#36604/signaling-pathway-for-butanol-production-in-clostridium-beijerinckii-nrrl-b598"],"model_score":["59.4487"],"default_version":["2"],"ModelFormat":["SBML"],"submitter_affiliation":[""],"submitter_email":[""],"version_id":["2"],"repository":["Cell Collective"],"version_url":["https://cellcollective.org/#36604:2/signaling-pathway-for-butanol-production-in-clostridium-beijerinckii-nrrl-b598"],"version_description":[""],"pubmed_abstract":["<h4>Background</h4>Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data.<h4>Results</h4>In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation.<h4>Conclusions</h4>We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.","Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium."],"pubmed_title":["Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level.","Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq."],"pubmed_authors":["Patakova Petra P, Branska Barbora B, Sedlar Karel K, Vasylkivska Maryna M, Jureckova Katerina K, Kolek Jan J, Koscova Pavlina P, Provaznik Ivo I","Sedlar Karel K, Koscova Pavlina P, Vasylkivska Maryna M, Branska Barbora B, Kolek Jan J, Kupkova Kristyna K, Patakova Petra P, Provaznik Ivo I"],"pubmed_title_synonyms":["Abiotic Stress Response, Metabolic Stress, lifespan, Biotic Stresses, Biological Stress, Physiological Stress Reactivity, solventogenesis, Physiological Stress Reaction, Stage, Life History, Metabolic Stresses, Physiological Stress Response, Physiological Stress, Abiotic Stress Reactions, Biological, Abiotic, Physiological Stress Responses, Cycle, Clostridium beijerinckii Donker 1926 (Approved Lists 1980)., Physiological Stress Reactions, Physiological Stresses, Biotic Stress, Abiotic Stress Responses, Metabolic Stress Responses, Life Cycle, Metabolic Stress Response, Biological Stresses, Life, Biotic, Cycles, Stress Response, History Stages, Reactions, Abiotic Stresses, Metabolic, entire lifespan, entire life cycle, Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001, life, Life Cycle Stage, History Stage, Clostridium rubrum, Abiotic Stress Reaction, Life History Stages, Abiotic Stress, acidogenesis, Life Cycles, Stages, Stress Reaction, Life History Stage, Reaction, Stress, Response, Physiological"],"name_synonyms":["signal transduction by protein phosphorylation, signal transduction by conformational transition, signal transduction by cis-phosphorylation, signaling cascade, signalling pathway, Clostridium rubrum, signalling cascade, signaling pathway, Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001, signal transduction by trans-phosphorylation, Clostridium beijerinckii Donker 1926 (Approved Lists 1980)."],"pubmed_abstract_synonyms":["biochemical pathways, Mental, Metabolic Process, Materials, Activity, determination, Effects, Land Supplies, Processes, dSmurf1, Metabolic Concepts, Gene, Selective, Metabolic Processes, regulation of gene product expression, Long Term, element, Processed, Fluorescence-Activated, DSmurf, Fluorescence-Activated Cell Sortings, Microfluorometry, Processed Genes, Metabolism, Engineerings., Land, Clostridium beijerinckii Donker 1926 (Approved Lists 1980), Concepts, Whole Transcriptome Shotgun Sequencing, Prophage, Flow Microfluorimetry, Metabolism Concept, Phenomenon, Sprains, Effect, Cell Sortings, Metabolism Phenomena, Resources, Cytofluorometry, Pseudogene, Supply, Genetic, Genomes, Fluorescence Activated Cell Sorting, Longterm, Flow Cytofluorometries, Natural, beta-Tubulin Pseudogene, catabolism, beta-Tubulin Pseudogenes, Microfluorometries, beta-Tubulin, Metabolic Concept, metabolic process resulting in cell growth, Long-Term, Supplies, ecotype, Genotypes, Social, d-smurf, Social Attention, Concentration, Smurf, Flow, Flow Microfluorometries, Cytometry, biotransformation, Pseudogenes, Long-Term Effect, Strains, elements, Behaviors, transcription from bacterial-type RNA polymerase promoter, Catabolism, Long-Term Effects, atom, Flow Cytofluorometry, CG4943, Cytometries, Sortings, single organism signaling, D-smurf, single-organism behavior, Cell Sorting, Fluorescence-Activated Cell Sorting, Papers, Data Set, degradation, Process, metabolism resulting in cell growth, Sprain, Liquid Chromatography, Longterm Effect, RNA-seq, Attention Focus, Flow Cytometries, Lack, Dsmurf, Fermentations, Cistrons, results, Acceptance Processes, strain, Concept, Metabolic Phenomena, Microfluorimetry, dSmurf, Metabolism Concepts, Acceptance Process, Experiment, Attention, Selective Attention, Resource, Genogroup, Natural Resource, Smurf ubiquitin ligase, Long Term Effects, chemical analysis, Strain, Phenomena, sequence, Genetic Materials, atomo, atomus, secretion, cultivar, gene regulation, background, Focus of Attention, Flow Microfluorometry, atome, Processed Gene, metabolism, Genetic Material, Metabolic Phenomenon, Acceptance, multicellular organism metabolic process, Cytofluorometries, Genes, Element, biodegradation, DmelCG4943, Metabolic, Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001, atoms, Mental Concentration, Clostridium rubrum, whole genome, Fluorescence-Activated Cell, primary structure of sequence macromolecule, introduction, regulation of protein expression, Longterm Effects, Land Supply, Phenotypes, Genogroups, signalling process, Material, bacterial transcription, Sorting, Cistron, assay, Strains and Sprains, General activity, beta Tubulin Pseudogene, Anabolism"],"citation_count":["896"],"additional_accession":[]},"is_claimable":false,"name":"Signaling Pathway for Butanol Production in Clostridium beijerinckii NRRL B-598","description":"","dates":{"created":"2019-03-21","publication":"","submission":"2019-04-03","last_modified":"2019-04-03"},"accession":"36604","cross_references":{"pubmed":["30718562","29843608"]}}