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1.
Biotechnol Bioeng ; 114(1): 106-112, 2017 01.
Artículo en Inglés | MEDLINE | ID: mdl-27474812

RESUMEN

Spo0A is a master regulator that governs the metabolic shift of solventogenic Clostridium species such as Clostridium beijerinckii. Its disruption can thus potentially cause a significant alteration of cellular physiology as well as metabolic patterns. To investigate the specific effect of spo0A disruption in C. beijerinckii, a spo0A mutant of C. beijerinckii was characterized in this study. In a batch fermentation with pH control at 6.5, the spo0A mutant accumulated butyrate and butanol up to 8.96 g/L and 3.32 g/L, respectively from 60 g/L glucose. Noticing the unique phenotype of the spo0A mutant accumulating both butyrate and butanol at significant concentrations, we decided to use the spo0A mutant for the production of butyl butyrate that can be formed by the condensation of butyrate and butanol during the ABE fermentation in the presence of the enzyme lipase. Butyl butyrate is a value-added chemical that has numerous uses in the food and fragrance industry. Moreover, butyl butyrate as a biofuel is compatible with Jet A-1 aviation kerosene and used for biodiesel enrichment. In an initial trial of small-scale extractive batch fermentation using hexadecane as the extractant with supplementation of lipase CalB, the spo0A mutant was subjected to acid crash due to the butyrate accumulation, and thus produced only 98 mg/L butyl butyrate. To alleviate the butyrate toxicity, the biphasic medium was supplemented with 10 g/L CaCO3 and 5 g/L butanol. The butyl butyrate production was then increased up to 2.73 g/L in the hexadecane layer. When continuous agitation was performed to enhance the esterification and extraction of butyl butyrate, 3.32 g/L butyl butyrate was obtained in the hexadecane layer. In this study, we successfully demonstrated the use of the C. beijerinckii spo0A mutant for the butyl butyrate production through the simultaneous ABE fermentation, condensation, and extraction. Biotechnol. Bioeng. 2017;114: 106-112. © 2016 Wiley Periodicals, Inc.


Asunto(s)
Reactores Biológicos/microbiología , Butiratos/metabolismo , Clostridium beijerinckii/genética , Clostridium beijerinckii/metabolismo , Butanoles/metabolismo , Butiratos/análisis , Carbonato de Calcio , Fermentación , Glucosa/metabolismo , Concentración de Iones de Hidrógeno , Mutación/genética
2.
Biotechnol Bioeng ; 113(12): 2739-2743, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27240718

RESUMEN

CRISPR-Cas9 has been explored as a powerful tool for genome engineering for many organisms. Meanwhile, dCas9 which lacks endonuclease activity but can still bind to target loci has been engineered for efficient gene transcription repression. Clostridium beijerinckii, an industrially significant species capable of biosolvent production, is generally difficult to metabolically engineer. Recently, we reported our work in developing customized CRISPR-Cas9 system for genome engineering in C. beijerinckii. However, in many cases, gene expression repression (rather than actual DNA mutation) is more desirable for various biotechnological applications. Here, we further demonstrated gene transcription repression in C. beijerinckii using CRISPR-dCas9. A small RNA promoter was employed to drive the expression of the single chimeric guide RNA targeting on the promoter region of amylase gene, while a constitutive thiolase promoter was used to drive Streptococcus pyogenes dCas9 expression. The growth assay on starch agar plates showed qualitatively significant repression of amylase activity in C. beijerinckii transformant with CRISPR-dCas9 compared to the control strain. Further amylase activity quantification demonstrated consistent repression (65-97% through the fermentation process) on the activity in the transformant with CRISPR-dCas9 versus in the control. Our results provided essential references for engineering CRISPR-dCas9 as an effective tool for tunable gene transcription repression in diverse microorganisms. Biotechnol. Bioeng. 2016;113: 2739-2743. © 2016 Wiley Periodicals, Inc.


