Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly

Background

Ogataea parapolymorpha DL-1 is a versatile thermotolerant organism with numerous applications in biotechnology, particularly in the production of recombinant proteins and the study of methanol metabolism and peroxisome functions. This study presents a comprehensive genome and methylome analysis of Ogataea parapolymorpha DL-1 using long-read sequencing technology. The research builds upon previous short-read sequencing efforts, revealing enhancements in genome assembly and epigenomic insights.

Methods

We used long-read sequencing technology to achieve a telomere-to-telomere (T2T) genome assembly of Ogataea parapolymorpha DL-1. High-quality reads were obtained and assembled de novo, followed by polishing to enhance accuracy. The genome was analyzed to identify coding genes, telomeric motifs, rRNA genes, and methylation patterns, including the detection of 5mC and 6 mA modifications. Epigenetic features were further assessed and validated through liquid chromatography-mass spectrometry.

Results

Key findings include the absence of 5 mC DNA modification and the presence of 6 mA in the genome, unusual telomere regulation mechanism based on the addition of non-telomeric dT and the introduction of long-read enhanced telomere-to-telomere assembly.

Conclusion

This work provides deeper insights into the yeast's genome organization and methylation patterns, contributing to the understanding of its genetics and therefore potential biotechnological applications.

Ogataea polymorpha as a next-generation chassis for industrial biotechnology

Ogataea (Hansenula) polymorpha is a nonconventional yeast with some unique characteristics, including fast growth, thermostability, and broad substrate spectrum. Other than common applications for protein production, O. polymorpha is attracting interest for chemical and protein production from methanol; a promising feedstock for the next-generation biomanufacturing due to its abundant sources and excellent characteristics. Benefiting from the development of synthetic biology, it has been engineered to produce value-added chemicals by extensively rewiring cellular metabolism. This Review discusses recently developed synthetic biology tools of O. polymorpha. The advances of chemicals production and systems biology were reviewed comprehensively. Finally, we look ahead to the developments of biomanufacturing in O. polymorpha to make an overall understanding of this chassis for academia and industry.

Genomic insights into fish pathogenic bacteria: A systems biology perspective for sustainable aquaculture

Fish diseases significantly challenge global aquaculture, causing substantial financial losses and impacting sustainability, trade, and socioeconomic conditions. Understanding microbial pathogenesis and virulence at the molecular level is crucial for disease prevention in commercial fish. This review provides genomic insights into fish pathogenic bacteria from a systems biology perspective, aiming to promote sustainable aquaculture. It covers the genomic characteristics of various fish pathogens and their industry impact. The review also explores the systems biology of zebrafish, fish bacterial pathogens, and probiotic bacteria, offering insights into fish production, potential vaccines, and therapeutic drugs. Genome-scale metabolic models aid in studying pathogenic bacteria, contributing to disease management and antimicrobial development. Researchers have also investigated probiotic strains to improve aquaculture health. Additionally, the review highlights bioinformatics resources for fish and fish pathogens, which are essential for researchers. Systems biology approaches enhance understanding of bacterial fish pathogens by revealing virulence factors and host interactions. Despite challenges from the adaptability and pathogenicity of bacterial infections, sustainable alternatives are necessary to meet seafood demand. This review underscores the potential of systems biology in understanding fish pathogen biology, improving production, and promoting sustainable aquaculture.

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains' growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.

Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha

BACKGROUND

One carbon (C1) molecules such as methanol have the potential to become sustainable feedstocks for biotechnological processes, as they can be derived from CO2 and green hydrogen, without the need for arable land. Therefore, we investigated the suitability of the methylotrophic yeast Ogataea polymorpha as a potential production organism for platform chemicals derived from methanol. We selected acetone, malate, and isoprene as industrially relevant products to demonstrate the production of compounds with 3, 4, or 5 carbon atoms, respectively.

RESULTS

We successfully engineered O. polymorpha for the production of all three molecules and demonstrated their production using methanol as carbon source. We showed that the metabolism of O. polymorpha is well suited to produce malate as a product and demonstrated that the introduction of an efficient malate transporter is essential for malate production from methanol. Through optimization of the cultivation conditions in shake flasks, which included pH regulation and constant substrate feeding, we were able to achieve a maximum titer of 13 g/L malate with a production rate of 3.3 g/L/d using methanol as carbon source. We further demonstrated the production of acetone and isoprene as additional heterologous products in O. polymorpha, with maximum titers of 13.6 mg/L and 4.4 mg/L, respectively.

CONCLUSION

These findings highlight how O. polymorpha has the potential to be applied as a versatile cell factory and contribute to the limited knowledge on how methylotrophic yeasts can be used for the production of low molecular weight biochemicals from methanol. Thus, this study can serve as a point of reference for future metabolic engineering in O. polymorpha and process optimization efforts to boost the production of platform chemicals from renewable C1 carbon sources.

Advances in genome-scale metabolic models of industrially important fungi

Many fungal species have been used industrially for production of biofuels and bioproducts. Developing strains with better performance in biomanufacturing contexts requires a systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated for several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. Here, we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design-build-test-learn cycles, ultimately advancing the field of fungal biomanufacturing.

C1-based biomanufacturing: Advances, challenges and perspectives

One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.

Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste

In our study, we used 16SrRNA and ITS to investigate the microbial community composition and the effect of compound bacterial agent on the microbial community composition in the aerobic composting process of food waste (FW). At the bacterial level, the main phyla of Group A (compost naturally) were Proteobacteria and Firmicutes, and the main species were Pseudomonas_sp._GR7, Bacillus licheniformis and Pediococcus acidilactici. The main phyla of Group B (compost with compound bacterial agent) were Proteobacteria, Firmicutes and Streptophyta, and the main species were Klebsiella pneumoniae, Cronobacter sakazakii, Macrococcus caseolyticus, Enterococcus faecalis, Citrobacter freundii and Bacillus velezensis. It is worth noting that M. caseolyticus may be able to improve the effect of odour which is an important sensory index during aerobic composting. At the fungal level, the main phylum of both Groups A and B was Ascomycota, and the main species of Group A were Paecilomyces variotii, Byssochlamys spectabilis and Aspergillus fumigatus. The main species of Group B were Ogataea polymorpha and Millerozyma farinosa. Finally, the degradation rate of Group B was 81% that was about 15% higher than that of Group A, indicating that the compound bacterial agent could effectively improve the degradation rate and the composting process, while the low abundance of the compound bacterial agent in the composting process might be due to the small initial addition or the inhibition of other bacteria or fungi in the composting process.