1
|
Perotti O, Esparza GV, Booth DS. A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594265. [PMID: 38798503 PMCID: PMC11118467 DOI: 10.1101/2024.05.14.594265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
We uncovered an interaction between a choanoflagellate and alga, in which porphyran, a polysaccharide produced by the red alga Porphyra umbilicalis, induces multicellular development in the choanoflagellate Salpingoeca rosetta. We first noticed this possible interaction when we tested the growth of S. rosetta in media that was steeped with P. umbilicalis as a nutritional source. Under those conditions, S. rosetta formed multicellular rosette colonies even in the absence of any bacterial species that can induce rosette development. In biochemical purifications, we identified porphyran, a extracellular polysaccharide produced by red algae, as the rosette inducing factor The response of S. rosetta to porphyran provides a biochemical insight for associations between choanoflagellates and algae that have been observed since the earliest descriptions of choanoflagellates. Moreover, this work provides complementary evidence to ecological and geochemical studies that show the profound impact algae have exerted on eukaryotes and their evolution, including a rise in algal productivity that coincided with the origin of animals, the closest living relatives of choanoflagellates.
Collapse
Affiliation(s)
- Olivia Perotti
- Chan Zuckerberg Biohub, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
- Present address: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Gabriel Viramontes Esparza
- Chan Zuckerberg Biohub, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
- Tetrad Graduate Group, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
| | - David S. Booth
- Chan Zuckerberg Biohub, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
- Tetrad Graduate Group, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine Genentech Hall, 600 16 St, San Francisco, CA 94143
| |
Collapse
|
2
|
Patwary ZP, Zhao M, Paul NA, Cummins SF. Identification of reproductive sex-biased gene expression in Asparagopsis taxiformis (lineage 6) gametophytes. JOURNAL OF PHYCOLOGY 2024; 60:327-342. [PMID: 38156746 DOI: 10.1111/jpy.13419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 01/03/2024]
Abstract
The sub-tropical red seaweed Asparagopsis taxiformis is of significant interest due to its ability to store halogenated compounds, including bromoform, which can mitigate methane production in ruminants. Significant scale-up of aquaculture production of this seaweed is required; however, relatively little is known about the molecular mechanisms that control fundamental physiological processes, including the regulatory factors that determine sexual dimorphism in gametophytes. In this study, we used comparative RNA-sequencing analysis between different morphological parts of mature male and female A. taxiformis (lineage 6) gametophytes that resulted in greater number of sex-biased gene expression in tips (containing the reproductive structures for both sexes), compared with the somatic main axis and rhizomes. Further comparative RNA-seq against immature tips was used to identify 62 reproductive sex-biased genes (59 male-biased, 3 female-biased). Of the reproductive male-biased genes, 46% had an unknown function, while others were predicted to be regulatory factors and enzymes involved in signaling. We found that bromoform content obtained from female samples (8.5 ± 1.0 mg·g-1 dry weight) was ~10% higher on average than that of male samples (6.5 ± 1.0 mg·g-1 dry weight), although no significant difference was observed (p > 0.05). There was also no significant difference in the marine bromoform biosynthesis locus gene expression. In summary, our comparative RNA-sequencing analysis provides a first insight into the potential molecular factors relevant to gametogenesis and sexual differentiation in A. taxiformis, with potential benefits for identification of sex-specific markers.