Asunto(s)
Amilasas/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Represión Epigenética/genética , Transcripción Genética/genética , Activación Transcripcional/genética , Amilasas/biosíntesis , Proteínas Asociadas a CRISPR/genética , Clostridium beijerinckii/genética , Regulación hacia Abajo/genética , Regulación Bacteriana de la Expresión Génica/genética
3.
Appl Environ Microbiol ; 79(19): 5853-63, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23872562

RESUMEN

Clostridium beijerinckii is a well-known solvent-producing microorganism with great potential for biofuel and biochemical production. To better understand and improve the biochemical pathway to solvents, the development of genetic tools for engineering C. beijerinckii is highly desired. Based on mobile group II intron technology, a targetron gene knockout system was developed for C. beijerinckii in this study. This system was successfully employed to disrupt acid production pathways in C. beijerinckii, leading to pta (encoding phosphotransacetylase)- and buk (encoding butyrate kinase)-negative mutants. In addition to experimental characterization, the mutant phenotypes were analyzed in the context of our C. beijerinckii genome-scale model. Compared to those of the parental strain (C. beijerinckii 8052), acetate production in the pta mutant was substantially reduced and butyrate production was remarkably increased, while solvent production was dependent on the growth medium. The pta mutant also produced much higher levels of lactate, suggesting that disrupting pta influenced the energy generation and electron flow pathways. In contrast, acetate and butyrate production in the buk mutant was generally similar to that of the wild type, but solvent production was consistently 20 to 30% higher and glucose consumption was more rapid and complete. Our results suggest that the acid and solvent production of C. beijerinckii can be effectively altered by disrupting the acid production pathways. As the gene disruption method developed in this study does not leave any antibiotic marker in a disrupted allele, multiple and high-throughput gene disruption is feasible for elucidating genotype and phenotype relationships in C. beijerinckii.


Asunto(s)
Ácidos Carboxílicos/metabolismo , Clostridium beijerinckii/genética , Clostridium beijerinckii/metabolismo , Técnicas de Inactivación de Genes/métodos , Intrones , Redes y Vías Metabólicas/genética , Medios de Cultivo/química , Ingeniería Metabólica/métodos , Solventes/metabolismo
4.
BMC Genomics ; 13: 102, 2012 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-22433311

RESUMEN

BACKGROUND: Clostridium beijerinckii is a prominent solvent-producing microbe that has great potential for biofuel and chemical industries. Although transcriptional analysis is essential to understand gene functions and regulation and thus elucidate proper strategies for further strain improvement, limited information is available on the genome-wide transcriptional analysis for C. beijerinckii. RESULTS: The genome-wide transcriptional dynamics of C. beijerinckii NCIMB 8052 over a batch fermentation process was investigated using high-throughput RNA-Seq technology. The gene expression profiles indicated that the glycolysis genes were highly expressed throughout the fermentation, with comparatively more active expression during acidogenesis phase. The expression of acid formation genes was down-regulated at the onset of solvent formation, in accordance with the metabolic pathway shift from acidogenesis to solventogenesis. The acetone formation gene (adc), as a part of the sol operon, exhibited highly-coordinated expression with the other sol genes. Out of the > 20 genes encoding alcohol dehydrogenase in C. beijerinckii, Cbei_1722 and Cbei_2181 were highly up-regulated at the onset of solventogenesis, corresponding to their key roles in primary alcohol production. Most sporulation genes in C. beijerinckii 8052 demonstrated similar temporal expression patterns to those observed in B. subtilis and C. acetobutylicum, while sporulation sigma factor genes sigE and sigG exhibited accelerated and stronger expression in C. beijerinckii 8052, which is consistent with the more rapid forespore and endspore development in this strain. Global expression patterns for specific gene functional classes were examined using self-organizing map analysis. The genes associated with specific functional classes demonstrated global expression profiles corresponding to the cell physiological variation and metabolic pathway switch. CONCLUSIONS: The results from this work provided insights for further C. beijerinckii strain improvement employing system biology-based strategies and metabolic engineering approaches.


