1
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Anjou C, Lotoux A, Morvan C, Martin-Verstraete I. From ubiquity to specificity: The diverse functions of bacterial thioredoxin systems. Environ Microbiol 2024; 26:e16668. [PMID: 38899743 DOI: 10.1111/1462-2920.16668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
The thioredoxin (Trx) system, found universally, is responsible for the regeneration of reversibly oxidized protein thiols in living cells. This system is made up of a Trx and a Trx reductase, and it plays a central role in maintaining thiol-based redox homeostasis by reducing oxidized protein thiols, such as disulfide bonds in proteins. Some Trxs also possess a chaperone function that is independent of thiol-disulfide exchange, in addition to their thiol-disulfide reductase activity. These two activities of the Trx system are involved in numerous physiological processes in bacteria. This review describes the diverse physiological roles of the Trx system that have emerged throughout bacterial evolution. The Trx system is essential for responding to oxidative and nitrosative stress. Beyond this primary function, the Trx system also participates in redox regulation and signal transduction, and in controlling metabolism, motility, biofilm formation, and virulence. This range of functions has evolved alongside the diversity of bacterial lifestyles and their specific constraints. This evolution can be characterized by the multiplication of the systems and by the specialization of cofactors or targets to adapt to the constraints of atypical lifestyles, such as photosynthesis, insect endosymbiosis, or spore-forming bacteria.
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Affiliation(s)
- Cyril Anjou
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Aurélie Lotoux
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Claire Morvan
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
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2
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Shen H, Li J, Chen L, Guo X. Insights into multiscale structure and digestive characteristic of starch from two cultivars of chestnut during kernel development. Int J Biol Macromol 2024; 269:131978. [PMID: 38692537 DOI: 10.1016/j.ijbiomac.2024.131978] [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: 01/22/2024] [Revised: 04/17/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Multiscale structure and digestive characteristic of starch during kernel development of Castanea henryi ('Jinzhui' (YS) and 'Baiyan No.1' (WS)) were investigated in this study. Structural analysis revealed that the surface of starch granules became smooth, the amylopectin content decreased (from 71.32 % to 70.47 %, from 71.44 % to 68.37 %, respectively), the chain length distribution of amylopectin reduced (the proportion of B1 chain decreased from 52.35 % to 50.60 %, from 52.22 % to 50.59 %, respectively) while the amorphous and semi-crystalline lamellae of starch increased during development, which was consistent with the decreasing relative crystallinity (from 28.79 % to 24.11 %, from 29.57 % to 23.66 %, respectively) and short-range ordering degree. The degradation of ordered structure further resulted in the increase of digestibility, especially in the late developmental stage, supported by a significant decrease of resistant starch content (from 70.21 % to 61.70 % and from 73.58 % to 58.86 %, respectively). Transcriptome analysis and RT-qPCR were performed to explore the possible molecular mechanisms affecting starch structure. The high expression of several key genes including AGPase, GBSS, SBE, SSS, ISA and PUL in late development stage might be the reason of structural changes during development. The results provided valuable information for starch accumulation during kernel development of Castanea henryi.
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Affiliation(s)
- Haoran Shen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China
| | - Jiaqi Li
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China
| | - Ling Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China
| | - Xinbo Guo
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China.
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3
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Wang Y, Wang D, Du J, Wang Y, Shao C, Cui C, Xiao J, Wang X. Crucial role of SWL1 in chloroplast biogenesis and development in Arabidopsis thaliana. PLANT CELL REPORTS 2024; 43:135. [PMID: 38704787 DOI: 10.1007/s00299-024-03210-1] [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: 02/03/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE The disruption of the SWL1 gene leads to a significant down regulation of chloroplast and secondary metabolites gene expression in Arabidopsis thaliana. And finally results in a dysfunction of chloroplast and plant growth. Although the development of the chloroplast has been a consistent focus of research, the corresponding regulatory mechanisms remain unidentified. In this study, the CRISPR/Cas9 system was used to mutate the SWL1 gene, resulting in albino cotyledons and variegated true leaf phenotype. Confocal microscopy and western blot of chloroplast protein fractions revealed that SWL1 localized in the chloroplast stroma. Electron microscopy indicated chloroplasts in the cotyledons of swl1 lack well-defined grana and internal membrane structures, and similar structures have been detected in the albino region of variegated true leaves. Transcriptome analysis revealed that down regulation of chloroplast and nuclear gene expression related to chloroplast, including light harvesting complexes, porphyrin, chlorophyll metabolism and carbon metabolism in the swl1 compared to wild-type plant. In addition, proteomic analysis combined with western blot analysis, showed that a significant decrease in chloroplast proteins of swl1. Furthermore, the expression of genes associated with secondary metabolites and growth hormones was also reduced, which may be attributed to SWL1 associated with absorption and fixation of inorganic carbon during chloroplast development. Together, the above findings provide valuable information to elucidate the exact function of SWL1 in chloroplast biogenesis and development.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Dong Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingxia Du
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yan Wang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China
| | - Chunxue Shao
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chuwen Cui
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jianwei Xiao
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China.
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xinwei Wang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China.
- SENO Biotechnology Co., Ltd., Zhangjiakou, 075000, China.
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4
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K. Raval P, MacLeod AI, Gould SB. A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms. PLoS Biol 2024; 22:e3002608. [PMID: 38713727 PMCID: PMC11135702 DOI: 10.1371/journal.pbio.3002608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/29/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander I. MacLeod
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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5
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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6
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Goold HD, Moseley JL, Lauersen KJ. The synthetic future of algal genomes. CELL GENOMICS 2024; 4:100505. [PMID: 38395701 PMCID: PMC10943592 DOI: 10.1016/j.xgen.2024.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.
