Expressing Vitreoscilla hemoglobin in statically cultured Acetobacter xylinum with reduced O(2) tension maximizes bacterial cellulose pellicle production

Toward biomanufacturing of next-generation bacterial nanocellulose (BNC)-based materials with tailored properties: A review on genetic engineering approaches

Bacterial nanocellulose (BNC) is a biopolymer that is drawing significant attention for a wide range of applications thanks to its unique structure and excellent properties, such as high purity, mechanical strength, high water holding capacity and biocompatibility. Nevertheless, the biomanufacturing of BNC is hindered due to its low yield, the instability of microbial strains and cost limitations that prevent it from being mass-produced on a large scale. Various approaches have been developed to address these problems by genetically modifying strains and to produce BNC-based biomaterials with added value. These works are summarized and discussed in the present article, which include the overexpression and knockout of genes related and not related with the nanocellulose biosynthetic operon, the application of synthetic biology approaches and CRISPR/Cas techniques to modulate BNC biosynthesis. Further discussion is provided on functionalized BNC-based biomaterials with tailored properties that are incorporated in-vivo during its biosynthesis using genetically modified strains either in single or co-culture systems (in-vivo manufacturing). This novel strategy holds potential to open the road toward cost-effective production processes and to find novel applications in a variety of technology and industrial fields.

Enhanced bacterial cellulose production in Komagataeibacter sucrofermentans: impact of different PQQ-dependent dehydrogenase knockouts and ethanol supplementation

BACKGROUND

Bacterial cellulose (BC) is a biocompatible material with unique mechanical properties, thus holding a significant industrial potential. Despite many acetic acid bacteria (AAB) being BC overproducers, cost-effective production remains a challenge. The role of pyrroloquinoline quinone (PQQ)-dependent membrane dehydrogenases (mDH) is crucial in the metabolism of AAB since it links substrate incomplete oxidation in the periplasm to energy generation. Specifically, glucose oxidation to gluconic acid substantially lowers environmental pH and hinders BC production. Conversely, ethanol supplementation is known to enhance BC yields in Komagataeibacter spp. by promoting efficient glucose utilization.

RESULTS

K. sucrofermentans ATCC 700178 was engineered, knocking out the four PQQ-mDHs, to assess their impact on BC production. The strain KS003, lacking PQQ-dependent glucose dehydrogenase (PQQ-GDH), did not produce gluconic acid and exhibited a 5.77-fold increase in BC production with glucose as the sole carbon source, and a 2.26-fold increase under optimal ethanol supplementation conditions. In contrast, the strain KS004, deficient in the PQQ-dependent alcohol dehydrogenase (PQQ-ADH), showed no significant change in BC yield in the single carbon source experiment but showed a restrained benefit from ethanol supplementation.

CONCLUSIONS

The results underscore the critical influence of PQQ-GDH and PQQ-ADH and clarify the effect of ethanol supplementation on BC production in K. sucrofermentans ATCC 700178. This study provides a foundation for further metabolic pathway optimization, emphasizing the importance of diauxic ethanol metabolism for high BC production.

Vitreoscilla Hemoglobin Improves Sophorolipid Production in Starmerella Bombicola O-13-1 Under Oxygen Limited Conditions