Asunto(s)
Clostridium beijerinckii/genética , Perfilación de la Expresión Génica/métodos , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , ARN Bacteriano/genética , Análisis de Secuencia de ARN/métodos , Transcripción Genética/genética , Anaerobiosis/genética , Transporte Biológico/genética , Metabolismo de los Hidratos de Carbono/genética , Clostridium beijerinckii/citología , Clostridium beijerinckii/metabolismo , Clostridium beijerinckii/fisiología , Ácidos Grasos/metabolismo , Fermentación , Ingeniería Genética , Glucólisis/genética , Cinética , Percepción de Quorum/genética , Esporas Bacterianas/genética , Esporas Bacterianas/fisiología
5.
BMC Genomics ; 12: 479, 2011 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-21962126

RESUMEN

BACKGROUND: Clostridium beijerinckii is an important solvent producing microorganism. The genome of C. beijerinckii NCIMB 8052 has recently been sequenced. Although transcriptome structure is important in order to reveal the functional and regulatory architecture of the genome, the physical structure of transcriptome for this strain, such as the operon linkages and transcript boundaries are not well understood. RESULTS: In this study, we conducted a single-nucleotide resolution analysis of the C. beijerinckii NCIMB 8052 transcriptome using high-throughput RNA-Seq technology. We identified the transcription start sites and operon structure throughout the genome. We confirmed the structure of important gene operons involved in metabolic pathways for acid and solvent production in C. beijerinckii 8052, including pta-ack, ptb-buk, hbd-etfA-etfB-crt (bcs) and ald-ctfA-ctfB-adc (sol) operons; we also defined important operons related to chemotaxis/motility, transcriptional regulation, stress response and fatty acids biosynthesis along with others. We discovered 20 previously non-annotated regions with significant transcriptional activities and 15 genes whose translation start codons were likely mis-annotated. As a consequence, the accuracy of existing genome annotation was significantly enhanced. Furthermore, we identified 78 putative silent genes and 177 putative housekeeping genes based on normalized transcription measurement with the sequence data. We also observed that more than 30% of pseudogenes had significant transcriptional activities during the fermentation process. Strong correlations exist between the expression values derived from RNA-Seq analysis and microarray data or qRT-PCR results. CONCLUSIONS: Transcriptome structural profiling in this research provided important supplemental information on the accuracy of genome annotation, and revealed additional gene functions and regulation in C. beijerinckii.


Asunto(s)
Clostridium beijerinckii/genética , Análisis de Secuencia de ARN , Transcriptoma , Clostridium beijerinckii/crecimiento & desarrollo , Regulación Bacteriana de la Expresión Génica , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
6.
J Biotechnol ; 329: 49-55, 2021 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-33556425

RESUMEN

The acetone-butanol-ethanol (ABE) fermentation by solventogenic clostridia has a long history of industrial butanol production. The Clostridium beijerinckii mutant BA101 has been widely studied for ABE fermentation owing to its enhanced butanol production capacity. Here, we characterized the BA101 mutant under controlled environmental conditions in parallel with the parental strain C. beijerinckii NCIMB 8052. To investigate the correlation between phenotype and genotype, we carried out the genome sequencing of BA101. Through comparative genomic analysis, several mutations in the genes encoding transcriptional regulator, sensor kinase, and phosphatase were identified in the BA101 genome as well as other sibling mutants. Among them, the SNP in the Cbei_3078 gene encoding PAS/PAC sensor hybrid histidine kinase was unique to the BA101 strain. The identified mutations relevant to the observed physiological behaviors of BA101 could be potential genetic targets for rational engineering of solventogenic clostridia toward desired phenotypes.


Asunto(s)
Clostridium beijerinckii , Butanoles , Clostridium beijerinckii/genética , Fermentación , Genómica , Fenotipo , Solventes
7.
Appl Microbiol Biotechnol ; 85(6): 1697-712, 2010 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-20033401

RESUMEN

Anaerobic bacteria such as the solventogenic clostridia can ferment a wide range of carbon sources (e.g., glucose, galactose, cellobiose, mannose, xylose, and arabinose) to produce carboxylic acids (acetic and butyric) and solvents such as acetone, butanol, and ethanol (ABE). The fermentation process typically proceeds in two phases (acidogenic and solventogenic) in a batch mode. Poor solvent resistance by the solventogenic clostridia and other fermenting microorganisms is a major limiting factor in the profitability of ABE production by fermentation. The toxic effect of solvents, especially butanol, limits the concentration of these solvents in the fermentation broth, limiting solvent yields and adding to the cost of solvent recovery from dilute solutions. The accepted dogma is that toxicity in the ABE fermentation is due to chaotropic effects of butanol on the cell membranes of the fermenting microorganisms, which poses a challenge for the biotechnological whole-cell bio-production of butanol. This mini-review is focused on (1) the effects of solvents on inhibition of cell metabolism (nutrient transport, ion transport, and energy metabolism); (2) cell membrane fluidity, death, and solvent tolerance associated with the ability of cells to tolerate high concentrations of solvents without significant loss of cell function; and (3) strategies for overcoming poor solvent resistance in acetone and butanol-producing microorganisms.