Collapse
Affiliation(s)
- Zubaida Parveen Patwary
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Min Zhao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Nicholas A Paul
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Scott F Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| |
Collapse
|
3
|
Rana MM, De la Hoz Siegler H. Evolution of Hybrid Hydrogels: Next-Generation Biomaterials for Drug Delivery and Tissue Engineering. Gels 2024; 10:216. [PMID: 38667635 PMCID: PMC11049329 DOI: 10.3390/gels10040216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Hydrogels, being hydrophilic polymer networks capable of absorbing and retaining aqueous fluids, hold significant promise in biomedical applications owing to their high water content, permeability, and structural similarity to the extracellular matrix. Recent chemical advancements have bolstered their versatility, facilitating the integration of the molecules guiding cellular activities and enabling their controlled activation under time constraints. However, conventional synthetic hydrogels suffer from inherent weaknesses such as heterogeneity and network imperfections, which adversely affect their mechanical properties, diffusion rates, and biological activity. In response to these challenges, hybrid hydrogels have emerged, aiming to enhance their strength, drug release efficiency, and therapeutic effectiveness. These hybrid hydrogels, featuring improved formulations, are tailored for controlled drug release and tissue regeneration across both soft and hard tissues. The scientific community has increasingly recognized the versatile characteristics of hybrid hydrogels, particularly in the biomedical sector. This comprehensive review delves into recent advancements in hybrid hydrogel systems, covering the diverse types, modification strategies, and the integration of nano/microstructures. The discussion includes innovative fabrication techniques such as click reactions, 3D printing, and photopatterning alongside the elucidation of the release mechanisms of bioactive molecules. By addressing challenges, the review underscores diverse biomedical applications and envisages a promising future for hybrid hydrogels across various domains in the biomedical field.
Collapse
Affiliation(s)
- Md Mohosin Rana
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada;
- Centre for Blood Research, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hector De la Hoz Siegler
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
4
|
Park SJ, Sharma A, Lee HJ. An Update on the Chemical Constituents and Biological Properties of Selected Species of an Underpinned Genus of Red Algae: Chondrus. Mar Drugs 2024; 22:47. [PMID: 38248672 PMCID: PMC10817618 DOI: 10.3390/md22010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Macroalgae, particularly red seaweeds, have attracted significant attention due to their economic and health benefits. Chondrus, a red algae genus, despite its economic importance, seems to be undervalued. Among all its species, Chondrus crispus has been meticulously documented for its biological properties, and little is known about other species. No comprehensive review of the biological properties of this genus has been acknowledged. Thus, this review aimed to summarize the available information on the chemical constituents and biological properties of a few selected species, including Chondrus crispus, Chondrus ocellatus, Mazzaella canaliculata, and Chondrus armatus. We compiled and discovered that the genus is offering most of the important health-promoting benefits evidenced from in vitro and in vivo studies focused on antimicrobial, immunomodulation, neuroprotection, anti-atopic, anti-inflammatory, anti-viral, anti-diabetic, cytoprotective, antioxidant, anti-coagulation, nephroprotective, anti-tumor, and anti-venom activity, which speaks about the potential of this genus. Data on clinical studies are limited. Further, around 105 chemical constituents have been reported from Chondrus spp. Given its significance, further investigation is warranted, in the form of meticulously planned cell, animal, and clinical studies that concentrate on novel health-enhancing endeavors, in order to unveil the full potential of this genus. The review also outlines challenges and future directions.
Collapse
Affiliation(s)
- Seon-Joo Park
- Department of Food and Nutrition, College of Bionanotechnology, Gachon University, Seongnam-si 13120, Republic of Korea;
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam-si 13120, Republic of Korea
| | - Anshul Sharma
- Department of Food and Nutrition, College of Bionanotechnology, Gachon University, Seongnam-si 13120, Republic of Korea;
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam-si 13120, Republic of Korea
| | - Hae-Jeung Lee
- Department of Food and Nutrition, College of Bionanotechnology, Gachon University, Seongnam-si 13120, Republic of Korea;
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam-si 13120, Republic of Korea
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Science and Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
| |
Collapse
|
5
|
McKinnie LJ, Cummins SF, Zhao M. Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach. Mar Drugs 2023; 22:3. [PMID: 38276641 PMCID: PMC10817344 DOI: 10.3390/md22010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Rhodophytes (red algae) are an important source of natural products and are, therefore, a current research focus in terms of metabolite production. The recent increase in publicly available Rhodophyte whole genome and transcriptome assemblies provides the resources needed for in silico metabolic pathway analysis. Thus, this study aimed to create a Rhodophyte multi-omics resource, utilising both genomes and transcriptome assemblies with functional annotations to explore Rhodophyte metabolism. The genomes and transcriptomes of 72 Rhodophytes were functionally annotated and integrated with metabolic reconstruction and phylogenetic inference, orthology prediction, and gene duplication analysis to analyse their metabolic pathways. This resource was utilised via two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halide-associated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research revealed trends in Rhodophyte metabolic pathways that have been under-researched and require further functional analysis. Furthermore, the high duplication of haem peroxidases and other peroxidase enzymes offers insight into the potential drug development of Rhodophyte halogenated secondary metabolites.