Sophorolipids (SLs) are homologous microbial secondary metabolites produced by Starmerella bombicola and have been widely applied in many industrial fields. The biosynthesis of SLs is a highly aerobic process and is often limited by low dissolved oxygen (DO) levels. In this study, the Vitreoscilla hemoglobin (VHb) gene was transformed into S. bombicola O-13-1 by homologous recombination to alleviate oxygen limitation. VHb expression improved the intracellular oxygen utilization efficiency under either oxygen-rich or oxygen-limited conditions. In shake flask culture, the production of SLs was higher in the recombinant (VHb⁺) strain than in the wild-type (VHb^-) strain, while the oxygen uptake rate of the recombinant (VHb⁺) strain was significantly lower than that of the wild-type (VHb^-) strain. In a 5 L bioreactor, the production of SLs did not increase significantly, but the DO level in the fermentation broth of the VHb⁺ strain was 21.8% higher than that of VHb^- strain under oxygen-rich conditions. Compared to wide-type strains (VHb^-), VHb expression enhanced SLs production by 25.1% in the recombinants (VHb⁺) under oxygen-limited conditions. In addition, VHb expression raised the transcription levels of key genes involved in the electron transfer chain (NDH, SDH, COX), TCA cycle (CS, ICD, KDG1) and SL synthesis (CYP52M1 and UGTA1) in the recombinant (VHb⁺) strains. VHb expression in S. bombicola could enhance SLs biosynthesis and intracellular oxygen utilization efficiency by increasing ATP production and cellular respiration. Our findings highlight the potential use of VHb to improve the oxygen utilization efficiency of S. bombicola in the industrial-scale production of SLs using industrial and agricultural by-products like molasses and waste oil as fermentation feedstock.

On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases

Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an L-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. KEY POINTS: • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.

Towards control of cellulose biosynthesis by Komagataeibacter using systems-level and strain engineering strategies: current progress and perspectives

The strains of the Komagataeibacter genus have been shown to be the most efficient bacterial nanocellulose producers. Although exploited for many decades, the studies of these species focused mainly on the optimisation of cellulose synthesis process through modification of culturing conditions in the industrially relevant settings. Molecular physiology of Komagataeibacter was poorly understood and only a few studies explored genetic engineering as a strategy for strain improvement. Only since recently the systemic information of the Komagataeibacter species has been accumulating in the form of omics datasets representing sequenced genomes, transcriptomes, proteomes and metabolomes. Genetic analyses of the mutants generated in the untargeted strain modification studies have drawn attention to other important proteins, beyond those of the core catalytic machinery of the cellulose synthase complex. Recently, modern molecular and synthetic biology tools have been developed which showed the potential for improving targeted strain engineering. Taking the advantage of the gathered knowledge should allow for better understanding of the genotype–phenotype relationship which is necessary for robust modelling of metabolism as well as selection and testing of new molecular engineering targets. In this review, we discuss the current progress in the area of Komagataeibacter systems biology and its impact on the research aimed at scaled-up cellulose synthesis as well as BNC functionalisation.

Key points • The accumulated omics datasets advanced the systemic understanding of Komagataeibacter physiology at the molecular level. • Untargeted and targeted strain modification approaches have been applied to improve nanocellulose yield and properties. • The development of modern molecular and synthetic biology tools presents a potential for enhancing targeted strain engineering. • The accumulating omic information should improve modelling of Komagataeibacter’s metabolism as well as selection and testing of new molecular engineering targets.

Bacterial cellulose: Biosynthesis, production, and applications

Bacterial cellulose (BC) is a natural polymer produced by the acetic acid producing bacterium and has gathered much interest over the last decade for its biomedical and biotechnological applications. Unlike the plant derived cellulose nanofibres, which require pretreatment to deconstruct the recalcitrant lignocellulosic network, BC are 100% pure, and are extruded by cells as nanofibrils. Moreover, these nanofibrils can be converted to macrofibers that possess excellent material properties, surpassing even the strength of steel, and can be used as substitutes for fossil fuel derived synthetic fibers. The focus of the review is to present the fundamental long-term research on the influence of environmental factors on the organism's BC production capabilities, the production methods that are available for scaling up/scaled-up processes, and its use as a bulk commodity or for biomedical applications.

An Expanded Synthetic Biology Toolkit for Gene Expression Control in Acetobacteraceae