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Affiliation(s)
- Hugh D Goold
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia; ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Phycoil Biotechnology International, Inc., Fremont, CA 94538, USA
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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7
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Vuillemin M, Moreno Prieto ES, Pilgaard B, Siebenhaar S, Holck J, Henrissat B, Bahieldin A, Hakeem KR, Alghamdi KM. Biochemical exploration of family GH119 reveals a single α-amylase specificity and confirms shared catalytic machinery with GH57 enzymes. Int J Biol Macromol 2024; 262:129783. [PMID: 38280706 DOI: 10.1016/j.ijbiomac.2024.129783] [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: 10/10/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 01/29/2024]
Abstract
While hundreds of starch- and glycogen-degrading enzymes have been characterized experimentally in historical families such as GH13, GH14, GH15, GH57 and GH126 of the CAZy database (www.cazy.org), the α-amylase from Bacillus circulans is the only enzyme that has been characterized in family GH119. Since glycosidase families have been shown to often group enzymes with different substrates or products, a single characterized enzyme in a family is insufficient to extrapolate enzyme function based solely on sequence similarity. Here we report the rational exploration of family GH119 through the biochemical characterization of five GH119 members. All enzymes shared single α-amylase specificity but display distinct product profile. We also report the first kinetic constants in family GH119 and the first experimental validation of previously predicted catalytic residues in family GH119, confirming that families GH119 and GH57 can be grouped in the novel clan GH-T of the CAZy database.
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Affiliation(s)
- Marlene Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Eduardo S Moreno Prieto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Bo Pilgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Public Health, Daffodil International University, Dhaka 1341, Bangladesh; Centre of Research Impact and Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India.
| | - Khalid M Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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8
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Lee J, Yang JH, Weber APM, Bhattacharya D, Kim WY, Yoon HS. Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism. Mol Biol Evol 2024; 41:msae012. [PMID: 38267085 PMCID: PMC10853006 DOI: 10.1093/molbev/msae012] [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: 09/09/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 four), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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9
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Ahamed A, Hosea R, Wu S, Kasim V. The Emerging Roles of the Metabolic Regulator G6PD in Human Cancers. Int J Mol Sci 2023; 24:17238. [PMID: 38139067 PMCID: PMC10743588 DOI: 10.3390/ijms242417238] [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: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Metabolic reprogramming, especially reprogrammed glucose metabolism, is a well-known cancer hallmark related to various characteristics of tumor cells, including proliferation, survival, metastasis, and drug resistance. Glucose-6-phosphate dehydrogenase (G6PD) is the first and rate-limiting enzyme of the pentose phosphate pathway (PPP), a branch of glycolysis, that converts glucose-6-phosphate (G6P) into 6-phosphogluconolactone (6PGL). Furthermore, PPP produces ribose-5-phosphate (R5P), which provides sugar-phosphate backbones for nucleotide synthesis as well as nicotinamide adenine dinucleotide phosphate (NADPH), an important cellular reductant. Several studies have shown enhanced G6PD expression and PPP flux in various tumor cells, as well as their correlation with tumor progression through cancer hallmark regulation, especially reprogramming cellular metabolism, sustaining proliferative signaling, resisting cell death, and activating invasion and metastasis. Inhibiting G6PD could suppress tumor cell proliferation, promote cell death, reverse chemoresistance, and inhibit metastasis, suggesting the potential of G6PD as a target for anti-tumor therapeutic strategies. Indeed, while challenges-including side effects-still remain, small-molecule G6PD inhibitors showing potential anti-tumor effect either when used alone or in combination with other anti-tumor drugs have been developed. This review provides an overview of the structural significance of G6PD, its role in and regulation of tumor development and progression, and the strategies explored in relation to G6PD-targeted therapy.
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Affiliation(s)
- Alfar Ahamed
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Rendy Hosea
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
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10
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Launay H, Avilan L, Gérard C, Parsiegla G, Receveur-Brechot V, Gontero B, Carriere F. Location of the photosynthetic carbon metabolism in microcompartments and separated phases in microalgal cells. FEBS Lett 2023; 597:2853-2878. [PMID: 37827572 DOI: 10.1002/1873-3468.14754] [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: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid-liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin-Benson-Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.
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Affiliation(s)
- Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Luisana Avilan
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Cassy Gérard
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
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11
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Chang H, Bai J, Zhang H, Huang R, Chu H, Wang Q, Liu H, Cheng J, Jiang H. Origin and evolution of the main starch biosynthetic enzymes. Synth Syst Biotechnol 2023; 8:462-468. [PMID: 37692203 PMCID: PMC10485787 DOI: 10.1016/j.synbio.2023.05.006] [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: 04/03/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 09/12/2023] Open
Abstract
Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.
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Affiliation(s)
- Hong Chang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jie Bai
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Hejian Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Rong Huang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Huanyu Chu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Qian Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Hao Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jian Cheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
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Xiong L, Li Y, Yu H, Wei Y, Li H, Ji X. Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland. Sci Rep 2023; 13:14190. [PMID: 37648730 PMCID: PMC10468529 DOI: 10.1038/s41598-023-41323-x] [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: 01/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
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Tame A, Maruyama T, Ikuta T, Chikaraishi Y, Ogawa NO, Tsuchiya M, Takishita K, Tsuda M, Hirai M, Takaki Y, Ohkouchi N, Fujikura K, Yoshida T. mTORC1 regulates phagosome digestion of symbiotic bacteria for intracellular nutritional symbiosis in a deep-sea mussel. SCIENCE ADVANCES 2023; 9:eadg8364. [PMID: 37611098 PMCID: PMC10446485 DOI: 10.1126/sciadv.adg8364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/27/2023] [Indexed: 08/25/2023]
Abstract
Phagocytosis is one of the methods used to acquire symbiotic bacteria to establish intracellular symbiosis. A deep-sea mussel, Bathymodiolus japonicus, acquires its symbiont from the environment by phagocytosis of gill epithelial cells and receives nutrients from them. However, the manner by which mussels retain the symbiont without phagosome digestion remains unknown. Here, we show that controlling the mechanistic target of rapamycin complex 1 (mTORC1) in mussels leads to retaining symbionts in gill cells. The symbiont is essential for the host mussel nutrition; however, depleting the symbiont's energy source triggers the phagosome digestion of symbionts. Meanwhile, the inhibition of mTORC1 by rapamycin prevented the digestion of the resident symbionts and of the engulfed exogenous dead symbionts in gill cells. This indicates that mTORC1 promotes phagosome digestion of symbionts under reduced nutrient supply from the symbiont. The regulation mechanism of phagosome digestion by mTORC1 through nutrient signaling with symbionts is key for maintaining animal-microbe intracellular nutritional symbiosis.