Asunto(s)
Acetona/metabolismo , Biotecnología , Butanoles/metabolismo , Clostridium/metabolismo , Fermentación , Solventes/metabolismo , Membrana Celular/metabolismo , Clostridium/genética , Clostridium/crecimiento & desarrollo , Fluidez de la Membrana/genética
8.
Appl Environ Microbiol ; 74(24): 7709-14, 2008 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-18849451

RESUMEN

Clostridium beijerinckii is an anaerobic bacterium used for the fermentative production of acetone and butanol. The recent availability of genomic sequence information for C. beijerinckii NCIMB 8052 has allowed for an examination of gene expression during the shift from acidogenesis to solventogenesis over the time course of a batch fermentation using a ca. 500-gene set DNA microarray. The microarray was constructed using a collection of genes which are orthologs of members of gene families previously found to be important to the physiology of C. acetobutylicum ATCC 824. Similar to the onset of solventogenesis in C. acetobutylicum 824, the onset of solventogenesis in C. beijerinckii 8052 was concurrent with the initiation of sporulation. However, forespores and endospores developed more rapidly in C. beijerinckii 8052 than in C. acetobutylicum 824, consistent with the accelerated expression of the sigE- and sigG-regulated genes in C. beijerinckii 8052. The comparison of gene expression patterns and morphological changes in C. beijerinckii 8052 and the hyper-butanol-producing C. beijerinckii strain BA101 indicated that BA101 was less efficient in sporulation and phosphotransferase system-mediated sugar transport than 8052 but that it exhibited elevated expression of several primary metabolic genes and chemotaxis/motility genes.


Asunto(s)
Acetona/metabolismo , Butanoles/metabolismo , Clostridium beijerinckii/genética , Clostridium beijerinckii/metabolismo , Fermentación , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión Génica , Clostridium beijerinckii/citología , Análisis de Secuencia por Matrices de Oligonucleótidos , Esporas Bacterianas/crecimiento & desarrollo
9.
Bioresour Technol ; 99(12): 5232-42, 2008 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-17967532

RESUMEN

Pretreatment and hydrolysis of lignocellulosic biomass using either dilute acid, liquid hot water (LHW), or ammonium fiber expansion (AFEX) results in a complex mixture of sugars such as hexoses (glucose, galactose, mannose), and pentoses (xylose, arabinose). A detailed description of the utilization of representative mixed sugar streams (pentoses and hexoses) and their sugar preferences by the solventogenic clostridia (Clostridium beijerinckii BA101, C. acetobutylicum 260, C. acetobutylicum 824, Clostridium saccharobutylicum 262, and C. butylicum 592) is presented. In these experiments, all the sugars were utilized concurrently throughout the fermentation, although the rate of sugar utilization was sugar specific. For all clostridia tested, the rate of glucose utilization was higher than for the other sugars in the mixture. In addition, the availability of excess fermentable sugars in the bioreactor is necessary for both the onset and the maintenance of solvent production otherwise the fermentation will become acidogenic leading to premature termination of the fermentation process. During an investigation on the effect of some of the known lignocellulosic hydrolysate inhibitors on the growth and ABE production by clostridia, ferulic and p-coumaric acids were found to be potent inhibitors of growth and ABE production. Interestingly, furfural and HMF were not inhibitory to the solventogenic clostridia; rather they had a stimulatory effect on growth and ABE production at concentrations up to 2.0g/L.


