Engineering the phycosphere: fundamental concepts and tools for the bottom-up design of microalgal-bacterial consortia DOI Creative Commons

Austin Semple,

Jagroop Pandhal

Applied Phycology, Journal Year: 2024, Volume and Issue: 6(1), P. 21 - 51

Published: Dec. 23, 2024

Microalgae are a promising platform for the sustainable production of high-value compounds, while also serving as robust degraders toxic pollutants that accumulate in industrial waste streams. As synthetic biologists continue to optimize microalgae so they can compete with conventional microbial hosts, major limitation is compromised central metabolism, following transformation heterologous pathways interfere distribution cellular resources. The co-cultivation microorganisms, including bacteria, has emerged branch biology, rationale distributing metabolic burden inflicted by degradation and synthesis processes aid alleviating stress, polycultures reduce susceptibility contamination. Furthermore, bacteria have co-evolved share resources many aquatic ecosystems, playing pivotal role nutrient cycling. Recent studies these symbioses revealed exchange diverse growth-promoting probiotics, ranging from vitamins metals act co-substrates, amino acids small metabolite infochemicals which dictate population-level shifts phenotype. interface interactions termed phycosphere, dynamic hotspot symbiotic relationships, transient nature, highlighting difficulty establishing stable consortia fit use. Therefore, development interaction screens assays identifying strains optimizing culture conditions important suited desired functions. Equally application meta-omics tools decipher functional interactions, revealing targets improving functionality stability. Here, we review current understanding microalgal microbiome, well bottom-up alga-bacteria co-culture design. We finish perspectives on potential engineering phycosphere applications, where there an increasing need methods manufacturing using adopting circular economy.

Language: Английский

Where Biology Meets Engineering: Scaling Up Microbial Nutraceuticals to Bridge Nutrition, Therapeutics, and Global Impact DOI Creative Commons
Ahmed M. Elazzazy, Mohammed N. Baeshen,

Khalid M. Alasmi

et al.

Microorganisms, Journal Year: 2025, Volume and Issue: 13(3), P. 566 - 566

Published: March 2, 2025

The global nutraceutical industry is experiencing a paradigm shift, driven by an increasing demand for functional foods and dietary supplements that address malnutrition chronic diseases such as obesity, diabetes, cardiovascular conditions, cancer. Traditional plant- animal-derived nutraceuticals face limitations in scalability, cost, environmental impact, paving the way microbial biotechnology sustainable alternative. Microbial cells act bio-factories, converting nutrients like glucose amino acids into valuable products polyunsaturated fatty (PUFAs), peptides, other bioactive compounds. By harnessing their natural metabolic capabilities, microorganisms efficiently synthesize these compounds, making production effective approach development. This review explores transformative role of platforms nutraceuticals, emphasizing advanced fermentation techniques, synthetic biology, engineering. It addresses challenges optimizing strains, ensuring product quality, scaling while navigating regulatory frameworks. Furthermore, highlights cutting-edge technologies CRISPR/Cas9 genome editing, adaptive evolution strain enhancement, bioreactor innovations to enhance yield efficiency. With focus on sustainability precision, positioned game-changer industry, offering eco-friendly scalable solutions meet health needs. integration omics exploration novel sources hold potential revolutionize this field, aligning with growing consumer innovative products.

Language: Английский

Citations

3
Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae DOI Creative Commons
Marco Dueñas, Rory J. Craig, Sean D. Gallaher

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(9)

Published: Feb. 26, 2025

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent green algae, although the mechanism by which multiple polypeptides translated from a single transcript is unknown. Here, we used bioinformatic and vivo mutational analyses to evaluate competing mechanistic models for translation bicistronic mRNAs algae. High-confidence manually curated datasets loci two divergent Chlamydomonas reinhardtii Auxenochlorella protothecoides , revealed preference weak Kozak-like sequences ORF 1 an underrepresentation potential initiation codons before 2 start codon, suitable conditions leaky ribosome scanning allow translation. We analysis A. test mechanism. In manipulation sequence codon altered reporter expression at 2, with weaker enhancing stronger one diminishing it. A synthetic dual demonstrated inversely adjustable activity fluorescent protein expressed luciferase depending on strength sequence. Our findings demonstrate that ORFs algal consistent episodic 2. This work has implications functionality upstream open reading frames (uORFs) found across eukaryotic genomes transgene biology applications.

Language: Английский

Citations

1
Outlook on Synthetic Biology-Driven Hydrogen Production: Lessons from Algal Photosynthesis Applied to Cyanobacteria DOI Creative Commons
Alfonso Jaramillo, Alessandro Satta, Filipe Pinto

et al.

Energy & Fuels, Journal Year: 2025, Volume and Issue: 39(11), P. 4987 - 5006

Published: March 11, 2025

Photobiological hydrogen production offers a sustainable route to clean energy by harnessing solar through photosynthetic microorganisms. The pioneering sulfur-deprivation technique developed Melis and colleagues in the green alga Chlamydomonas reinhardtii successfully enabled sustained downregulating photosystem II (PSII) activity reduce oxygen evolution, creating anaerobic conditions necessary for hydrogenase activity. Inspired this approach, we present project of European consortium PhotoSynH2, which builds on these biological insights employs synthetic biology replicate enhance strategy cyanobacteria, specifically, Synechocystis sp. PCC 6803. By genetically engineering precise downregulation PSII, aim evolution without unintended effects associated with nutrient deprivation, enabling efficient production. Additionally, re-engineering endogenous respiration continuously replenish glycogen consumed during allows matching consumption, maintaining conducive This review discusses how focusing molecular-level processes leveraging advanced genetic tools can lead new methodology that potentially improved results over traditional approaches. redirecting electron flow optimizing redox pathways, seek efficiency cyanobacteria. Our approach demonstrates photosynthesis contribute scalable production, addressing growing demand renewable advancing toward carbon-neutral future.