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Affiliation(s)
- Akihiro Tame
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
- School of Marine Biosciences, University of Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
- Faculty of Medical Sciences, Life Science Research Laboratory, University of Fukui, 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui 910-1193, Japan
| | - Tadashi Maruyama
- School of Marine Biosciences, University of Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Tetsuro Ikuta
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yoshihito Chikaraishi
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Nanako O. Ogawa
- Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Kiyotaka Takishita
- Department of Environmental Science, Fukuoka Women's University, Kasumigaoka 1-1-1, Higashi-ku, Fukuoka 813-8529, Japan
| | - Miwako Tsuda
- Institute for Extra-cutting-edge Science and Technology Avant-grade Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Miho Hirai
- Institute for Extra-cutting-edge Science and Technology Avant-grade Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-grade Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Naohiko Ohkouchi
- Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katsunori Fujikura
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Takao Yoshida
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
- School of Marine Biosciences, University of Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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Yamada R, Han SR, Park H, Oh TJ. Complete Genome Analysis of Subtercola sp. PAMC28395: Genomic Insights into Its Potential Role for Cold Adaptation and Biotechnological Applications. Microorganisms 2023; 11:1480. [PMID: 37374983 DOI: 10.3390/microorganisms11061480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
This study reports the complete genome sequence of Subtercola sp. PAMC28395, a strain isolated from cryoconite in Uganda. This strain possesses several active carbohydrate-active enzyme (CAZyme) genes involved in glycogen and trehalose metabolism. Additionally, two specific genes associated with α-galactosidase (GH36) and bacterial alpha-1,2-mannosidase (GH92) were identified in this strain. The presence of these genes indicates the likelihood that they can be expressed, enabling the strain to break down specific polysaccharides derived from plants or the shells of nearby crabs. The authors performed a comparative analysis of CAZyme patterns and biosynthetic gene clusters (BGCs) in several Subtercola strains and provided annotations describing the unique characteristics of these strains. The comparative analysis of BGCs revealed that four strains, including PAMC28395, have oligosaccharide BGCs, and we confirmed that the pentose phosphate pathway was configured perfectly in the genome of PAMC28395, which may be associated with adaptation to low temperatures. Additionally, all strains contained antibiotic resistance genes, indicating a complex self-resistance system. These results suggest that PAMC28395 can adapt quickly to the cold environment and produce energy autonomously. This study provides valuable information on novel functional enzymes, particularly CAZymes, that operate at low temperatures and can be used for biotechnological applications and fundamental research purposes.
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Affiliation(s)
- Ryoichi Yamada
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan 31460, Republic of Korea
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
| | - So-Ra Han
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan 31460, Republic of Korea
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan 31460, Republic of Korea
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea
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Muizelaar W, van Duinkerken G, Khan Z, Dijkstra J. Evaluation of 3 northwest European seaweed species on enteric methane production and lactational performance of Holstein-Friesian dairy cows. J Dairy Sci 2023:S0022-0302(23)00270-9. [PMID: 37225576 DOI: 10.3168/jds.2022-22749] [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: 09/09/2022] [Accepted: 01/23/2023] [Indexed: 05/26/2023]
Abstract
Seaweeds have been studied for their ability to reduce enteric methane emissions of ruminants when fed as a feed supplement. In vivo research with dairy cattle is mainly limited to the seaweed species Ascophyllum nodosum and Asparagopsis taxiformis, whereas in vitro gas production research covers a broader range of brown, red, and green seaweed species from different regions. The objective of the present study was to determine the effect of Chondrus crispus (Rhodophyta), Saccharina latissima (Phaeophyta), and Fucus serratus (Phaeophyta), 3 common northwest European seaweeds, on enteric methane production and lactational performance of dairy cattle. Sixty-four Holstein-Friesian dairy cattle (16 primiparous, 48 multiparous) averaging (mean ± standard deviation) 91 ± 22.6 d in milk and 35.4 ± 8.13 kg/d fat- and protein-corrected milk yield (FPCM) were randomly assigned to 1 of 4 treatments in a randomized complete block design. Cows were fed a partial mixed ration [54.2% grass silage, 20.8% corn silage, and 25.0% concentrate; dry matter (DM) basis] with additional concentrate bait in the milking parlor and the GreenFeed system (C-Lock Inc.). The 4 treatments consisted of a control diet without seaweed supplement (CON), or CON supplemented with 150 g/d (fresh weight of dried seaweed) of either C. crispus (CC), S. latissima (SL), or a 50/50 mix (DM basis) of F. serratus and S. latissima. Milk yield (28.7 vs. 27.5 kg/d, respectively), fat- and protein-corrected milk (FPCM) yield (31.4 vs. 30.2 kg/d, respectively), milk lactose content (4.57 vs. 4.52%, respectively), and lactose yield (1,308 vs. 1,246 g/d, respectively) increased for SL compared with CON. Milk protein content was lower for SL compared with the other treatments. Milk fat and protein contents; yields of fat, protein, lactose, and FPCM; feed efficiency; milk nitrogen efficiency; and somatic cell count did not differ between CON and the other treatments. Depending on week of experiment, milk urea content was higher for SL compared with CON and CC. No effects were observed of the treatments compared with CON for DM intake, number of visits to the GreenFeed, or gas emission (production, yield, or intensity) of CO2, CH4, and H2. In conclusion, the seaweeds evaluated did not decrease enteric CH4 emissions and did not negatively affect feed intake and lactational performance of dairy cattle. Milk yield, FPCM yield, milk lactose content, and lactose yield increased, and milk protein content decreased, with S. latissima.