Collapse
Affiliation(s)
- Lachlan J. McKinnie
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| | - Scott F. Cummins
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| | - Min Zhao
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| |
Collapse
|
6
|
Borg M, Krueger-Hadfield SA, Destombe C, Collén J, Lipinska A, Coelho SM. Red macroalgae in the genomic era. THE NEW PHYTOLOGIST 2023; 240:471-488. [PMID: 37649301 DOI: 10.1111/nph.19211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.
Collapse
Affiliation(s)
- Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Stacy A Krueger-Hadfield
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Virginia Institute of Marine Science Eastern Shore Laboratory, Wachapreague, VA, 23480, USA
| | - Christophe Destombe
- International Research Laboratory 3614 (IRL3614) - Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, 29680, France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff, Sorbonne Université, Roscoff, 29680, France
| | - Agnieszka Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| |
Collapse
|
7
|
Garcia-Perez P, Cassani L, Garcia-Oliveira P, Xiao J, Simal-Gandara J, Prieto MA, Lucini L. Algal nutraceuticals: A perspective on metabolic diversity, current food applications, and prospects in the field of metabolomics. Food Chem 2023; 409:135295. [PMID: 36603477 DOI: 10.1016/j.foodchem.2022.135295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The current consumers' demand for food naturalness is urging the search for new functional foods of natural origin with enhanced health-promoting properties. In this sense, algae constitute an underexplored biological source of nutraceuticals that can be used to fortify food products. Both marine macroalgae (or seaweeds) and microalgae exhibit a myriad of chemical constituents with associated features as a result of their primary and secondary metabolism. Thus, primary metabolites, especially polysaccharides and phycobiliproteins, present interesting properties to improve the rheological and nutritional properties of food matrices, whereas secondary metabolites, such as polyphenols and xanthophylls, may provide interesting bioactivities, including antioxidant or cytotoxic effects. Due to the interest in algae as a source of nutraceuticals by the food and related industries, novel strategies should be undertaken to add value to their derived functional components. As a result, metabolomics is considered a high throughput technology to get insight into the full metabolic profile of biological samples, and it opens a wide perspective in the study of algae metabolism, whose knowledge is still little explored. This review focuses on algae metabolism and its applications in the food industry, paying attention to the promising metabolomic approaches to be developed aiming at the functional characterization of these organisms.
Collapse
Affiliation(s)
- Pascual Garcia-Perez
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Lucia Cassani
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Centro de Investigação de Montanha (CIMO-IPB), Campus de Santa Apolónia, Bragança, Portugal
| | - Paula Garcia-Oliveira
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Centro de Investigação de Montanha (CIMO-IPB), Campus de Santa Apolónia, Bragança, Portugal
| | - Jianbo Xiao
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain
| | - Miguel A Prieto
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, Ourense Campus, Universidade de Vigo, E32004 Ourense, Spain; Centro de Investigação de Montanha (CIMO-IPB), Campus de Santa Apolónia, Bragança, Portugal
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| |
Collapse
|
8
|
Chevenier A, Jouanneau D, Ficko-Blean E. Carrageenan biosynthesis in red algae: a review. Cell Surf 2023. [DOI: 10.1016/j.tcsw.2023.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
9
|
