A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum

ABSTRACTEngineering industrial microorganisms for ambitious applications, for example, the production of second-generation biofuels such as butanol, is impeded by a lack of knowledge of primary metabolism and its regulation. A quantitative system-scale analysis was applied to the biofuel-producing bacteriumClostridium acetobutylicum, a microorganism used for the industrial production of solvent. An improved genome-scale model,iCac967, was first developed based on thorough biochemical characterizations of 15 key metabolic enzymes and on extensive literature analysis to acquire accurate fluxomic data. In parallel, quantitative transcriptomic and proteomic analyses were performed to assess the number of mRNA molecules per cell for all genes under acidogenic, solventogenic, and alcohologenic steady-state conditions as well as the number of cytosolic protein molecules per cell for approximately 700 genes under at least one of the three steady-state conditions. A complete fluxomic, transcriptomic, and proteomic analysis applied to different metabolic states allowed us to better understand the regulation of primary metabolism. Moreover, this analysis enabled the functional characterization of numerous enzymes involved in primary metabolism, including (i) the enzymes involved in the two different butanol pathways and their cofactor specificities, (ii) the primary hydrogenase and its redox partner, (iii) the major butyryl coenzyme A (butyryl-CoA) dehydrogenase, and (iv) the major glyceraldehyde-3-phosphate dehydrogenase. This study provides important information for further metabolic engineering ofC. acetobutylicumto develop a commercial process for the production ofn-butanol.IMPORTANCECurrently, there is a resurgence of interest inClostridium acetobutylicum, the biocatalyst of the historical Weizmann process, to producen-butanol for use both as a bulk chemical and as a renewable alternative transportation fuel. To develop a commercial process for the production ofn-butanol via a metabolic engineering approach, it is necessary to better characterize both the primary metabolism ofC. acetobutylicumand its regulation. Here, we apply a quantitative system-scale analysis to acidogenic, solventogenic, and alcohologenic steady-stateC. acetobutylicumcells and report for the first time quantitative transcriptomic, proteomic, and fluxomic data. This approach allows for a better understanding of the regulation of primary metabolism and for the functional characterization of numerous enzymes involved in primary metabolism.

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Functional Characterization of a 28-Kilobase Catabolic Island from Pseudomonas sp. Strain M1 Involved in Biotransformation of β-Myrcene and Related Plant-Derived Volatiles

Applied and Environmental Microbiology ◽

10.1128/aem.03112-16 ◽

2017 ◽

Vol 83 (9) ◽

Cited By ~ 3

Author(s):

Pedro Soares-Castro ◽

Pedro Montenegro-Silva ◽

Hermann J. Heipieper ◽

Pedro M. Santos

Keyword(s):

Metabolic Engineering ◽

Functional Characterization ◽

Regulatory Protein ◽

Model Organism ◽

Detailed Knowledge ◽

Initial Oxidation ◽

Content Type ◽

Cell Factories ◽

Analytical Approaches

ABSTRACT Pseudomonas sp. strain M1 is able to mineralize highly hydrophobic and recalcitrant compounds, such as benzene, phenol, and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such a spectrum of compounds as the sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of strain M1 regarding β-myrcene catabolism was elucidated in this work, with a focus on the biocatalytical potential of the β-myrcene-associated core code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units. Functional characterization of this locus with promoter probes and analytical approaches validated the genetic organization predicted in silico and associated the β-myrcene-induced promoter activity to the production of β-myrcene derivatives. Notably, by using a whole-genome mutagenesis strategy, different genotypes of the 28-kb GI were generated, resulting in the identification of a novel putative β-myrcene hydroxylase, responsible for the initial oxidation of β-myrcene into myrcen-8-ol, and a sensor-like regulatory protein, whose inactivation abolished the myr + trait of M1 cells. Moreover, it was demonstrated that the range of monoterpene substrates of the M1 enzymatic repertoire, besides β-myrcene, also includes other acyclic (e.g., β-linalool) and cyclic [e.g., R-(+)-limonene and (−)-β-pinene] molecules. Our findings are the cornerstone for following metabolic engineering approaches and hint at a major role of the 28-kb GI in the biotransformation of a broad monoterpene backbone spectrum for its future biotechnological applications. IMPORTANCE Information regarding microbial systems able to biotransform monoterpenes, especially β-myrcene, is limited and focused mainly on nonsystematic metabolite identification. Complete and detailed knowledge at the genetic, protein, metabolite, and regulatory levels is essential in order to set a model organism or a catabolic system as a biotechnology tool. Moreover, molecular characterization of reported systems is scarce, almost nonexistent, limiting advances in the development of optimized cell factories with strategies based on the new generation of metabolic engineering platforms. This study provides new insights into the intricate molecular functionalities associated with β-myrcene catabolism in Pseudomonas, envisaging the production of a molecular knowledge base about the underlying catalytic and regulatory mechanisms of plant-derived volatile catabolic pathways.