Asunto(s)
Clostridium/metabolismo , Fermentación , Residuos Industriales , Solventes/metabolismo , Zea mays/metabolismo , 1-Butanol/síntesis química , Acetona/síntesis química , Clostridium/citología , Clostridium/crecimiento & desarrollo , Etanol/química , Etanol/metabolismo , Hidrólisis , Monosacáridos/metabolismo , Solubilidad
10.
Bioresour Technol ; 99(13): 5915-22, 2008 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18061440

RESUMEN

Fermentation of sulfuric acid treated corn fiber hydrolysate (SACFH) inhibited cell growth and butanol production (1.7+/-0.2g/L acetone butanol ethanol or ABE) by Clostridium beijerinckii BA101. Treatment of SACFH with XAD-4 resin removed some of the inhibitors resulting in the production of 9.3+/-0.5 g/L ABE and a yield of 0.39+/-0.015. Fermentation of enzyme treated corn fiber hydrolysate (ETCFH) did not reveal any cell inhibition and resulted in the production of 8.6+/-1.0 g/L ABE and used 24.6g/L total sugars. ABE production from fermentation of 25 g/L glucose and 25 g/L xylose was 9.9+/-0.4 and 9.6+/-0.4 g/L, respectively, suggesting that the culture was able to utilize xylose as efficiently as glucose. Production of only 9.3+/-0.5 g/L ABE (compared with 17.7 g/L ABE from fermentation of 55 g/L glucose-control) from the XAD-4 treated SACFH suggested that some fermentation inhibitors may still be present following treatment. It is suggested that inhibitory components be completely removed from the SACFH prior to fermentation with C. beijerinckii BA101. In our fermentations, an ABE yield ranging from 0.35 to 0.39 was obtained, which is higher than reported by the other investigators.


Asunto(s)
Butanoles/metabolismo , Clostridium beijerinckii/metabolismo , Hidrolasas/metabolismo , Zea mays/enzimología , Acetona/metabolismo , Etanol/metabolismo , Fermentación , Hidrólisis , Microbiología Industrial , Cinética , Estructuras de las Plantas/metabolismo
11.
J Biotechnol ; 265: 119-126, 2018 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-29158189

RESUMEN

Clostridium beijerinckii is a predominant solventogenic clostridia with great attraction for renewable liquid biofuel and biochemical production. Metabolic engineering and synthetic biology can be employed to engineer the strain toward desirable phenotypes. However, current limited information such as promoter strength and gene regulation may hinder the efficient engineering of the strain. To investigate genetic information and complex cellular bioprocesses of C. beijerinckii, an in vivo fluorescence reporter system can be employed. In general, green fluorescence protein (GFP) and relative analogs have been widely used as real-time reporters. However, GFP-family proteins require molecular oxygen for fluorescence maturation. Considering the strict anaerobic growth requirement of the clostridia, an oxygen-independent fluorescence reporter such as a flavin mononucleotide-based fluorescent protein (FbFP) can be used as an alternative fluorescence reporter. In this study, we synthesized and expressed the codon-optimized FbFP gene for C. beijerinckii (CbFbFP) based on the nucleotide sequence of Bacillus subtilis YtvA variant EcFbFP in C. beijerinckii NCIMB 8052 wild-type. Protein expression and in vivo fluorescence of CbFbFP in C. beijeirnckii were confirmed under anaerobic growth conditions. Through fluorescence-activated cell sorting (FACS), we isolated the bright cells from the heterogenous population of C. beijerinckii cells expressing CbFbFP. Several mutations were found in the isolated plasmid which may be responsible for the high-level expression of CbFbFP in C. beijerinckii. The mutant plasmid and CbFbFP reporter were further utilized for strain selection, real-time fluorescence measurement, population analysis, and metabolic engineering in this study.


Asunto(s)
Proteínas Bacterianas/genética , Clostridium beijerinckii/genética , Mononucleótido de Flavina/genética , Proteínas Bacterianas/metabolismo , Clostridium beijerinckii/metabolismo , Mononucleótido de Flavina/metabolismo , Genes Reporteros , Mutación , Plásmidos
12.
Methods Mol Biol ; 1772: 297-325, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29754236

RESUMEN

CRISPR-Cas9 has been explored as a transformative genome engineering tool for many eukaryotic organisms. However, its utilization in bacteria remains limited and ineffective. This chapter, taking Clostridium beijerinckii as an example, describes the use of Streptococcus pyogenes CRISPR-Cas9 system guided by the single chimeric guide RNA (gRNA) for diverse genome-editing purposes, including chromosomal gene deletion, integration, single nucleotide modification, as well as "clean" mutant selection. The general principle is to use CRISPR-Cas9 as an efficient selection tool for the edited mutant (whose CRISPR-Cas9 target site has been disrupted through a homologous recombination event and thus can survive selection) against? the wild type background cells. This protocol is broadly applicable to other microorganisms for genome-editing purposes.