Gregersen Echers S, Abdul-Khalek N, Mikkelsen RK, Holdt SL, Jacobsen C, Hansen EB, Olsen TH, Sejberg JJ, Overgaard MT. Is Gigartina a potential source of food protein and functional peptide-based ingredients? Evaluating an industrial, pilot-scale extract by proteomics and bioinformatics. FUTURE FOODS 2022. [DOI: 10.1016/j.fufo.2022.100189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
|
10
|
Compositional and rheological analysis of carrageenan from the gametophyte phase of the red seaweed Chondrus crispus neutrally extracted at varying temperatures and time. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
11
|
Shao Z, Duan D. The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:902823. [PMID: 35620682 PMCID: PMC9127767 DOI: 10.3389/fpls.2022.902823] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/15/2022] [Indexed: 05/16/2023]
Abstract
Cell wall polysaccharides (CWPS) of seaweeds play crucial roles in mechanical shear resistance, cell-cell adhesion and the interactions with changeable marine environments. They have diverse applications in food, cosmetics, agriculture, pharmaceuticals and therapeutics. The recent boost of multi-omics sequence analysis has rapidly progressed the mining of presumed genes encoding enzymes involved in CWPS biosynthesis pathways. In this review, we summarize the biosynthetic pathways of alginate, fucoidan, agar, carrageenan and ulvan in seaweeds referred to the literatures on published genomes and biochemical characterization of encoded enzymes. Some transcriptomic data were briefly reported to discuss the correlation between gene expression levels and CWPS contents. Mannuronan C-5 epimerase (MC5E) and carbohydrate sulfotransferase (CST) are crucial enzymes for alginate and sulfated CWPS, respectively. Nonetheless, most CWPS-relevant genes were merely investigated by gene mining and phylogenetic analysis. We offer an integrative view of CWPS biosynthesis from a molecular perspective and discuss about the underlying regulation mechanism. However, a clear understanding of the relationship between chemical structure and bioactivities of CWPS is limited, and reverse genetic manipulation and effective gene editing tools need to be developed in future.
Collapse
Affiliation(s)
- Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao, China
| |
Collapse
|
12
|
Carrageenan‐based Hybrids with Biopolymers and Nano‐structured Materials for Biomimetic Applications. STARCH-STARKE 2022. [DOI: 10.1002/star.202200018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
13
|
Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
Collapse
Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
14
|
Torres MD, Flórez-Fernández N, Domínguez H. Chondrus crispus treated with ultrasound as a polysaccharides source with improved antitumoral potential. Carbohydr Polym 2021; 273:118588. [PMID: 34560989 DOI: 10.1016/j.carbpol.2021.118588] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Ultrasound-assisted extraction was used to recover gelling biopolymers and antioxidant compounds from Chondrus crispus with improved biological potential. The optimal processing conditions were evaluated using a Box-Behnken design, and the impact on the biological and thermo-rheological properties of the carrageenan fraction and on the bioactive features of the soluble extracts were studied. The optimum extraction parameters were defined by extraction time of ~34.7 min; solid liquid ratio of ~2.1 g/100 g and ultrasound amplitude of ~79.0% with a maximum power of 1130 W. The dependent variables exhibited maximum carrageenan yields (44.3%) and viscoelastic modulus (925.9 Pa) with the lowest gelling temperatures (38.7 °C) as well as maximum content of the extract in protein (22.4 mg/g), gallic acid (13.4 mg/g) and Trolox equivalents antioxidant capacity (182.4 mg TEAC/g). Tested hybrid carrageenans exhibited promising biological activities (% of growth inhibition around 91% for four human cancer cellular lines: A549; A2780; HeLa 229; HT-29).
Collapse
Affiliation(s)
- M D Torres
- Department of Chemical Engineering, Universidade de Vigo (Campus Ourense), Edificio Politécnico, As Lagoas, 32004 Ourense, Spain; CINBIO, Universidade de Vigo, 32004 Ourense, Spain.