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N-Acetylglucosamine-1-Phosphate Transferase, WecA, as a Validated Drug Target in Mycobacterium tuberculosis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01310-17 ◽

2017 ◽

Vol 61 (11) ◽

Cited By ~ 6

Author(s):

Stanislav Huszár ◽

Vinayak Singh ◽

Alica Polčicová ◽

Peter Baráth ◽

María Belén Barrio ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Drug Target ◽

Functional Characterization ◽

Drug Candidate ◽

Content Type ◽

Chemical Libraries ◽

Whole Cells ◽

Encoding Gene

ABSTRACT The mycobacterial phosphoglycosyltransferase WecA, which initiates arabinogalactan biosynthesis in Mycobacterium tuberculosis, has been proposed as a target of the caprazamycin derivative CPZEN-45, a preclinical drug candidate for the treatment of tuberculosis. In this report, we describe the functional characterization of mycobacterial WecA and confirm the essentiality of its encoding gene in M. tuberculosis by demonstrating that the transcriptional silencing of wecA is bactericidal in vitro and in macrophages. Silencing wecA also conferred hypersensitivity of M. tuberculosis to the drug tunicamycin, confirming its target selectivity for WecA in whole cells. Simple radiometric assays performed with mycobacterial membranes and commercially available substrates allowed chemical validation of other putative WecA inhibitors and resolved their selectivity toward WecA versus another attractive cell wall target, translocase I, which catalyzes the first membrane step in the biosynthesis of peptidoglycan. These assays and the mutant strain described herein will be useful for identifying potential antitubercular leads by screening chemical libraries for novel WecA inhibitors.

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Biomechanical and hydrodynamic characterization of the hydrocephalic infant

Journal of Neurosurgery ◽

10.3171/jns.1985.63.1.0069 ◽

1985 ◽

Vol 63 (1) ◽

pp. 69-75 ◽

Cited By ~ 67

Author(s):

Kenneth Shapiro ◽

Arno Fried ◽

Anthony Marmarou

Keyword(s):

Steady State ◽

Ventricular Volume ◽

Volume Index ◽

Injection Technique ◽

Infantile Hydrocephalus ◽

Content Type ◽

Two Factors ◽

The Mean ◽

Fine Print

✓ The pressure-volume index (PVI) technique of bolus manipulation of cerebrospinal fluid (CSF) was used to measure neural axis volume-buffering capacity and resistance to the absorption of CSF in 16 hydrocephalic infants prior to shunting. The mean steady-state intracranial pressure (ICP) was 11.7 ± 5.7 mm Hg (± standard deviation (SD)), representing a modest elevation of ICP in infants. The mean measured PVI was 28.1 ± 1.5 ml (± standard error of the mean (SEM)) compared to the predicted normal level for these infants of 12.1 ± 2.7 ml (± SD) (p < 0.001). This resulted from an enhanced volume storage capacity in the hydrocephalic infants. The PVI was not related to ventricular size in these hydrocephalic infants. Although absorption of the additional bolus of fluid did not occur at steady-state ICP, it was readily absorbed once ICP was raised above a mean threshold pressure of 16.0 ± 5.0 mm Hg (± SD) in 13 of the 16 infants. Above this pressure, the mean CSF absorption resistance was 7.2 ± 1.3 mm Hg/ml/min (± SEM) which is twice the normal values as measured by the bolus injection technique. The biomechanical profile of infantile hydrocephalus described in this study indicates that two factors are required for progression of ventricular volume. While an absorptive defect may initiate the hydrocephalic process, progressive volume storage requires an alteration in the mechanical properties of the intracranial compartment.