Asunto(s)
Sistemas CRISPR-Cas/genética , Clostridium beijerinckii/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Genoma Bacteriano/genética , Deleción Cromosómica , Recombinación Homóloga/genética , ARN Guía de Kinetoplastida/genética , Streptococcus pyogenes/genética
13.
Biotechnol J ; 12(11)2017 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-28762642

RESUMEN

Clostridium beijerinckii is a predominant solventogenic bacterium that is used for the ABE fermentation. Various C. beijerinckii mutants are constructed for desirable phenotypes. The C. beijerinckii mutant BA105 harboring a glucose derepression phenotype was previously isolated and demonstrated the enhanced amylolytic activity in the presence of glucose. Despite its potential use, BA105 is not further characterized and utilized. Therefore, the authors investigate fermentation phenotypes of BA105 in this study. Under the typical batch fermentation conditions, BA105 consistently exhibits acid crash phenotype resulting in limited glucose uptake and cell growth. However, when the culture pH is maintained above 5.5, BA105 exhibits the increased glucose uptake and butanol production than did the wild-type. To further analyze BA105, the authors perform genome sequencing and RNA sequencing. Genome analysis identifies two SNPs unique to BA105, in the upstream region of AbrB regulator (Cbei_4885) and the ROK family glucokinase (Cbei_4895) which are involved in catabolite repression and regulation of sugar metabolism. Transcriptional analysis of BA105 reveals significant differential expression of the genes associated with the PTS sugar transport system and acid production. This study improves understanding of the acid crash phenomenon and provides the genetic basis underlying the catabolite derepression phenotype of C. beijericnkii.


Asunto(s)
Clostridium beijerinckii/genética , Clostridium beijerinckii/metabolismo , Glucosa/metabolismo , Mutación/genética , Acetona/metabolismo , Alcoholes/metabolismo , Fermentación , Perfilación de la Expresión Génica , Genoma Bacteriano/genética , Genómica , Concentración de Iones de Hidrógeno , Mutación/fisiología , Fenotipo , Polimorfismo de Nucleótido Simple/genética
14.
ACS Synth Biol ; 5(7): 721-32, 2016 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-27115041

RESUMEN

CRISPR-Cas9 has been demonstrated as a transformative genome engineering tool for many eukaryotic organisms; however, its utilization in bacteria remains limited and ineffective. Here we explored Streptococcus pyogenes CRISPR-Cas9 for genome editing in Clostridium beijerinckii (industrially significant but notorious for being difficult to metabolically engineer) as a representative attempt to explore CRISPR-Cas9 for genome editing in microorganisms that previously lacked sufficient genetic tools. By combining inducible expression of Cas9 and plasmid-borne editing templates, we successfully achieved gene deletion and integration with high efficiency in single steps. We further achieved single nucleotide modification by applying innovative two-step approaches, which do not rely on availability of Protospacer Adjacent Motif sequences. Severe vector integration events were observed during the genome engineering process, which is likely difficult to avoid but has never been reported by other researchers for the bacterial genome engineering based on homologous recombination with plasmid-borne editing templates. We then further successfully employed CRISPR-Cas9 as an efficient tool for selecting desirable "clean" mutants in this study. The approaches we developed are broadly applicable and will open the way for precise genome editing in diverse microorganisms.


