Complete genome sequences of strains isolated from Shirahama Hot Spring in Japan.

We isolated six strains from Shirahama Hot Spring in Japan. Complete genome sequences, determined by combining Oxford Nanopore long-read and Illumina short-read sequence data, revealed that they showed >99.9% average nucleotide identities with each other and approximately 97% to the genome of the type strain HB8.

Stability and release mechanism of double emulsification (W1/O/W2) for biodegradable pH-responsive polyhydroxybutyrate/cellulose acetate phthalate microbeads loaded with the water-soluble bioactive compound niacinamide.

Microbeads of biodegradable polyhydroxybutyrate (PHB) offer environmental benefits and economic competitiveness. The aim of this study was to encapsulate a water-soluble bioactive compound, niacinamide (NIA), in a pH-responsive natural matrix composed of PHB and cellulose acetate phthalate (CAP) by double emulsification (W1/O/W2) to improve the encapsulation efficiency (%EE) and loading capacity (%LC). PHB was produced in-house by Escherichia coli JM109 pUC19-23119phaCAB without the inducing agent isopropyl β-D-1-thiogalactopyranoside (IPTG).

Precise microbiome engineering using natural and synthetic bacteriophages targeting an artificial bacterial consortium.

In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising method to elucidate the functions of targeted bacteria in microbiomes. However, few methods to selectively kill target microorganisms in the microbiome without affecting the growth of nontarget microorganisms are available.

Subtractive modification of bacterial consortium using antisense peptide nucleic acids.

Microbiome engineering is an emerging research field that aims to design an artificial microbiome and modulate its function. In particular, subtractive modification of the microbiome allows us to create an artificial microbiome without the microorganism of interest and to evaluate its functions and interactions with other constituent bacteria. However, few techniques that can specifically remove only a single species from a large number of microorganisms and can be applied universally to a variety of microorganisms have been developed.

Effects of small heat shock proteins from thermotolerant bacteria on the stress resistance of Escherichia coli to temperature, pH, and hyperosmolarity.

Small heat shock proteins (HSPs), such as HSP20, represent cellular thermal resistance mechanisms, to avoid protein aggregation at elevated temperatures. Recombinantly expressed HSP20s serve as a molecular tool for improving the tolerance of living cells to various physical and chemical stressors. Here, we aimed to heterologously express 18 HSP20s from 12 thermotolerant bacteria in Escherichia coli and evaluate their effects on various physical and chemical cellular stresses.

Valorization of agro-industrial waste from the cassava industry as esterified cellulose butyrate for polyhydroxybutyrate-based biocomposites.

The aim of this study was to utilize cassava pulp to prepare biocomposites comprising microcrystalline cellulose from cassava pulp (CP-MCC) as a filler and polyhydroxybutyrate (PHB) synthesized in-house by Cupriavidus necator strain A-04. The CP-MCC was extracted from fresh cassava pulp. Next, the CP-MCC surface was modified with butyryl chloride (esterified to CP-MCC butyrate) to improve dissolution and compatibility with the PHB.

Bio-coatings in permeated cultivation systems: Unprecedented impacts on microalgal monoculture growth and organic matter yield.

Bio-coating, a recent and promising approach in attached microalgal cultivation systems, has garnered attention due to its efficiency in enhancing immobilized algal growth, particularly in submerged cultivation systems. However, when the cells are cultured on thin solid microporous substrates that physically separate them from the nutrient medium, it remains unclear whether the applied bio-coatings still have a significant impact on algal growth or the subsequent rates of algal organic matter (AOM) release. Therefore, this current work investigated the role of bio-coatings on the microalgal monoculture growth of one freshwater species, Chlorella vulgaris ESP 31, and one marine species, Cylindrotheca fusiformis on a hydrophilic substrate, polyvinylidene fluoride membrane in a permeated cultivation system.

Enhancing organic matter productivity in microalgal-bacterial biofilm using novel bio-coating.

Research on renewable energy from microalgae has led to a growing interest in porous substrate photobioreactors, but their widespread adoption is currently limited to pure microalgal biofilm cultures. The behavior of microalgal-bacterial biofilms immobilized on microporous substrates remains as a research challenge, particularly in uncovering their mutualistic interactions in environment enriched with dissolved organic matter. Therefore, this study established a novel culture platform by introducing microalgal-derived bio-coating that preconditioned hydrophilic polyvinylidene fluoride membranes for the microalgal-bacterial biofilm growth of freshwater microalgae, Chlorella vulgaris ESP 31 and marine microalgae, Cylindrotheca fusiformis with bacteria, Escherichia coli.

