Microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. Advances in protein engineering, metabolic engineering, ...and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. In this review, we describe the recent progress on engineering microbial factories for synthesis of valued-added products including alkaloids, terpenoids, flavonoids, polyketides, non-ribosomal peptides, biofuels, and chemicals. Related topics on lignocellulose degradation, sugar utilization, and microbial tolerance improvement will also be discussed.
Celotno besedilo
Dostopno za:
CEKLJ, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production ...titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
Here we report an efficient CRISPR-Cas9 knock-in strategy to activate silent biosynthetic gene clusters (BGCs) in streptomycetes. We applied this one-step strategy to activate multiple BGCs of ...different classes in five Streptomyces species and triggered the production of unique metabolites, including a novel pentangular type II polyketide in Streptomyces viridochromogenes. This potentially scalable strategy complements existing activation approaches and facilitates discovery efforts to uncover new compounds with interesting bioactivities.
DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen ...bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages,
phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.
In a continuous effort to emulate the efficiency of biosynthetic pathways, considerable progress has been made in developing one-pot chemoenzymatic processes that take full advantage of the chemo-, ...regio-, and stereoselectivity of biocatalysts and the productivity of chemical catalysts. Over the last 20 years, research in this area has provided us with proof of concept examples in which chemical and biological transformations occur in one vessel, sequentially or concurrently. These transformations typically access products with high enantiopurity and chemical diversity. In this perspective, we present some of the most successful reports in this field.
Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin ...dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
Saccharomyces cerevisiae has increasingly been engineered as a cell factory for efficient and economic production of fuels and chemicals from renewable resources. Notably, a wide variety of ...industrially important products are derived from the same precursor metabolite, acetyl-CoA. However, the limited supply of acetyl-CoA in the cytosol, where biosynthesis generally happens, often leads to low titer and yield of the desired products in yeast. In the present work, combined strategies of disrupting competing pathways and introducing heterologous biosynthetic pathways were carried out to increase acetyl-CoA levels by using the CoA-dependent n-butanol production as a reporter. By inactivating ADH1 and ADH4 for ethanol formation and GPD1 and GPD2 for glycerol production, the glycolytic flux was redirected towards acetyl-CoA, resulting in 4-fold improvement in n-butanol production. Subsequent introduction of heterologous acetyl-CoA biosynthetic pathways, including pyruvate dehydrogenase (PDH), ATP-dependent citrate lyase (ACL), and PDH-bypass, further increased n-butanol production. Recombinant PDHs localized in the cytosol (cytoPDHs) were found to be the most efficient, which increased n-butanol production by additional 3 fold. In total, n-butanol titer and acetyl-CoA concentration were increased more than 12 fold and 3 fold, respectively. By combining the most effective and complementary acetyl-CoA pathways, more than 100mg/L n-butanol could be produced using high cell density fermentation, which represents the highest titer ever reported in yeast using the clostridial CoA-dependent pathway.
•Saccharomyces cerevisiae was engineered to increase the supply of acetyl-CoA.•Competing pathways were blocked to redirect the flux towards acetyl-CoA.•Various acetyl-CoA biosynthetic pathways were systematically evaluated.•PDH complexes were functionally reconstituted in the cytosol of yeast.•Acetyl-CoA level and n-butanol titer were increased more than 3- and 12-fold, respectively.
Hyperspectral imaging (HSI) classification has become a popular research topic in recent years, and effective feature extraction is an important step before the classification task. Traditionally, ...spectral feature extraction techniques are applied to the HSI data cube directly. This paper presents a novel algorithm for HSI feature extraction by exploiting the curvelet-transformed domain via a relatively new spectral feature processing technique-singular spectrum analysis (SSA). Although the wavelet transform has been widely applied for HSI data analysis, the curvelet transform is employed in this paper since it is able to separate image geometric details and background noise effectively. Using the support vector machine classifier, experimental results have shown that features extracted by SSA on curvelet coefficients have better performance in terms of classification accuracy over features extracted on wavelet coefficients. Since the proposed approach mainly relies on SSA for feature extraction on the spectral dimension, it actually belongs to the spectral feature extraction category. Therefore, the proposed method has also been compared with some state-of-the-art spectral feature extraction techniques to show its efficacy. In addition, it has been proven that the proposed method is able to remove the undesirable artifacts introduced during the data acquisition process. By adding an extra spatial postprocessing step to the classified map achieved using the proposed approach, we have shown that the classification performance is comparable with several recent spectral-spatial classification methods.
Graphitic carbon nitride (g-C3N4) is defined as an emerging semiconductor for applications in photocatalytic and photoelectrochemical analysis. In our previous report, it is found that 3D branched ...crystalline carbon nitride with 1D nanoneedles (3DBC-C3N4) has the features of large surface area, improved light-harvest properties, fast charge mobility, and effective charge separation. Therefore, it could be served as an ideal photoactive material. In this study, the novel photoelectrode (3DBC-C3N4/FTO) exhibits desirable photoelectrochemical behavior towards the reduction of Cu2+. The developed photoelectrochemical sensing platform for detecting trace Cu2+ in aqueous environment shows a linear response ranging from 1 to 100 nM (R2 = 0.9938), with the limit of detection of 0.38 nM (signal-to-noise ratio = 3). Additionally, with the help of density functional theory calculations, the mechanism of selective detection is also explored. This work suggests that such 3D branched structural carbon nitride holds great promises for applying in photoelectrochemical biosensing with high photo-electron conversion efficiency.
PDF