Asunto(s)
Sistemas CRISPR-Cas , Clostridium beijerinckii/genética , Ingeniería Genética/métodos , Roturas del ADN de Doble Cadena , Eliminación de Gen , Edición Génica , Vectores Genéticos , Genoma Bacteriano , Recombinación Homóloga , Nucleótidos/genética , Plásmidos , Regiones Promotoras Genéticas , ARN Guía de Kinetoplastida
15.
J Food Prot ; 68(3): 521-7, 2005 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-15771176

RESUMEN

Shigella boydii CDPH (Chicago Department of Public Health) serotype 18 was implicated in an outbreak of foodborne illness in 1998. The suspected food vehicles were parsley and cilantro imported from Mexico used to prepare bean salad. Previous studies revealed that S. boydii CDPH serotype 18 can survive in bean salad, which contains organic acids and whose pH decreases over time. Acid challenge assays in acidified tryptic soy broth at pH 4.5, acidified Luria-Bertani broth at pH 4.5, and acidified M9 minimal salts medium at pH 2.5 containing amino acids, arginine, or glutamic acid were performed using S. boydii CDPH, S. boydii ATCC 35966, S. flexneri 3136, Escherichia coli O157:H7 dd8872, and E. coli O157:H7 dd642 to compare differences in acid tolerance. Differences in survival of exponential-phase cells were detected in acidified tryptic soy broth and Luria-Bertani broth at pH 4.5. In acidified minimal medium containing arginine, S. boydii strains were able to survive at pH 2.5. The arginine decarboxylase gene (adiA) present in S. boydii is involved in survival at extremely low pH. The discovery of adiA expression in S. boydii serotype 18 by use of an acidified minimal medium challenge and arginine decarboxylase biochemical assay is significant because arginine decarboxylase activity was thought to be unique to E. coli. Sequencing of the rpoS gene from the S. boydii outbreak strain indicates that it is 99% conserved compared with the E. coli K-12 rpoS gene and plays a vital role in survival under acidic conditions.


Asunto(s)
Ácidos/farmacología , Disentería Bacilar/epidemiología , Regulación Bacteriana de la Expresión Génica , Shigella boydii/aislamiento & purificación , Secuencia de Aminoácidos , Arginina/metabolismo , Chicago/epidemiología , Medios de Cultivo , Brotes de Enfermedades , Genes Bacterianos , Humanos , Concentración de Iones de Hidrógeno , Datos de Secuencia Molecular , Alineación de Secuencia , Shigella boydii/clasificación , Shigella boydii/genética
16.
J Food Prot ; 68(4): 838-40, 2005 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-15830680

RESUMEN

A strain of Shigella boydii 18 involved in a bean salad outbreak and S. boydii 18 ATCC 35966 were used to inoculate bean salad. Bean salad samples were stored at 4 or 23 degrees C. At 4 degrees C, the S. boydii survived for the duration of the shelf life of the salad but did not grow. At 23 degrees C, both strains increased by two orders of magnitude by day 2 and decreased rapidly thereafter. This demonstrates the importance of proper storage in preventing the outgrowth of foodborne pathogens.


Asunto(s)
Fabaceae/microbiología , Microbiología de Alimentos , Shigella boydii/crecimiento & desarrollo , Recuento de Colonia Microbiana , Brotes de Enfermedades , Conservación de Alimentos/métodos , Cinética , Shigella boydii/aislamiento & purificación , Temperatura , Factores de Tiempo
17.
J Biotechnol ; 200: 1-5, 2015 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-25680931

RESUMEN

The anaerobic spore-forming, gram-positive, solventogenic clostridia are notorious for being difficult to genetically engineer. Based on CRISPR/Cas9 assisted homologous recombination, we demonstrated that clean markerless gene deletion from the chromosome can be easily achieved with a high efficiency through a single-step transformation in Clostridium beijerinckii NCIMB 8052, one of the most prominent strains for acetone, butanol and ethanol (ABE) production. This highly efficient genome engineering system can be further explored for multiplex genome engineering purposes. The protocols and principles developed in this study provided valuable references for genome engineering in other microorganisms lacking developed genetic engineering tools.


Asunto(s)
Clostridium beijerinckii/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Eliminación de Gen , Cromosomas Bacterianos , Genes Bacterianos , Ingeniería Genética , Genoma Bacteriano
18.
J Agric Food Chem ; 50(20): 5676-82, 2002 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-12236697