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Affiliation(s)
- W Muizelaar
- Wageningen Livestock Research, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, the Netherlands; Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, the Netherlands.
| | - G van Duinkerken
- Wageningen Livestock Research, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - Z Khan
- Foundation BlueO2, Oude Haagweg 679, 2552 GM Den Haag, the Netherlands
| | - J Dijkstra
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, the Netherlands
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Zhang Z, Qian H, Wang Z, Pang Y, Guan X, Poetsch A, Wang D. Characterization of histone acetyltransferases and deacetylases and their roles in response to dehydration stress in Pyropia yezoensis (Rhodophyta). FRONTIERS IN PLANT SCIENCE 2023; 14:1133021. [PMID: 37260940 PMCID: PMC10227436 DOI: 10.3389/fpls.2023.1133021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/12/2023] [Indexed: 06/02/2023]
Abstract
Histone acetylation is one of the most pivotal epigenetic mechanisms in eukaryotes and has been tightly linked to the regulation of various genes controlling growth, development and response to environmental stresses in both animals and plants. Till date, the association of histone acetylation to dehydration stress in red algae and genes encoding the enzymes responsible for histone acetylation: histone acetyltransferases (HATs) or histone deacetylases (HDACs), remains largely unknown. In this study, in silico analysis of the red seaweed Pyropia yezoensis identified 6 HAT genes and 10 HDAC genes. These genes displayed good synteny in genome loci with their Pyropia haitanensis orthologs except for a putative gene duplication event in HDAC and a loss of one HAT gene in P. yezoensis. According to the conserved domains and phylogenetic analysis, they encoded three GCNA5-, one TAFII250- and one MYST-HAT, as well as five HDA1-and five SIRT-HDACs. The sirtuin-domain of Py06502 harbored a ~100 aa insert and interestingly, this insertion was specifically observed in Bangiales species. Two nuclear-localized HATs were transcriptionally up-regulated at the early stage of dehydration and so were two nuclear HDA1s when moderate dehydration started, suggesting their potential roles in modulating downstream gene expression to facilitate dehydration adaptation by changing histone acetylation patterns on relevant regulatory elements. This was experimentally confirmed by the increased decline in photosynthesis efficiency during dehydration when HAT and HDAC activities were inhibited by SAHA and MB-3, respectively. Transcriptional patterns of multiple dehydration-responsive genes after water loss were strongly affected by MB-3 or SAHA treatment. This study provides the first insight into the regulation and function of HAT/HDAC during stress adaptation in red algae.
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Affiliation(s)
- Zehao Zhang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huijuan Qian
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongshi Wang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Pang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaowei Guan
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ansgar Poetsch
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, North Rhine-Westphalia, Germany
| | - Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Phycobilisomes and Phycobiliproteins in the Pigment Apparatus of Oxygenic Photosynthetics: From Cyanobacteria to Tertiary Endosymbiosis. Int J Mol Sci 2023; 24:ijms24032290. [PMID: 36768613 PMCID: PMC9916406 DOI: 10.3390/ijms24032290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Eukaryotic photosynthesis originated in the course of evolution as a result of the uptake of some unstored cyanobacterium and its transformation to chloroplasts by an ancestral heterotrophic eukaryotic cell. The pigment apparatus of Archaeplastida and other algal phyla that emerged later turned out to be arranged in the same way. Pigment-protein complexes of photosystem I (PS I) and photosystem II (PS II) are characterized by uniform structures, while the light-harvesting antennae have undergone a series of changes. The phycobilisome (PBS) antenna present in cyanobacteria was replaced by Chl a/b- or Chl a/c-containing pigment-protein complexes in most groups of photosynthetics. In the form of PBS or phycobiliprotein aggregates, it was inherited by members of Cyanophyta, Cryptophyta, red algae, and photosynthetic amoebae. Supramolecular organization and architectural modifications of phycobiliprotein antennae in various algal phyla in line with the endosymbiotic theory of chloroplast origin are the subject of this review.
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Murakami M, Osanai T. Biochemical Properties of β-Amylase from Red Algae and Improvement of Its Thermostability through Immobilization. ACS OMEGA 2022; 7:36195-36205. [PMID: 36278071 PMCID: PMC9583313 DOI: 10.1021/acsomega.2c03315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
β-Amylase hydrolyzes polysaccharides, such as starch, into maltose. It is used as an industrial enzyme in the production of food and pharmaceuticals. The eukaryotic red alga Cyanidioschyzon merolae is a unicellular alga that grows at an optimum pH of 2.0-3.0 and an optimum temperature of 40-50 °C. By focusing on the thermostability and acid resistance of the proteins of C. merolae, we investigated the properties of β-amylase from C. merolae (hereafter CmBAM) and explored the possibility of using CmBAM as an industrial enzyme. CmBAM showed the highest activity at 47 °C and pH 6.0. CmBAM had a relatively higher specificity for amylose as a substrate than for starch. Immobilization of CmBAM on a silica gel carrier improved storage stability and thermostability, allowing the enzyme to be reused. The optimum temperature and pH of CmBAM were comparable to those of existing β-amylases from barley and wheat. C. merolae does not use amylose, but CmBAM has a substrate specificity for both amylose and amylopectin but not for glycogen. Among the several β-amylases reported, CmBAM was unique, with a higher specificity for amylose than for starch. The high specificity of CmBAM for amylose suggests that isoamylase and pullulanase, which cleave the α-1,6 bonds of starch, may act together in vivo. Compared with several reported immobilized plant-derived β-amylases, immobilized CmBAM was comparable to β-amylase, with the highest reusability and the third-highest storage stability at 30 days of storage. In addition, immobilized CmBAM has improved thermostability by 15-20 °C, which can lead to wider applications and easier handling.