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Functional Characterization of AbaQ, a Novel Efflux Pump Mediating Quinolone Resistance inAcinetobacter baumannii

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00906-18 ◽

2018 ◽

Vol 62 (9) ◽

Cited By ~ 8

Author(s):

María Pérez-Varela ◽

Jordi Corral ◽

Jesús Aranda ◽

Jordi Barbé

Keyword(s):

Acinetobacter Baumannii ◽

Antimicrobial Agents ◽

Efflux Pump ◽

Functional Characterization ◽

Multidrug Resistant ◽

Quinolone Resistance ◽

Nosocomial Pathogen ◽

Content Type ◽

Mfs Transporter

ABSTRACTAcinetobacter baumanniihas emerged as an important multidrug-resistant nosocomial pathogen. In previous work, we identified a putative MFS transporter, AU097_RS17040, involved in the pathogenicity ofA. baumannii(M. Pérez-Varela, J. Corral, J. A. Vallejo, S. Rumbo-Feal, G. Bou, J. Aranda, and J. Barbé, Infect Immun 85:e00327-17, 2017,https://doi.org/10.1128/IAI.00327-17). In this study, we analyzed the susceptibility to diverse antimicrobial agents ofA. baumanniicells defective in this transporter, referred to as AbaQ. Our results showed that AbaQ is mainly involved in the extrusion of quinolone-type drugs inA. baumannii.

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Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B

Nucleic Acids Research ◽

10.1093/nar/gkaa353 ◽

2020 ◽

Vol 48 (11) ◽

pp. 6157-6169 ◽

Cited By ~ 2

Author(s):

Elisa Vilardo ◽

Fabian Amman ◽

Ursula Toth ◽

Annika Kotter ◽

Mark Helm ◽

...

Keyword(s):

Protein Synthesis ◽

Steady State ◽

Human Genome ◽

Functional Significance ◽

Functional Characterization ◽

Trna Methyltransferase ◽

Steady State Levels

Abstract The TRM10 family of methyltransferases is responsible for the N1-methylation of purines at position 9 of tRNAs in Archaea and Eukarya. The human genome encodes three TRM10-type enzymes, of which only the mitochondrial TRMT10C was previously characterized in detail, whereas the functional significance of the two presumably nuclear enzymes TRMT10A and TRMT10B remained unexplained. Here we show that TRMT10A is m1G9-specific and methylates a subset of nuclear-encoded tRNAs, whilst TRMT10B is the first m1A9-specific tRNA methyltransferase found in eukaryotes and is responsible for the modification of a single nuclear-encoded tRNA. Furthermore, we show that the lack of G9 methylation causes a decrease in the steady-state levels of the initiator tRNAiMet-CAT and an alteration in its further post-transcriptional modification. Our work finally clarifies the function of TRMT10A and TRMT10B in vivo and provides evidence that the loss of TRMT10A affects the pool of cytosolic tRNAs required for protein synthesis.

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Metabolic Engineering of Clostridium acetobutylicum ATCC 824 for Isopropanol-Butanol-Ethanol Fermentation

Applied and Environmental Microbiology ◽

10.1128/aem.06382-11 ◽

2011 ◽

Vol 78 (5) ◽

pp. 1416-1423 ◽

Cited By ~ 162

Author(s):

Joungmin Lee ◽

Yu-Sin Jang ◽

Sung Jun Choi ◽

Jung Ae Im ◽

Hyohak Song ◽

...

Keyword(s):

Metabolic Engineering ◽

Clostridium Acetobutylicum ◽

Secondary Alcohol ◽

Clostridium Beijerinckii ◽

Fuel Additive ◽

Gas Stripping ◽

Alcohol Fermentation ◽

Content Type ◽

Formation Pathway ◽

Total Alcohol

ABSTRACTClostridium acetobutylicumnaturally produces acetone as well as butanol and ethanol. Since acetone cannot be used as a biofuel, its production needs to be minimized or suppressed by cell or bioreactor engineering. Thus, there have been attempts to disrupt or inactivate the acetone formation pathway. Here we present another approach, namely, converting acetone to isopropanol by metabolic engineering. Since isopropanol can be used as a fuel additive, the mixture of isopropanol, butanol, and ethanol (IBE) produced by engineeredC. acetobutylicumcan be directly used as a biofuel. IBE production is achieved by the expression of a primary/secondary alcohol dehydrogenase gene fromClostridium beijerinckiiNRRL B-593 (i.e.,adhB-593) inC. acetobutylicumATCC 824. To increase the total alcohol titer, a synthetic acetone operon (actoperon;adc-ctfA-ctfB) was constructed and expressed to increase the flux toward isopropanol formation. When this engineering strategy was applied to the PJC4BK strain lacking in thebukgene (encoding butyrate kinase), a significantly higher titer and yield of IBE could be achieved. The resulting PJC4BK(pIPA3-Cm2) strain produced 20.4 g/liter of total alcohol. Fermentation could be prolonged byin situremoval of solvents by gas stripping, and 35.6 g/liter of the IBE mixture could be produced in 45 h.