The availability of different host chassis will greatly expand the range of applications in synthetic biology. Members of the Acetobacteraceae family of Gram-negative bacteria form an attractive class of nonmodel microorganisms that can be exploited to produce industrial chemicals, food and beverage, and biomaterials. One such biomaterial is bacterial cellulose, which is a strong and ultrapure natural polymer used in tissue engineering scaffolds, wound dressings, electronics, food additives, and other products. However, despite the potential of Acetobacteraceae in biotechnology, there has been considerably little effort to fundamentally reprogram the bacteria for enhanced performance. One limiting factor is the lack of a well-characterized, comprehensive toolkit to control expression of genes in biosynthetic pathways and regulatory networks to optimize production and cell viability. Here, we address this shortcoming by building an expanded genetic toolkit for synthetic biology applications in Acetobacteraceae. We characterized the performance of multiple natural and synthetic promoters, ribosome binding sites, terminators, and degradation tags in three different strains, namely, Gluconacetobacter xylinus ATCC 700178, Gluconacetobacter hansenii ATCC 53582, and Komagataeibacter rhaeticus iGEM. Our quantitative data revealed strain-specific and common design rules for the precise control of gene expression in these industrially relevant bacterial species. We further applied our tools to synthesize a biodegradable cellulose-chitin copolymer, adjust the structure of the cellulose film produced, and implement CRISPR interference for ready down-regulation of gene expression. Collectively, our genetic parts will enable the efficient engineering of Acetobacteraceae bacteria for the biomanufacturing of cellulose-based materials and other commercially valuable products.

Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582

Bacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in addition to the previously described cellulose synthase operon, ATCC 53582 contains two additional cellulose synthase operons and several previously undescribed genes associated with cellulose production. In parallel, we also develop optimized protocols and identify plasmid backbones suitable for transformation of ATCC 53582, albeit with low efficiencies. Together, these results provide important information for further studies into cellulose synthesis and for future studies aiming to genetically engineer G. hansenii ATCC 53582 for increased cellulose productivity.

The single-domain globin of Vitreoscilla: augmentation of aerobic metabolism for biotechnological applications

Extensive studies have revealed that large-scale, high-cell density bioreactor cultivations have significant impact on metabolic networks of oxygen-requiring production organisms. Oxygen transfer problems associated with fluid dynamics and inefficient mixing efficiencies result in oxygen gradients, which lead to reduced performance of the bioprocess, decreased product yields, and increased production costs. These problems can be partially alleviated by improving bioreactor configuration and setting, but significant improvements have been achieved by metabolic engineering methods, especially by heterologously expressing Vitreoscilla hemoglobin (VHb). Vast numbers of studies have been accumulating during the past 20 years showing the applicability of VHb to improve growth and product yields in a variety of industrially significant prokaryotic and eukaryotic hosts. The global view on the metabolism of globin-expressing Escherichia coli cells depicts increased energy generation, higher oxygen uptake rates, and a decrease in fermentative by-product excretion. Transcriptome and metabolic flux analysis clearly demonstrate the multidimensional influence of heterologous VHb on the expression of stationary phase-specific genes and on the regulation of cellular metabolic networks. The exact biochemical mechanisms by which VHb is able to improve the oxygen-limited growth remain poorly understood. The suggested mechanisms propose either the delivery of oxygen to the respiratory chain or the detoxification of reactive nitrogen species for the protection of cytochrome activity. The expression of VHb in E. coli bioreactor cultures is likely to assist bacterial growth through providing an increase in available intracellular oxygen, although to fully understand the exact role of VHb in vivo, further analysis will be required.

Production of L-DOPA and dopamine in recombinant bacteria bearing the Vitreoscilla hemoglobin gene

Given the well-established beneficial effects of Vitreoscilla hemoglobin (VHb) on heterologous organisms, the potential of this protein for the production of L-DOPA and dopamine in two bacteria, Citrobacter freundii and Erwinia herbicola, was investigated. The constructed recombinants bearing the VHb gene (vgb(+)) had substantially higher levels of cytoplasmic L-DOPA (112 mg/L for C. freundii and 97 mg/L for E. herbicola) than their respective hosts (30.4 and 33.8 mg/L) and the vgb(-) control strains (35.6 and 35.8 mg/L). Further, the vgb(+) recombinants of C. freundii and E. herbicola had 20-fold and about two orders of magnitude higher dopamine levels than their hosts, repectively. The activity of tyrosine phenol-lyase, the enzyme converting L-tyrosine to L-DOPA, was well-correlated to cytoplasmic L-DOPA levels. As cultures aged, higher tyrosine phenol-lyase activity of the vgb(+) strains was more apparent.