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Dynamics of the Glycogen β-Particle Number in Rat Hepatocytes during Glucose Refeeding. Int J Mol Sci 2022; 23:ijms23169263. [PMID: 36012534 PMCID: PMC9409161 DOI: 10.3390/ijms23169263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Glycogen is an easily accessible source of energy for various processes. In hepatocytes, it can be found in the form of individual molecules (β-particles) and their agglomerates (α-particles). The glycogen content in hepatocytes depends on the physiological state and can vary due to the size and number of the particles. Using biochemical, cytofluorometric, interferometric and morphometric methods, the number of β-particles in rat hepatocytes was determined after 48 h of fasting at different time intervals after glucose refeeding. It has been shown that after starvation, hepatocytes contain ~1.6 × 108 β-particles. During refeeding, their number of hepatocytes gradually increases and reaches a maximum (~5.9 × 108) at 45 min after glucose administration, but then quickly decreases. The data obtained suggest that in cells there is a continuous synthesis and degradation of particles, and at different stages of life, one or another process predominates. It has been suggested that in the course of glycogenesis, pre-existing β-particles are replaced by those formed de novo. The main contribution to the deposition of glycogen is made by an increase in the glucose residue number in its molecules. The average diameter of β-particles of glycogen during glycogenesis increases from ~11 nm to 21 nm.
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Apriyanto A, Compart J, Fettke J. A review of starch, a unique biopolymer - Structure, metabolism and in planta modifications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111223. [PMID: 35351303 DOI: 10.1016/j.plantsci.2022.111223] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have α-1,4- and α-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.
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Affiliation(s)
- Ardha Apriyanto
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany
| | - Julia Compart
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany.
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21
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Mérida A, Fettke J. Starch granule initiation in Arabidopsis thaliana chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:688-697. [PMID: 34051021 DOI: 10.1111/tpj.15359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/14/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs.
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Affiliation(s)
- Angel Mérida
- Institute of Plant Biochemistry and Photosynthesis (IBVF), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla (US), Avda Américo Vespucio, 49, Sevilla, 41092, Spain
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, Potsdam-Golm, 14476, Germany
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Mak CA, Weis K, Henao T, Kuchtova A, Chen T, Sharma S, Meekins DA, Thalmann M, Vander Kooi CW, Raththagala M. Cooperative Kinetics of the Glucan Phosphatase Starch Excess4. Biochemistry 2021; 60:2425-2435. [PMID: 34319705 DOI: 10.1021/acs.biochem.1c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glucan phosphatases are members of a functionally diverse family of dual-specificity phosphatase (DSP) enzymes. The plant glucan phosphatase Starch Excess4 (SEX4) binds and dephosphorylates glucans, contributing to processive starch degradation in the chloroplast at night. Little is known about the complex kinetics of SEX4 when acting on its complex physiologically relevant glucan substrate. Therefore, we explored the kinetics of SEX4 against both insoluble starch and soluble amylopectin glucan substrates. SEX4 displays robust activity and a unique sigmoidal kinetic response to amylopectin, characterized by a Hill coefficient of 2.77 ± 0.63, a signature feature of cooperativity. We investigated the basis for this positive kinetic cooperativity and determined that the SEX4 carbohydrate-binding module (CBM) dramatically influences the binding cooperativity and substrate transformation rates. These findings provide insights into a previously unknown but important regulatory role for SEX4 in reversible starch phosphorylation and further advances our understanding of atypical kinetic mechanisms.
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Affiliation(s)
- Claudia A Mak
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
| | - Kenyon Weis
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
| | - Tiffany Henao
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
| | - Andrea Kuchtova
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Tiantian Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Savita Sharma
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - David A Meekins
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Matthias Thalmann
- The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40506, United States
| | - Madushi Raththagala
- Department of Chemistry, Skidmore College, Saratoga Springs, New York 12866, United States
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Ralton JE, Sernee MF, McConville MJ. Evolution and function of carbohydrate reserve biosynthesis in parasitic protists. Trends Parasitol 2021; 37:988-1001. [PMID: 34266735 DOI: 10.1016/j.pt.2021.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/28/2022]
Abstract
Nearly all eukaryotic cells synthesize carbohydrate reserves, such as glycogen, starch, or low-molecular-weight oligosaccharides. However, a number of parasitic protists have lost this capacity while others have lost, and subsequently evolved, entirely new pathways. Recent studies suggest that retention, loss, or acquisition of these pathways in different protists is intimately linked to their lifestyle. In particular, parasites with carbohydrate reserves often establish long-lived chronic infections and/or produce environmental cysts, whereas loss of these pathways is associated with parasites that have highly proliferative and metabolically active life-cycle stages. The evolution of mannogen biosynthesis in Leishmania and related parasites indicates that these pathways have played a role in defining the host range and niches occupied by some protists.
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Affiliation(s)
- Julie E Ralton
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia
| | - M Fleur Sernee
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia.
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Growth under Different Trophic Regimes and Synchronization of the Red Microalga Galdieria sulphuraria. Biomolecules 2021; 11:biom11070939. [PMID: 34202768 PMCID: PMC8301940 DOI: 10.3390/biom11070939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
The extremophilic unicellular red microalga Galdieria sulphuraria (Cyanidiophyceae) is able to grow autotrophically, or mixo- and heterotrophically with 1% glycerol as a carbon source. The alga divides by multiple fission into more than two cells within one cell cycle. The optimal conditions of light, temperature and pH (500 µmol photons m-2 s-1, 40 °C, and pH 3; respectively) for the strain Galdieria sulphuraria (Galdieri) Merola 002 were determined as a basis for synchronization experiments. For synchronization, the specific light/dark cycle, 16/8 h was identified as the precondition for investigating the cell cycle. The alga was successfully synchronized and the cell cycle was evaluated. G. sulphuraria attained two commitment points with midpoints at 10 and 13 h of the cell cycle, leading to two nuclear divisions, followed subsequently by division into four daughter cells. The daughter cells stayed in the mother cell wall until the beginning of the next light phase, when they were released. Accumulation of glycogen throughout the cell cycle was also described. The findings presented here bring a new contribution to our general understanding of the cell cycle in cyanidialean red algae, and specifically of the biotechnologically important species G. sulphuraria.
