Abstract：
BACKGROUND:The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. RESULTS:Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. CONCLUSIONS:iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.
journal_name
Microb Cell Factjournal_title
Microbial cell factoriesauthors
Nagarajan H,Sahin M,Nogales J,Latif H,Lovley DR,Ebrahim A,Zengler Kdoi
10.1186/1475-2859-12-118subject
Has Abstractpub_date
2013-11-25 00:00:00pages
118issn
1475-2859pii
1475-2859-12-118journal_volume
12pub_type
杂志文章abstract：:A growing number of insights on the biology of bacterial inclusion bodies (IBs) have revealed intriguing utilities of these protein particles. Since they combine mechanical stability and protein functionality, IBs have been already exploited in biocatalysis and explored for bottom-up topographical modification in tiss...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-76
更新日期：2012-06-11 00:00:00
abstract：BACKGROUND:In spite of the substantial metabolic engineering effort previously devoted to the development of Saccharomyces cerevisiae strains capable of fermenting both the hexose and pentose sugars present in lignocellulose hydrolysates, the productivity of reported strains for conversion of the naturally most abundan...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-9-16
更新日期：2010-03-10 00:00:00
abstract：BACKGROUND:Fatty aldehydes are industrially relevant compounds, which also represent a common metabolic intermediate in the microbial synthesis of various oleochemicals, including alkanes, fatty alcohols and wax esters. The key enzymes in biological fatty aldehyde production are the fatty acyl-CoA/ACP reductases (FARs)...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0869-z
更新日期：2018-02-08 00:00:00
abstract：BACKGROUND:The deep-sea environment harbors a vast pool of novel enzymes. Owing to the limitations of cultivation, cultivation-independent has become an effective method for mining novel enzymes from the environment. Based on a deep-sea sediment metagenomics library, lipolytic-positive clones were obtained by activity-...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0864-4
更新日期：2018-01-30 00:00:00
abstract：BACKGROUND:A cellular stress response is triggered upon induction of recombinant protein expression which feedback inhibits both growth as well as protein synthesis. In order to separate these two effects, it was decided to study "quiescent cultures" which continue to be metabolically active and express recombinant pro...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-017-0744-3
更新日期：2017-07-28 00:00:00
abstract：BACKGROUND:L-arabinose is an important intermediate for anti-virus drug synthesis and has also been used in food additives for diets-controlling in recent years. Commercial production of L-arabinose is a complex progress consisting of acid hydrolysis of gum arabic, followed by multiple procedures of purification, thus ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-43
更新日期：2011-06-07 00:00:00
abstract：BACKGROUND:Recent interest has been focused on the production of platform chemicals from renewable biomass due to increasing concerns on global warming and depletion of fossil fuel reserves. Microbial production of platform chemicals in biorefineries has been suggested to be a promising solution for these problems. Gam...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0977-9
更新日期：2018-08-21 00:00:00
abstract：BACKGROUND:The sesquiterpenoid abscisic acid (ABA) is mostly known for regulating developmental processes and abiotic stress responses in higher plants. Recent studies show that ABA also exhibits a variety of pharmacological activities. Affordable and sustainable production will be required to utilize the compound in a...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-019-1257-z
更新日期：2019-11-25 00:00:00
abstract：BACKGROUND:Lipases (EC 3.1.1.3) catalyze the hydrolysis of triacyl glycerol to glycerol and are involved in the synthesis of both short chain and long chain acylglycerols. They are widely used industrially in various applications, such as baking, laundry detergents and as biocatalysts in alternative energy strategies. ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-72
更新日期：2012-06-01 00:00:00
abstract：BACKGROUND:Plasmid expression is a popular method in studies of MVA pathway for isoprenoid production in Escherichia coli. However, heterologous gene expression with plasmid is often not stable and might burden growth of host cells, decreases cell mass and product yield. In this study, MVA pathway was divided into thre...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-016-0607-3
更新日期：2016-12-01 00:00:00
abstract：:Controlling harmful algae blooms (HABs) using microbial algicides is cheap, efficient and environmental-friendly. However, obtaining high yield of algicidal microbes to meet the need of field test is still a big challenge since qualitative and quantitative analysis of algicidal compounds is difficult. In this study, w...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-13-75
更新日期：2014-05-24 00:00:00
abstract：BACKGROUND:Under aerobic conditions, acetic acid is the major byproduct produced by E. coli during the fermentation. And acetic acid is detrimental to cell growth as it destroys transmembrane pH gradients. Hence, how to reduce the production of acetic acid and how to utilize it as a feedstock are of intriguing interest...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-016-0475-x
更新日期：2016-05-05 00:00:00
abstract：BACKGROUND:D-Lactate is a valued chemical which can be produced by some bacteria including Klebsiella pneumoniae. However, only a few studies have focused on K. pneumoniae for D-lactate production with a significant amount of by-products, which complicated the purification process and decreased the yield of D-lactate. ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-017-0822-6
更新日期：2017-11-21 00:00:00
abstract：BACKGROUND:Strains with increased alkali tolerance have a broad application in industrial, especially for bioremediation, biodegradation, biocontrol and production of bio-based chemicals. A novel synthetic chromosome recombination and modification by LoxP-mediated evolution (SCRaMbLE) system has been introduced in the ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-019-1102-4
更新日期：2019-03-11 00:00:00
abstract：:The biotechnology industry has become a key element in modern societies. Within this industry, the production of recombinant enzymes and biopharmaceutical proteins is of major importance. The global markets for such recombinant proteins are growing rapidly and, accordingly, there is a continuous need for new productio...