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Functional Characterization of Burkholderia pseudomallei Trimeric Autotransporters

Infection and Immunity ◽

10.1128/iai.00526-13 ◽

2013 ◽

Vol 81 (8) ◽

pp. 2788-2799 ◽

Cited By ~ 15

Author(s):

Cristine G. Campos ◽

Matthew S. Byrd ◽

Peggy A. Cotter

Keyword(s):

Burkholderia Pseudomallei ◽

Functional Characterization ◽

A549 Cells ◽

Content Type ◽

Tier 1 ◽

Type V ◽

Mouse Model Of Infection ◽

Encoding Genes

ABSTRACTBurkholderia pseudomalleiis a tier 1 select agent and the causative agent of melioidosis, a severe and often fatal disease with symptoms ranging from acute pneumonia and septic shock to a chronic infection characterized by abscess formation in the lungs, liver, and spleen. Autotransporters (ATs) are exoproteins belonging to the type V secretion system family, with many playing roles in pathogenesis. The genome ofB. pseudomalleistrain 1026b encodes nine putative trimeric AT proteins, of which only four have been described. Using a bioinformatic approach, we annotated putative domains within each trimeric AT protein, excluding the well-studied BimA protein, and found short repeated sequences unique toBurkholderiaspecies, as well as an unexpectedly large proportion of ATs with extended signal peptide regions (ESPRs). To characterize the role of trimeric ATs in pathogenesis, we constructed disruption or deletion mutations in each of eight AT-encoding genes and evaluated the resulting strains for adherence to, invasion of, and plaque formation in A549 cells. The majority of the ATs (and/or the proteins encoded downstream) contributed to adherence to and efficient invasion of A549 cells. Using a BALB/c mouse model of infection, we determined the contributions of each AT to bacterial burdens in the lungs, liver, and spleen. At 48 h postinoculation, only one strain, Bp340::pDbpaC, demonstrated a defect in dissemination and/or survival in the liver, indicating that BpaC is required for wild-type virulence in this model.

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Functional Characterization of EscK (Orf4), a Sorting Platform Component of the Enteropathogenic Escherichia coli Injectisome

Journal of Bacteriology ◽

10.1128/jb.00538-16 ◽

2016 ◽

Vol 199 (1) ◽

Cited By ~ 7

Author(s):

Eduardo Soto ◽

Norma Espinosa ◽

Miguel Díaz-Guerrero ◽

Meztlli O. Gaytán ◽

José L. Puente ◽

...

Keyword(s):

Escherichia Coli ◽

Type Iii Secretion ◽

Diarrheal Disease ◽

Functional Characterization ◽

Type Iii Secretion System ◽

Secretion System ◽

Effector Proteins ◽

Content Type ◽

Enterocyte Effacement

ABSTRACT The type III secretion system (T3SS) is a supramolecular machine used by many bacterial pathogens to translocate effector proteins directly into the eukaryotic host cell cytoplasm. Enteropathogenic Escherichia coli (EPEC) is an important cause of infantile diarrheal disease in underdeveloped countries. EPEC virulence relies on a T3SS encoded within a chromosomal pathogenicity island known as the locus of enterocyte effacement (LEE). In this work, we pursued the functional characterization of the LEE-encoded protein EscK (previously known as Orf4). We provide evidence indicating that EscK is crucial for efficient T3S and belongs to the SctK (OrgA/YscK/MxiK) protein family, whose members have been implicated in the formation of a sorting platform for secretion of T3S substrates. Bacterial fractionation studies showed that EscK localizes to the inner membrane independently of the presence of any other T3SS component. Combining yeast two-hybrid screening and pulldown assays, we identified an interaction between EscK and the C-ring/sorting platform component EscQ. Site-directed mutagenesis of conserved residues revealed amino acids that are critical for EscK function and for its interaction with EscQ. In addition, we found that T3S substrate overproduction is capable of compensating for the absence of EscK. Overall, our data suggest that EscK is a structural component of the EPEC T3SS sorting platform, playing a central role in the recruitment of T3S substrates for boosting the efficiency of the protein translocation process. IMPORTANCE The type III secretion system (T3SS) is an essential virulence determinant for enteropathogenic Escherichia coli (EPEC) colonization of intestinal epithelial cells. Multiple EPEC effector proteins are injected via the T3SS into enterocyte cells, leading to diarrheal disease. The T3SS is encoded within a genomic pathogenicity island termed the locus of enterocyte effacement (LEE). Here we unravel the function of EscK, a previously uncharacterized LEE-encoded protein. We show that EscK is central for T3SS biogenesis and function. EscK forms a protein complex with EscQ, the main component of the cytoplasmic sorting platform, serving as a docking site for T3S substrates. Our results provide a comprehensive functional analysis of an understudied component of T3SSs.