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Han SR, Kim B, Jang JH, Park H, Oh TJ. Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. BMC Genomics 2021; 22:403. [PMID: 34078272 PMCID: PMC8171050 DOI: 10.1186/s12864-021-07734-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. RESULTS Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. CONCLUSIONS We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.
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Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Jong Hwa Jang
- Department of Dental Hygiene, College of Health Science, Dankook University, 119 Dandae-ro, Dongnam-gu, 31116, Cheonan-si, Chungnam, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, 02841, Seoul, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea.
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de Freitas KEJ, dos Santos RS, Busanello C, de Carvalho Victoria F, Lopes JL, Wing RA, de Oliveira AC. Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza. PLANTS 2021; 10:plants10061057. [PMID: 34070565 PMCID: PMC8229393 DOI: 10.3390/plants10061057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/18/2022]
Abstract
Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar’s genetics, but the way in which their genes express different phenotypes is not well understood. Further analysis of variation of grain quality genes using new information obtained from the wild relatives of rice should provide important insights into the evolution and potential use of these genetic resources. All analyses were conducted using bioinformatics approaches. The analysis of the protein sequences of grain quality genes across the Oryza suggest that the deletion/mutation of amino acids in active sites result in variations that can negatively affect specific steps of starch biosynthesis in the endosperm. On the other hand, the complete deletion of some genes in the wild species may not affect the amylose content. Here we present new insights for Starch Synthesis-Related Genes (SSRGs) evolution from starch-specific rice phenotypes.
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Affiliation(s)
- Karine E. Janner de Freitas
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | | | - Carlos Busanello
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Filipe de Carvalho Victoria
- Núcleo de Estudos da Vegetação Antártica—NEVA, Campus São Gabriel Federal do Pampa (UNIPAMPA), São Gabriel 97030, Brazil;
| | - Jennifer Luz Lopes
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Rod A. Wing
- The School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, AZ 97030, USA;
- Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal 23955, Saudi Arabia
| | - Antonio Costa de Oliveira
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
- Correspondence:
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Photosynthetic monitoring techniques indicate maximum glycogen accumulation in nitrogen-limited Synechocystis sp. PCC 6803 culture. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gupta JK, Srivastava S. The Effect of Promoter and RBS Combination on the Growth and Glycogen Productivity of Sodium-Dependent Bicarbonate Transporter (SbtA) Overexpressing Synechococcus sp. PCC 7002 Cells. Front Microbiol 2021; 12:607411. [PMID: 33927699 PMCID: PMC8076525 DOI: 10.3389/fmicb.2021.607411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Sodium dependent bicarbonate transporter, SbtA is a high-affinity, inducible bicarbonate transporter in cyanobacterial cells. Our previous work has shown that overexpression of this transporter can significantly increase growth and glycogen accumulation in Synechococcus sp. PCC 7002 cells. In this work, we have tested the effect of two different RBS sequences (RBS1: GGAGGA and RBS2: AGGAGA) and three different promoters (PcpcB, PcpcB560, and PrbcL2) on the growth and glycogen production in SbtA-overexpressing Synechococcus sp. PCC 7002 cells. Our results show that PcpcB or PcpcB560 were more effective than PrbcL2 in increasing the growth and glycogen content. The choice of RBS sequence had relatively minor effect, though RBS2 was more effective than RBS1. The transformant E, with PcpcB560 and RBS2, showed the highest growth. The biomass after 5 days of growth on air or 1% CO2 was increased by about 90% in the strain E compared to PCC 7002 cells. All transformants overexpressing SbtA had higher glycogen content. However, growing the cells with bubbling of 1% CO2 did not increase cellular glycogen content any further. The strain E had about 80% higher glycogen content compared to WT PCC 7002 cells. Therefore, the glycogen productivity of the strain E grown with air-bubbling was about 2.5-fold that of the WT PCC 7002 cells grown similarly. Additionally, some of the transformants had higher chlorophyll content while all the transformants had higher carotenoid content compared to the PCC 7002 cells, suggesting interaction between carbon transport and pigment levels. Thus, this work shows that the choice of photosynthetic promoters and RBSs sequences can impact growth and glycogen accumulation in SbtA-overexpressing cells.