RESUMEN

Food ingredients containing alpha-1,6-galactoside bonds elicit gastrointestinal disturbances in monogastric animals, including humans. Pretreatment of such ingredients with alpha-galactosidase (EC 3.2.1.22) has the potential to alleviate this condition. For this purpose, a thermostable alpha-galactosidase from Thermoanaerobacterium polysaccharolyticum was purified by a combination of anion exchange and size exclusion chromatographies. The enzyme has a monomeric molecular weight of approximately 80 kDa; however, it is active as a dimer. The optimum temperature for enzyme activity is 77.5 degrees C. Approximately 84 and 88% of enzyme activity remained after 36.5 h of incubation at 70 and 65 degrees C, respectively. Optimum activity was observed at pH 8.0, with a broad range of activity from pH 5.0 to 9.0. Different transition metals had weak to strong inhibitory effects on enzyme activity. The K(m) and V(max) of the enzyme are 0.29-0.345 mM and 200-232 micromol/min/mg of protein, respectively. Importantly, enzyme activity was only slightly inhibited by 75-100 mM galactose, an end product of hydrolysis. Enzyme activity was specific for the alpha-1,6-galactosyl bond, and activity was demonstrated on melibiose and soy molasses.


Asunto(s)
Clostridium/enzimología , alfa-Galactosidasa/aislamiento & purificación , alfa-Galactosidasa/metabolismo , Secuencia de Aminoácidos , Dimerización , Estabilidad de Enzimas , Concentración de Iones de Hidrógeno , Datos de Secuencia Molecular , Peso Molecular , alfa-Galactosidasa/química
19.
Appl Biochem Biotechnol ; 98-100: 553-61, 2002.
Artículo en Inglés | MEDLINE | ID: mdl-12018281

RESUMEN

In this article we report on acetone butanol ethanol (ABE) fermentation characteristics of degermed corn when using Clostridium beijerinckii BA101. Recent economic studies suggested that recovery of germ from corn and hence corn oil would help to make the ABE fermentation process more economical. C. beijerinckii BA101 ferments corn mash efficiently to produce ABE under appropriate nutritional and environmental conditions. Corn mash contains germ/corn oil that is, possibly, ancillary to the production of butanol during the ABE fermentation process. Since the presence of corn oil is not a critical factor in solvent fermentation, it can be removed and this will allow for byproduct credit. Batch fermentation of degermed corn resulted in 8.93 g/L of total ABE production as compared with 24.80 g/L of total ABE when supplemented with P2 medium nutrients. During the course of the germ separation process, corn steeping is required prior to grinding and removing the germ. It is likely that some nutrients from the corn are leached out during the steeping process. This may reduce the rate of fermentation and impact the final concentration of butanol/ABE that can be achieved. Fermentation of degermed corn with corn steep liquor resulted in the production of 19.28 g/L of ABE.


Asunto(s)
Acetona/metabolismo , Butanoles/metabolismo , Clostridium/metabolismo , Etanol/metabolismo , Semillas/química , Zea mays/química , Fermentación , Cinética
20.
Appl Biochem Biotechnol ; 98-100: 591-8, 2002.
Artículo en Inglés | MEDLINE | ID: mdl-12018285

RESUMEN

Acetone butanol ethanol was produced in a continuous immobilized cell (biofilm) plug-flow reactor inoculated with Clostridium beijerinckii BA101. To achieve high reactor productivity, C. beijerinckii BA101 cells were immobilized by adsorption onto clay brick. The continuous plug-flow reactor offers high productivities owing to reduced butanol inhibition and increased cell concentration. Although high productivity was achieved, it was at the expense of low sugar utilization (30.3%). To increase sugar utilization, the reactor effluent was recycled. However, this approach is complicated by butanol toxicity. The effluent was recycled after removal of butanol by pervaporation to reduce butanol toxicity in the reactor. Recycling of butanol-free effluent resulted in a sugar utilization of 100.7% in addition to high productivity of 10.2 g/(L x h) at a dilution rate of 1.5 h(-1). A dilution rate of 2.0 h(-1) resulted in a reactor productivity of 16.2 g/(L x h) and sugar utilization of 101.4%. It is anticipated that this reactor-recovery system would be economical for butanol production when using C. beijerinckii BA101.


Asunto(s)
Alcoholes/metabolismo , Butanoles/metabolismo , Metabolismo de los Hidratos de Carbono , Células Inmovilizadas/metabolismo , Clostridium/metabolismo , Glucosa/metabolismo , Adsorción , Técnicas Bacteriológicas/métodos , Biopelículas , Reactores Biológicos , Glucólisis
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