Current advances in alteration of fatty acid profile in Rhodotorula toruloides: a mini-review.

Microbial lipids are considered promising and environmentally friendly substitutes for fossil fuels and plant-derived oils. They alleviate the depletion of limited petroleum storage and the decrement of arable lands resulting from the greenhouse effect. Microbial lipids derived from oleaginous yeasts provide fatty acid profiles similar to plant-derived oils, which are considered as sustainable and alternative feedstocks for use in the biofuel, cosmetics, and food industries.

Cell-Free Production and Regeneration of Cofactors.

Cofactors, such as adenosine triphosphate, nicotinamide adenine dinucleotide, and coenzyme A, are involved in nearly 50% of enzymatic reactions and widely used in biocatalytic production of useful chemicals. Although commercial production of cofactors has been mostly dependent on extraction from microbial cells, this approach has a theoretical limitation to achieve a high-titer, high-yield production of cofactors owing to the tight regulation of cofactor biosynthesis in living cells. Besides the cofactor production, their regeneration is also a key challenge to enable continuous use of costly cofactors and improve the feasibility of enzymatic chemical manufacturing.

Chitin- and Streptavidin-Mediated Affinity Purification Systems: A Screening Platform for Enzyme Discovery.

Affinity purification of recombinant proteins is an essential technique in biotechnology. However, current affinity purification methods are very cost-intensive, and this imposes limits on versatile use of affinity purification for obtaining purified proteins for a variety of applications. To overcome this problem, we developed a new affinity purification system which we call CSAP (chitin- and streptavidin-mediated affinity purification) for low-cost purification of Strep-tag II fusion proteins.

A review on microalgal-bacterial co-culture: The multifaceted role of beneficial bacteria towards enhancement of microalgal metabolite production.

Mass microalgal-bacterial co-cultures have come to the fore of applied physiological research, in particularly for the optimization of high-value metabolite from microalgae. These co-cultures rely on the existence of a phycosphere which harbors unique cross-kingdom associations that are a prerequisite for the cooperative interactions. However, detailed mechanisms underpinning the beneficial bacterial effects onto microalgal growth and metabolic production are rather limited at the moment.

Green composites made of polyhydroxybutyrate and long-chain fatty acid esterified microcrystalline cellulose from pineapple leaf.

Pineapple leaf fibres are an abundant agricultural waste product that contains 26.9% cellulose. The objective of this study was to prepare fully degradable green biocomposites made of polyhydroxybutyrate (PHB) and microcrystalline cellulose from pineapple leaf fibres (PALF-MCC).

Characterization of thermostable serine hydroxymethyltransferase for β-hydroxy amino acids synthesis.

β-hydroxy amino acids, such as serine, threonine, and phenylserine, are important compounds for medical purposes. To date, there has been only limited exploration of thermostable serine hydroxylmethyltransferase (SHMT) for the synthesis of these amino acids, despite the great potential that thermostable enzymes may offer for commercial use due to their high stability and catalytic efficiencies. ITBSHMT_1 (ITB serine hydroxylmethyltransferase clone number 1) from thermophilic and methanol-tolerant bacteria Pseudoxanthomonas taiwanensis AL17 was successfully cloned.

One-Step Preparation of Cell-Free ATP Regeneration Module Based on Non-Oxidative Glycolysis Using Thermophilic Enzymes.

Adenosine triphosphate (ATP) is an essential cofactor for energy-dependent enzymatic reactions that occur during in vitro biochemical conversion. Recently, an enzyme cascade based on non-oxidative glycolysis, which uses starch and orthophosphate as energy and phosphate sources, respectively, for the regeneration of ATP from adenosine diphosphate, has been developed (Wei et al., ChemCatChem 2018, 10, 5597-5601).

l-Lactate oxidase-mediated removal of l-lactic acid derived from fermentation medium for the production of optically pure D-lactic acid.