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Affiliation(s)
- Jai Kumar Gupta
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.,Department of Biotechnology-International Centre for Genetic Engineering and Biotechnology (DBT-ICGEB), Centre for Advanced Bioenergy Research, New Delhi, India
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29
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Ye SQ, Zou Y, Zheng QW, Liu YL, Li RR, Lin JF, Guo LQ. TMT-MS/MS proteomic analysis of the carbohydrate-active enzymes in the fruiting body of Pleurotus tuoliensis during storage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:1879-1891. [PMID: 32894778 DOI: 10.1002/jsfa.10803] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 08/21/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The fruiting body of Pleurotus tuoliensis deteriorates rapidly after harvest, causing a decline in its commercial value and a great reduction in its shelf life. According to the present research, carbohydrate-active enzymes (CAZymes) may cause the softening, liquefaction and autolysis of mature mushrooms after harvest. To further understand the in vivo molecular mechanism of CAZymes affecting the postharvest quality of P. tuoliensis fruiting bodies, a tandem mass tags labelling combined liquid chromatography-tandem mass spectrometry (TMT-MS/MS) proteomic analysis was performed on P. tuoliensis fruiting bodies during storage at 25 °C. RESULTS A total of 4737 proteins were identified, which had at least one unique peptide and had a confidence level above 95%. Consequently, 1307 differentially expressed proteins (DEPs) were recruited using the criteria of abundance fold change (FC) >1.5 or < 0.67 and P < 0.05. The identified proteins were annotated by dbCAN2, a meta server for automated CAZymes annotation. Subsequently, 222 CAZymes were obtained. Several CAZymes participating in the cell wall degradation process, including β-glucosidase, glucan 1,3-β-glucosidase, endo-1,3(4)-β-glucanase and chitinases, were significantly upregulated during storage. The protein expression level of CAZymes, such as xylanase, amylase and glucoamylase, were upregulated significantly, which may participate in the P. tuoliensis polysaccharide degradation. CONCLUSIONS The identified CAZymes degraded the polysaccharides and lignin, destroying the cell wall structure, preventing cell wall remodeling, causing a loss of nutrients and the browning phenomenon, accelerating the deterioration of P. tuoliensis fruiting body. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Si-Qiang Ye
- College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, 510640, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510640, China
| | - Yuan Zou
- College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, 510640, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510640, China
| | - Qian-Wang Zheng
- College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, 510640, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510640, China
| | - Ying-Li Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Rui-Rong Li
- College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, 510640, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510640, China
| | - Jun-Fang Lin
- College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, 510640, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510640, China
| | - Li-Qiong Guo
- College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, 510640, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510640, China
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Hinchliffe JD, Parassini Madappura A, Syed Mohamed SMD, Roy I. Biomedical Applications of Bacteria-Derived Polymers. Polymers (Basel) 2021; 13:1081. [PMID: 33805506 PMCID: PMC8036740 DOI: 10.3390/polym13071081] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Plastics have found widespread use in the fields of cosmetic, engineering, and medical sciences due to their wide-ranging mechanical and physical properties, as well as suitability in biomedical applications. However, in the light of the environmental cost of further upscaling current methods of synthesizing many plastics, work has recently focused on the manufacture of these polymers using biological methods (often bacterial fermentation), which brings with them the advantages of both low temperature synthesis and a reduced reliance on potentially toxic and non-eco-friendly compounds. This can be seen as a boon in the biomaterials industry, where there is a need for highly bespoke, biocompatible, processable polymers with unique biological properties, for the regeneration and replacement of a large number of tissue types, following disease. However, barriers still remain to the mass-production of some of these polymers, necessitating new research. This review attempts a critical analysis of the contemporary literature concerning the use of a number of bacteria-derived polymers in the context of biomedical applications, including the biosynthetic pathways and organisms involved, as well as the challenges surrounding their mass production. This review will also consider the unique properties of these bacteria-derived polymers, contributing to bioactivity, including antibacterial properties, oxygen permittivity, and properties pertaining to cell adhesion, proliferation, and differentiation. Finally, the review will select notable examples in literature to indicate future directions, should the aforementioned barriers be addressed, as well as improvements to current bacterial fermentation methods that could help to address these barriers.
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Affiliation(s)
| | | | | | - Ipsita Roy
- Department of Materials Science and Engineering, Faculty of Engineering, University of Sheffield, Sheffield S1 3JD, UK; (J.D.H.); (A.P.M.); (S.M.D.S.M.)
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He Z, Zou T, Xiao Q, Yuan G, Liu M, Tao Y, Zhou D, Zhang X, Deng Q, Wang S, Zheng A, Zhu J, Liang Y, Yu X, Wang A, Liu H, Wang L, Li P, Li S. An L-type lectin receptor-like kinase promotes starch accumulation during rice pollen maturation. Development 2021; 148:dev.196378. [PMID: 33658224 DOI: 10.1242/dev.196378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 02/22/2021] [Indexed: 01/27/2023]
Abstract
Starch accumulation is key for the maturity of rice pollen grains; however, the regulatory mechanism underlying this process remains unknown. Here, we have isolated a male-sterile rice mutant, abnormal pollen 1 (ap1), which produces nonviable pollen grains with defective starch accumulation. Functional analysis revealed that AP1 encodes an active L-type lectin receptor-like kinase (L-LecRLK). AP1 is localized to the plasma membrane and its transcript is highly accumulated in pollen during the starch synthesis phase. RNA-seq and phosphoproteomic analysis revealed that the expression/phosphorylation levels of numerous genes/proteins involved in starch and sucrose metabolism pathway were significantly altered in the mutant pollen, including a known rice UDP-glucose pyrophosphorylase (OsUGP2). We further found that AP1 physically interacts with OsUGP2 to elevate its enzymatic activity, likely through targeted phosphorylation. These findings revealed a novel role of L-LecRLK in controlling pollen maturity via modulating sucrose and starch metabolism.
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Affiliation(s)
- Zhiyuan He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiao Xiao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqiang Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Tao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Dan Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Aiping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yueyang Liang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiumei Yu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Aijun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lingxia Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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Colpaert M, Kadouche D, Ducatez M, Pillonel T, Kebbi-Beghdadi C, Cenci U, Huang B, Chabi M, Maes E, Coddeville B, Couderc L, Touzet H, Bray F, Tirtiaux C, Ball S, Greub G, Colleoni C. Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae. Commun Biol 2021; 4:296. [PMID: 33674787 PMCID: PMC7935935 DOI: 10.1038/s42003-021-01794-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
The order Chlamydiales includes obligate intracellular pathogens capable of infecting mammals, fishes and amoeba. Unlike other intracellular bacteria for which intracellular adaptation led to the loss of glycogen metabolism pathway, all chlamydial families maintained the nucleotide-sugar dependent glycogen metabolism pathway i.e. the GlgC-pathway with the notable exception of both Criblamydiaceae and Waddliaceae families. Through detailed genome analysis and biochemical investigations, we have shown that genome rearrangement events have resulted in a defective GlgC-pathway and more importantly we have evidenced a distinct trehalose-dependent GlgE-pathway in both Criblamydiaceae and Waddliaceae families. Altogether, this study strongly indicates that the glycogen metabolism is retained in all Chlamydiales without exception, highlighting the pivotal function of storage polysaccharides, which has been underestimated to date. We propose that glycogen degradation is a mandatory process for fueling essential metabolic pathways that ensure the survival and virulence of extracellular forms i.e. elementary bodies of Chlamydiales.