journal_title：Microbial cell factories
pub_type： 社论
doi：10.1186/1475-2859-12-3
更新日期：2013-01-14 00:00:00
abstract：BACKGROUND:The discovery of the autotransporter family has provided a mechanism for surface expression of proteins in laboratory strains of Escherichia coli. We have previously reported the use of the AIDA-I autotransport system to express the Salmonella enterica serovar Enteritidis proteins SefA and H:gm. The SefA pro...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-118
更新日期：2012-09-03 00:00:00
abstract：BACKGROUND:Variations in codon usage between species are one of the major causes affecting recombinant protein expression levels, with a significant impact on the economy of industrial enzyme production processes. The use of codon-optimized genes may overcome this problem. However, designing a gene for optimal expressi...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-15
更新日期：2011-03-03 00:00:00
abstract：BACKGROUND:Bacillus subtilis has been widely used as a host for heterologous protein expression in food industry. B. subtilis ATCC6051 is an alternative expression host for the production of industrial enzymes, and exhibits favorable growth properties compared to B. subtilis 168. Extracellular expression of pullulanase...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-1011-y
更新日期：2018-10-22 00:00:00
abstract：BACKGROUND:The production of high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences that has yet to be addressed in a truly rational manner. Typically eukaryotic protein production experiments have relied on varying expression construct cassettes such as promoters and tags, or cultur...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-8-10
更新日期：2009-01-29 00:00:00
abstract：BACKGROUND:Membrane proteins are important drug targets in many human diseases and gathering structural information regarding these proteins encourages the pharmaceutical industry to develop new molecules using structure-based drug design studies. Specifically, membrane-bound catechol-O-methyltransferase (MBCOMT) is an...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-015-0304-7
更新日期：2015-08-07 00:00:00
abstract：BACKGROUND:Colorectal cancer (CRC) is a major clinical challenge, and the gut microbiome plays important roles in the occurrence and metastasis of CRC. Lactobacillus and their metabolites are thought to be able to suppress the growth of CRC cells. However, the antimetastatic mechanism of Lactobacillus or their metaboli...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-020-01466-2
更新日期：2020-11-23 00:00:00
abstract：BACKGROUND:The unicellular cyanobacterium Synechocystis sp. PCC 6803 has been widely used as a photoautotrophic host for synthetic biology studies. However, as a green chassis to capture CO2 for biotechnological applications, the genetic toolbox for Synechocystis 6803 is still a limited factor. RESULTS:We systematical...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0897-8
更新日期：2018-03-26 00:00:00
abstract：BACKGROUND:Erythritol is a four-carbon sugar alcohol with sweetening properties that is used by the agro-food industry as a food additive. In the yeast Yarrowia lipolytica, the last step of erythritol synthesis involves the reduction of erythrose by specific erythrose reductase(s). In the earlier report, an erythrose r...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0982-z
更新日期：2018-08-29 00:00:00
abstract：BACKGROUND:Corynebacterium glutamicum is a well-known producer of various L-amino acids in industry. During the fermenting process, C. glutamicum unavoidably encounters oxidative stress due to a specific reactive oxygen species (ROS) produced by consistent adverse conditions. To combat the ROS, C. glutamicum has develo...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-1048-y
更新日期：2018-12-26 00:00:00
abstract：BACKGROUND:Most bacteria can use various compounds as carbon sources. These carbon sources can be either co-metabolized or sequentially metabolized, where the latter phenomenon typically occurs as catabolite repression. From the practical application point of view of utilizing lignocellulose for the production of biofu...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-67
更新日期：2011-08-11 00:00:00
abstract：BACKGROUND:Aspergillus terreus is a natural producer of itaconic acid and is currently used to produce itaconic acid on an industrial scale. The metabolic process for itaconic acid biosynthesis is very similar to the production of citric acid in Aspergillus niger. However, a key enzyme in A. niger, cis-aconitate decarb...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-13-11
更新日期：2014-01-17 00:00:00
abstract：BACKGROUND:High-throughput screening methods assume that the output measured is representative of changes in metabolic flux toward the desired product and is not affected by secondary phenotypes. However, metabolic engineering can result in unintended phenotypes that may go unnoticed in initial screening. The red pigme...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-015-0381-7
更新日期：2015-11-26 00:00:00
abstract：:Innovative new genome engineering technologies for manipulating chromosomes have appeared in the last decade. One of these technologies, recombination mediated genetic engineering (recombineering) allows for precision DNA engineering of chromosomes and plasmids in Escherichia coli. Single-stranded DNA recombineering (...
journal_title：Microbial cell factories
pub_type： 杂志文章,评审
doi：10.1186/1475-2859-13-S1-S10
更新日期：2014-08-29 00:00:00
abstract：BACKGROUND:Sabinene, one kind of monoterpene, accumulated limitedly in natural organisms, is being explored as a potential component for the next generation of aircraft fuels. And demand for advanced fuels impels us to develop biosynthetic routes for the production of sabinene from renewable sugar. RESULTS:In this stu...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-13-20
更新日期：2014-02-10 00:00:00
abstract：BACKGROUND:Fine-tuning the aeration for cultivations when oxygen-limited conditions are demanded (such as the production of vaccines, isobutanol, 2-3 butanediol, acetone, and bioethanol) is still a challenge in the area of bioreactor automation and advanced control. In this work, an innovative control strategy based on...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-019-1198-6
更新日期：2019-09-04 00:00:00