| | - N Flórez-Fernández
- Department of Chemical Engineering, Universidade de Vigo (Campus Ourense), Edificio Politécnico, As Lagoas, 32004 Ourense, Spain; CINBIO, Universidade de Vigo, 32004 Ourense, Spain
| | - H Domínguez
- Department of Chemical Engineering, Universidade de Vigo (Campus Ourense), Edificio Politécnico, As Lagoas, 32004 Ourense, Spain; CINBIO, Universidade de Vigo, 32004 Ourense, Spain
| |
Collapse
|
15
|
Pacheco D, Cotas J, Rocha CP, Araújo GS, Figueirinha A, Gonçalves AM, Bahcevandziev K, Pereira L. Seaweeds’ carbohydrate polymers as plant growth promoters. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2021. [DOI: 10.1016/j.carpta.2021.100097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
16
|
Role and Evolution of the Extracellular Matrix in the Acquisition of Complex Multicellularity in Eukaryotes: A Macroalgal Perspective. Genes (Basel) 2021; 12:genes12071059. [PMID: 34356075 PMCID: PMC8307928 DOI: 10.3390/genes12071059] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Multicellular eukaryotes are characterized by an expanded extracellular matrix (ECM) with a diversified composition. The ECM is involved in determining tissue texture, screening cells from the outside medium, development, and innate immunity, all of which are essential features in the biology of multicellular eukaryotes. This review addresses the origin and evolution of the ECM, with a focus on multicellular marine algae. We show that in these lineages the expansion of extracellular matrix played a major role in the acquisition of complex multicellularity through its capacity to connect, position, shield, and defend the cells. Multiple innovations were necessary during these evolutionary processes, leading to striking convergences in the structures and functions of the ECMs of algae, animals, and plants.
Collapse
|
17
|
Rhein-Knudsen N, Meyer AS. Chemistry, gelation, and enzymatic modification of seaweed food hydrocolloids. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
18
|
Krueger-Hadfield SA, Flanagan BA, Godfroy O, Hill-Spanik KM, Nice CC, Murren CJ, Strand AE, Sotka EE. Using RAD-seq to develop sex-linked markers in a haplodiplontic alga. JOURNAL OF PHYCOLOGY 2021; 57:279-294. [PMID: 33098662 DOI: 10.1111/jpy.13088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to identify sex-linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD-seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non-native site (N = 40 gametophytes and N = 32 tetrasporophytes total). We identified seven putatively female-linked and 19 putatively male-linked sequences. Four female- and eight male-linked markers amplified in all three life cycle stages. Using one female- and one male-linked marker that were sex-specific, we developed a duplex PCR and tested the efficacy of this assay on a subset of thalli sampled at two sites in the non-native range. We confirmed ploidy based on the visual observation of reproductive structures and previous microsatellite genotyping at 10 polymorphic loci. For 32 vegetative thalli, we were able to assign sex and confirm ploidy in these previously genotyped thalli. These markers will be integral to ongoing studies of A. vermiculophyllum invasion. We discuss the utility of RAD-seq over other approaches previously used, such as RAPDs (random amplified polymorphic DNA), for future work designing sex-linked markers in other haplodiplontic macroalgae for which genomes are lacking.
Collapse
Affiliation(s)
- Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, Alabama, 35294, USA
| | - Ben A Flanagan
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Olivier Godfroy
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Kristina M Hill-Spanik
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, Texas, 78666, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Allan E Strand
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| | - Erik E Sotka
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| |
Collapse
|
19
|
Wallace MD, Ficko-Blean E, Stubbs KA. Red Algal Molecules - Synthesis of Methyl Neo-β-carrabioside and Its S-Linked Variant via Two Synthetic Routes: A Late Stage Ring Closure and Using a 3,6-Anhydro-d-galactosyl Donor. J Org Chem 2020; 85:16182-16195. [PMID: 33182999 DOI: 10.1021/acs.joc.0c02339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methyl neo-β-carrabioside has been synthesized for the first time, employing either a late stage ring closure to install the required 3,6-anhydro-bridge or a suitable 3,6-anhydro-galactosyl donor to form the unfavored 1,2-cis-equatorial α-linkage. Using the late stage ring closure approach, an S-linked analogue of methyl neo-β-carrabioside was also realized. These compounds have applications in the identification and characterization of marine bacterial exo-α-3,6-anhydro-d-galactosidases that have specific activity on red algal neo-carrageenan oligosaccharides, such as those found in both family 127 and 129 of the glycoside hydrolases. In addition a biochemical assay using the synthesized methyl neo-β-carrabioside and the marine bacterial exo-α-3,6-anhydro-d-galactosidase ZgGH129 demonstrates that the minimum substrate unit for the enzyme is neo-β-carrabiose.
Collapse
Affiliation(s)
- Michael D Wallace
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Elizabeth Ficko-Blean
- CNRS, Sorbonne Université, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| |
Collapse
|