Background: There has been an increasing demand for optically pure d-lactic and l-lactic acid for the production of stereocomplex-type polylactic acid. The d-lactic acid production from lignocellulosic biomass is important owing to its great abundance in nature. Corn steep liquor (CSL) is a cheap nitrogen source used for industrial fermentation, though it contains a significant amount of l-lactic acid, which decreases the optical purity of d-lactic acid produced.

Improvement of production yield of l-cysteine through in vitro metabolic pathway with thermophilic enzymes.

The demand for the amino acid l-cysteine is increasing in the food, cosmetic, and pharmaceutical industries. Conventionally, the commercial production of l-cysteine is achieved by its extraction from the acid hydrolysate of hair and feathers. However, this production method is associated with the release of environmentally hazardous wastewater.

Heterologous gene expression and characterization of two serine hydroxymethyltransferases from Thermoplasma acidophilum.

Serine hydroxymethyltransferase (SHMT) and threonine aldolase are classified as fold type I pyridoxal-5'-phosphate-dependent enzymes and engaged in glycine biosynthesis from serine and threonine, respectively. The acidothermophilic archaeon Thermoplasma acidophilum possesses two distinct SHMT genes, while there is no gene encoding threonine aldolase in its genome. In the present study, the two SHMT genes (Ta0811 and Ta1509) were heterologously expressed in Escherichia coli and Thermococcus kodakarensis, respectively, and biochemical properties of their products were investigated.

Strategies for Poly(3-hydroxybutyrate) Production Using a Cold-Shock Promoter in .

The present study attempted to increase poly(3-hydroxybutyrate) (PHB) production by improving expression of PHB biosynthesis operon derived from strain A-04 using various types of promoters. The intact PHB biosynthesis operon of A-04, an alkaline tolerant strain isolated in Thailand with a high degree of 16S rRNA sequence similarity with H16, was subcloned into pGEX-6P-1, pColdI, pColdTF, pBAD/Thio-TOPO, and pUC19 (native promoter) and transformed into JM109. While the gene was insoluble in most expression systems tested, it became soluble when it was expressed as a fusion protein with trigger factor (TF), a ribosome associated bacterial chaperone, under the control of a cold shock promoter.

Genome editing by miniature CRISPR/Cas12f1 enzyme in Escherichia coli.

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system is a valuable genome editing tool for microorganisms. However, the commonly used Cas9 nuclease derived from Streptococcus pyogenes (SpCas9) is not applicable to many industrially relevant bacteria, due to its cytotoxicity and large size (1368 amino acids [aa]). We developed an alternative genome editing system using a miniature Cas12f1 nuclease (529 aa) derived from an uncultured archaeon, Un1Cas12f1.

Polyhydroxybutyrate (PHB) Production Using an Arabinose-Inducible Expression System in Comparison With Cold Shock Inducible Expression System in .

strain A-04 has shown 16S rRNA gene identity to the well-known industrial strain H16. Nevertheless, the cell characteristics and polyhydroxyalkanoate (PHA) production ability of strain A-04 were different from those of H16. This study aimed to express PHA biosynthesis genes of strain A-04 in via an arabinose-inducible expression system.

Production of Coenzyme A Using Thermophilic Enzymes.

Coenzyme A (CoA) is an essential cofactor present in all domains of life and is involved in numerous metabolic pathways, including fatty acid metabolism, pyruvate oxidation through the tricarboxylic acid (TCA) cycle, and the production of secondary metabolites. This characteristic makes CoA a commercially valuable compound in the pharmaceutical, cosmetic, and clinical industries. However, CoA is difficult to accumulate in living cells at a high level, since it is consumed in multiple metabolic pathways, hampering its manufacturing by typical cell cultivation and extraction approaches.

Functional characterization and overexpression of Δ12-desaturase in the oleaginous yeast Rhodotorula toruloides for production of linoleic acid-rich lipids.

Linoleic acid (LA) has garnered much attention due to its potential applications in the oleochemical and nutraceutical industries. The oleaginous yeast Rhodotorula toruloides has outstanding lipogenecity, and is considered a potential alternative to the current plant-based platforms for LA production. Δ12-fatty acid desaturases (Δ12-Fads) are involved in LA synthesis in various fungi and yeasts, but their functions in R.

TEMPURA: Database of Growth TEMPeratures of Usual and RAre Prokaryotes.

Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.