Language: Английский

Citations

1
Immunomodulatory Compounds from the Sea: From the Origins to a Modern Marine Pharmacopoeia DOI Creative Commons
Edoardo Andrea Cutolo, Rosanna Campitiello, Roberto Caferri

et al.

Marine Drugs, Journal Year: 2024, Volume and Issue: 22(7), P. 304 - 304

Published: June 28, 2024

From sea shores to the abysses of deep ocean, marine ecosystems have provided humanity with valuable medicinal resources. The use organisms is discussed in ancient pharmacopoeias different times and geographic regions still deeply rooted traditional medicine. Thanks present-day, large-scale bioprospecting rigorous screening for bioactive metabolites, ocean coming back as an untapped resource natural compounds therapeutic potential. This renewed interest drugs propelled by a burgeoning research field investigating molecular mechanisms which newly identified intervene pathophysiology human diseases. Of great clinical relevance are molecules endowed anti-inflammatory immunomodulatory properties emerging applications management chronic inflammatory disorders, autoimmune diseases, cancer. Here, we review historical development pharmacology Eastern Western worlds describe status drug discovery. Finally, discuss importance conducting sustainable exploitation resources through biotechnology.

Language: Английский

Citations

4
The design and engineering of synthetic genomes DOI
Joshua S. James, Junbiao Dai, Wei Leong Chew

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 6, 2024

Language: Английский

Citations

4
Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome DOI Creative Commons
Hugh D. Goold, Heinrich Kroukamp, Paige E. Erpf

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 20, 2025

Abstract The Sc2.0 global consortium to design and construct a synthetic genome based on the Saccharomyces cerevisiae commenced in 2006, comprising 16 chromosomes new-to-nature tRNA neochromosome. In this paper we describe assembly debugging of 902,994-bp chromosome synXVI project. Application CRISPR D-BUGS protocol identified defective loci, which were modified improve sporulation recover wild-type like growth when grown glycerol as sole carbon source at 37˚C. LoxPsym sites inserted downstream dubious open reading frames impacted 5’ UTR genes required for optimal systematic cause growth. Based lessons learned from analysis defects , an in-silico redesign was performed, can be used blueprint future yeast designs. includes reduced PCR tag frequency, chunk megachunk termini, adjustments allocation loxPsym TAA stop codons ORFs. This provides roadmap into applications strategies non-yeast organisms.

Language: Английский

Citations

0
Methods for Mass Cultivation of Algae for Various Applications DOI

J. Paul,

M. Lakshmi Priyaa,

Manjupriya Ayyanar

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Genetic engineering in diatoms: advances and prospects DOI Creative Commons
Yixuan Li,

Longji Deng,

E. Walker

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(6)

Published: March 1, 2025

SUMMARY Diatoms are among the most diverse and ecologically significant groups of photosynthetic microalgae, contributing over 20% global primary productivity. Their ecological significance, unique biology, genetic tractability make them ideal targets for genomic engineering metabolic reprogramming. Over past few decades, numerous methods have been developed applied to these organisms better understand function individual genes how they underpin diatom metabolism. Additionally, ability diatoms synthesize high‐value metabolites elaborate mineral structures offers potential applications in biotechnology, including synthesis novel pharmaceuticals, nutraceuticals, biomaterials. This review discusses latest developments provides prospects not only promote use fields biotechnology but also deepen our understanding their role natural ecosystems.

Language: Английский

Citations

0
Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii DOI Open Access
Antoine Van de Vloet, Lucas Prost‐Boxoen, Quinten Bafort

et al.

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Whole-genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications ploidy shifts on short- long-term evolution remains fragmentary, necessitating further investigations across multiple levels. Chlamydomonas reinhardtii is a valuable model organism with profound potential to study impact increase longer term laboratory environment. This partly due ability level. We developed strategy engineer C. using noninterfering, antibiotic, selectable markers. approach allows us induce higher levels applicable field isolates, which expands beyond specific auxotroph strains broadens genetic diversity parental haploid that can be crossed. implement flow cytometry for precise measurement genome size different ploidy. demonstrate creation diploids, triploids, tetraploids by engineering North American broadening application synthetic biology principles reinhardtii. However, newly formed triploids show signs rapid aneuploidization. Our greatly facilitates polyploidy, both fundamental applied settings.

Language: Английский

Citations

0
Importance of Advanced Detection Methodologies from Plant Cells to Human Microsystems Targeting Anticancer Applications DOI Open Access
Mostafa Gouda, Eman Ramadan Elsharkawy, Yong He

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(10), P. 4691 - 4691

Published: May 14, 2025

The growing global demand for phytochemicals as bioactive sources is prompting scientists to develop methods that link their sensory properties mechanisms of action in cancer treatment. Recent techniques tracking the actions small plant metabolites (SPMs) from single-cell molecular anticancer biomarkers could provide valuable insights this field. Among critical discussed review are real-time cell components through stable isotope probing (Sis) and microspectroscopy, which has attracted attention biotechnologists. Additionally, precise pathways required studying new into functional materials discussed, based on high-resolution accurate technologies, aid categorization. Notably, molecules under study have recently garnered applications due advancements effective evaluation surpass traditional methods. In December 2020, Food Drug Administration (FDA) authorized 89 SPMs safe natural molecules. conclusion, by combining spatiotemporal SPMs’ mechanisms, they facilitate development more exceptional, bio-efficient materials.

Language: Английский

Citations

0