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A Mycobacterial Systems Resource for the Research Community

mBio ◽

10.1128/mbio.02401-20 ◽

2021 ◽

Vol 12 (2) ◽

Author(s):

J. A. Judd ◽

J. Canestrari ◽

R. Clark ◽

A. Joseph ◽

P. Lapierre ◽

...

Keyword(s):

Mycobacterium Smegmatis ◽

Protein Localization ◽

Functional Characterization ◽

Model Organism ◽

Research Community ◽

Mycobacterial Species ◽

Biological Resource ◽

Content Type ◽

Core Genes

ABSTRACT Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis. To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis. This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulcerans. IMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.

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Genome and Functional Characterization of Colonization Factor Antigen I- and CS6-Encoding Heat-Stable Enterotoxin-Only EnterotoxigenicEscherichia coliReveals Lineage and Geographic Variation

mSystems ◽

10.1128/msystems.00329-18 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 8

Author(s):

Tracy H. Hazen ◽

Sushma Nagaraj ◽

Sunil Sen ◽

Jasnehta Permala-Booth ◽

Felipe Del Canto ◽

...

Keyword(s):

Functional Characterization ◽

Geographic Location ◽

Childhood Diarrhea ◽

Content Type ◽

Colonization Factor ◽

Heat Stable ◽

Colonization Factor Antigen I ◽

Factor Antigen ◽

Current Report

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a significant cause of childhood diarrhea and is a leading cause of traveler’s diarrhea. ETEC strains encoding the heat-stable enterotoxin (ST) are more often associated with childhood diarrhea than ETEC strains that encode only the heat-labile enterotoxin (LT). Colonization factors (CFs) also have a demonstrated role in ETEC virulence, and two of the most prevalent CFs among ETEC that have caused diarrhea are colonization factor antigen I (CFA/I) and CS6. In the current report, we describe the genomes of 269 CS6- or CFA/I-encoding ST-only ETEC isolates that were associated with human diarrhea. While the CS6 and CFA/I ETEC were identified in at least 13 different ETEC genomic lineages, a majority (85%; 229/269) were identified in only six lineages. Complete genome sequencing of selected isolates demonstrated that a conserved plasmid contributed to the dissemination of CFA/I whereas at least five distinct plasmids were involved in the dissemination of ST and/or CS6. Additionally, there were differences in gene content between CFA/I and CS6 ETEC at the phylogroup and lineage levels and in association with their geographic location of isolation as well as lineage-related differences in ST production. Thus, we demonstrate that genomically diverseE. colistrains have acquired ST, as well as CFA/I or CS6, via one or more plasmids and that, in some cases, isolates of a particular lineage or geographic location have undergone additional modifications to their genome content. These findings will aid investigations of virulence and the development of improved diagnostics and vaccines against this important human diarrheal pathogen.IMPORTANCEComparative genomics and functional characterization were used to analyze a global collection of CFA/I and CS6 ST-only ETEC isolates associated with human diarrhea, demonstrating differences in the genomic content of CFA/I and CS6 isolates related to CF type, lineage, and geographic location of isolation and also lineage-related differences in ST production. Complete genome sequencing of selected CFA/I and CS6 isolates enabled descriptions of a highly conserved ST-positive (ST+) CFA/I plasmid and of at least five diverse ST and/or CS6 plasmids among the CS6 ETEC isolates. There is currently no approved vaccine for ST-only ETEC, or for any ETEC for that matter, and as such, the current report provides functional verification of ST and CF production and antimicrobial susceptibility testing and an in-depth genomic characterization of a collection of isolates that could serve as representatives of CFA/I- or CS6-encoding ST-only ETEC strains for future studies of ETEC pathogenesis, vaccine studies, and/or clinical trials.

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