Journal of Industrial Microbiology & Biotechnology最新文献

Bacterial DNA methylation is involved in diverse cellular functions, including modulation of gene expression, DNA repair, and restriction-modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation. Methylome analysis allows identification of motifs within a bacterial chromosome that may be targeted by native restriction enzymes. Further expression of the corresponding methyltransferases in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism, thereby drastically enhancing transformation efficiency. Nanopore sequencing can detect methylated bases, but software is needed to transform modified base coordinates into methylated motifs. Here, we develop MIJAMP (MIJAMP Is Just A  MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT's Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating incorrect motifs. MIJAMP also reports methylation data on specific, user-defined motifs. Using MIJAMP, we determined the methylated motifs both in a control strain (wild-type E. coli) and in Synecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/. One Sentence Summary: Here we describe software written to discover DNA methylation motifs from nanopore sequencing data.

The variety of microorganisms represents the most prevalent sources utilized within diverse industries and research fields. Enzymes with microorganisms are applied in the use of industrial biotechnology. Since the dawn of civilization, there are techniques like extraction and fermentation that use plant or bacterial enzymes as well as other byproducts. Enzymes, the natural catalysts, are intricately involved in many aspects of life. Enzymes pose remarkable specificity for their substrate, which implies that these metabolic cycles in a living cell need to be executed by a team working in collaboration. The major sources of these enzymes are yeast, some fungi and bacteria. Just like all living forms, microbes interact with their environment in which they must live in order to survive. A large number of microorganisms that are capable of producing great varieties of enzymes are important in the production of bread, cheese, yogurt, beer, and many other foods. One of the most widely used lipolytic enzyme is lipase from various sources including food and dairy industry, leather, detergent, pulp and paper, bioenergy and even pharma. With the latest innovation in biotechnology, the need for organisms that produce different commercially important lipases which other strains of lipases do is increasing. Lipases produced from microbial cells have a major industrial significance because of their property of versatility and ease of mass production. This review seeks to clarify the sources of microorganisms, lipase production and purification processes, as well as the environmental and industrial uses of lipase enzymes.

One-sentence summary: This manuscript explores the diverse microbial sources of lipase, their production processes and the crucial applications in industries such as food, pharmaceuticals, and biofuels.

4-Hydroxy-2-pyridone alkaloids have attracted considerable attention because of their intriguing structures and diverse bioactivities. In our previous study, 4-hydroxy-2-pyridone alkaloids were shown to exhibit potent activity against neuron-associated targets. To discover this class of neuroactive compounds, an array of endolichenic fungal extracts was screened by analyzing liquid chromatography-ultraviolet-mass spectrometry (LC-UV-MS) profiles. The screening yielded strain Tolypocladium sp. (strain CNC14), which produced compounds with characteristic Ultraviolet patterns for 4-hydroxy-2-pyridone alkaloids using our in-house library. Based on these findings, we conducted a chemical investigation, which led to the isolation of four new (1-4) and ten known (5-14) compounds. Their structures were elucidated via spectroscopic methods such as nuclear magnetic resonance and mass spectrometry. The stereochemistry of the new compounds (1-4) was established using rotating frame overhauser effect spectroscopy (ROESY), and the electronic circular dichrosim (ECD) was compared with the calculated data. Interestingly, the side chains of 4-hydroxy-2-pyridone in 1 and 2 were cyclized in different directions to form benzopyrano[3,4-b]pyridinol from previously reported compounds, and all the new compounds were predicted to be biosynthesized from reduced tolypyridone C (7) via the hetero-Diels-Alder reaction. Among the isolated compounds, 4 significantly protected neuronal cells against treatment with 1-methyl-4-phenylpyridinium (MPP+), a Parkinsonian neurotoxin, in an in vitro Parkinson's disease model. One-Sentence Summary: Four new neuroprotective 4-hydroxy-2-pyridone alkaloids were discovered from an endolichenic fungus Tolypocladium sp.

This paper presents the Multi Clone Kinetic Model (MCKM), a novel generalized kinetic mechanistic model for fed-batch cultivations of diverse Chinese hamster ovary (CHO) cell lines, producing different recombinant monoclonal antibodies (mAbs). Unlike traditional kinetic models requiring multiple cultures for one parameter regression, MCKM derives a complete set of 13 kinetic parameters from a single fed-batch cell line culture of 49 data points. This enables per-cell-line metabolic characterization during cell line development, as well as direct comparisons of kinetics across clones, passages, and different recombinant mAbs. To enable MCKM to be broadly applicable across many cell lines and mAbs, and to address the high-dimensional challenge of estimating 13 kinetic parameters from a small number of datapoints, the model uniquely incorporates a mechanistic growth constraint, a glucose-dependent lactate switch, and automated parameter balancing. MCKM demonstrated successful regression of 656 fed-batch culture runs of 157 unique CHO cell lines across four passage generations, recombinant for three different mAbs, achieving high accuracy in biomass and mAb titre (average ${rm{bar{R}}}_{{{{rm{X}}}_{rm{v}}}}^2$ ≈ 0.96 ± 0.07 and ${rm{bar{R}}}_{rm{P}}^2$ ≈ 0.97 ± 0.05, respectively). MCKM could facilitate automated cell line selection, identification of critical process parameters and biomarkers, guide media and feeding strategies, predict metabolite profiles, and support scale-up and quality-by-design studies, delivering overall reduction of experimental workload. One-Sentence Summary: This paper presents a novel kinetic model that derives distinct parameter sets from a single fed-batch run, enabling characterization of individual CHO clones across different mAb targets.

Despite their prevalent use in drug discovery and protein biochemistry, non-canonical amino acids are still challenging to synthesize through purely chemical means. In recent years, biocatalysis has emerged as a transformative paradigm for small-molecule synthesis. One strategy to further empower biocatalysis is to use it in combination with modern chemical reactions and take advantage of the strengths of each method to enable access to challenging structural motifs that were previously unattainable using each method alone. In this Mini-Review, we highlight several recent case studies that feature the synergistic use of chemical and enzymatic transformations in one pot to synthesize novel non-canonical amino acids.

One-sentence summary: This Mini-Review highlights several recent case studies that feature the synergistic use of chemical and enzymatic transformations in one pot to synthesize novel non-canonical amino acids.