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Affiliation(s)
- Matthieu Colpaert
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Derifa Kadouche
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mathieu Ducatez
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Ugo Cenci
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Binquan Huang
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/School of Agriculture, Yunnan University, Kunming, China
| | - Malika Chabi
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Emmanuel Maes
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Bernadette Coddeville
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Loïc Couderc
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Hélène Touzet
- University of Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Fabrice Bray
- University of Lille, CNRS, USR 3290-MSAP-Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Catherine Tirtiaux
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Steven Ball
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Christophe Colleoni
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
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Cyanobacterial branching enzymes bind to α-glucan via surface binding sites. Arch Biochem Biophys 2021; 702:108821. [PMID: 33662318 DOI: 10.1016/j.abb.2021.108821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
Besides their catalysis, specific interactions between starch/glycogen processing enzymes and their substrates have been reported. Multiple branching enzyme (BE) isoforms, BE1, BE2, and BE3, have been found in a limited number of cyanobacterial species that are characterized by amylopectin accumulation. Seven surface binding sites (SBSs) located away from the active site have been identified in crystal structures of cyanobacterial BE1 from Crocosphaera subtropica (Cyanothece sp.) ATCC 51142 (51142BE1). In the present study, binding affinity toward amylopectin, amylose, and glycogen was investigated for wild-type 51142BE1 and its mutants (residues at SBSs important for sugar-binding were replaced by alanine). These enzymes showed retarded mobility during electrophoresis in non-denaturing polyacrylamide gels in the presence of polysaccharides. This was caused by interactions between the enzymes and the polysaccharides, enabling calculation of the dissociation constants (Kd values) of the enzymes toward the polysaccharides. Mutational analysis indicated that particular domains of the protein (domains A and C) were involved in the polysaccharide binding. Kd values toward the polysaccharides were also measured for 10 BE isoforms (five BE1, three BE2, and two BE3) from 5 cyanobacterial strains. All BEs displayed much lower Kd values (higher affinity) toward amylopectin and amylose than toward glycogen, as described for plant BEs. In addition, one BE2 displayed exceptionally high Kd values (low affinity), while two BE3 exhibited multiple Kd values to all polysaccharides. These results could be ascribed to sequence variations in the SBSs, irrespective of the catalytic specificity.
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Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability. Sci Rep 2021; 11:4836. [PMID: 33649356 PMCID: PMC7921382 DOI: 10.1038/s41598-021-84286-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/15/2021] [Indexed: 12/23/2022] Open
Abstract
To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary insights of Bacillus species from cold environments. Bacillus sp. TK-2, isolated from the soil of Changbai Mountain, is a gram-positive bacterium with cold adaptation characteristics. In this study, we present the annotated complete genome sequence of Bacillus sp. TK-2. The genome comprised 5,286,177 bp with a GC content of 35.88%, 5293 protein-encoding genes, 32 rRNA, and 77 tRNA. Numerous genes related to cold adaptation were detected in the genome of Bacillus sp. TK-2, mainly involving in energy supply, regulation of cell membrane fluidity, antioxidant, and molecular chaperones. In addition, the strain TK-2 classified in the Bacillus groups was distributed on a terminal branch with Bacillus cereus A1 by Blastn and phylogenetic analysis in NCBI database. Complete genome sequences of the strain TK-2 and Bacillus cereus A1 were compared by the online tool "Average Nucleotide Identity", showing that the average nucleotide identity of these two strains was 98.26%. In parallel, A comparative analysis of the genomes of both Bacillus sp. TK-2 and Bacillus cereus A1 was conducted. Through the analysis of core and specific genes with cd-hit, it was found that the two strains had 5691 pan gene, 4524 core gene, and 1167 specific gene clusters. Among the 624 specific gene clusters of Bacillus sp. TK-2, some cold tolerance genes were detected, which implied the unique adaptability of Bacillus sp. TK-2 in long-term low temperature environments. Importantly, enzyme-encoding genes related to the degradation of polysaccharides such as cellulose and hemicellulose were detected in the 477 CAZyme genes of this genome. This work on sequencing and bioinformatics analysis of the complete sequence of Bacillus sp. TK-2 promote the application and in-depth research of low-temperature biotechnology.
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Chabi M, Leleu M, Fermont L, Colpaert M, Colleoni C, Ball SG, Cenci U. Retracing Storage Polysaccharide Evolution in Stramenopila. FRONTIERS IN PLANT SCIENCE 2021; 12:629045. [PMID: 33747010 PMCID: PMC7965971 DOI: 10.3389/fpls.2021.629045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 05/10/2023]
Abstract
Eukaryotes most often synthesize storage polysaccharides in the cytosol or vacuoles in the form of either alpha (glycogen/starch)- or beta-glucosidic (chrysolaminarins and paramylon) linked glucan polymers. In both cases, the glucose can be packed either in water-soluble (glycogen and chrysolaminarins) or solid crystalline (starch and paramylon) forms with different impacts, respectively, on the osmotic pressure, the glucose accessibility, and the amounts stored. Glycogen or starch accumulation appears universal in all free-living unikonts (metazoa, fungi, amoebozoa, etc.), as well as Archaeplastida and alveolata, while other lineages offer a more complex picture featuring both alpha- and beta-glucan accumulators. We now infer the distribution of these polymers in stramenopiles through the bioinformatic detection of their suspected metabolic pathways. Detailed phylogenetic analysis of key enzymes of these pathways correlated to the phylogeny of Stramenopila enables us to retrace the evolution of storage polysaccharide metabolism in this diverse group of organisms. The possible ancestral nature of glycogen metabolism in eukaryotes and the underlying source of its replacement by beta-glucans are discussed.
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Affiliation(s)
- Malika Chabi
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marie Leleu
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Léa Fermont
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Matthieu Colpaert
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Christophe Colleoni
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Steven G. Ball
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Ugo Cenci
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- *Correspondence: Ugo Cenci,
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Chistyakova L, Bezborodkina N, Berdieva M, Radaev A, Goodkov A. The nature and features of organization of reserve polysaccharides in three Pelomyxa species (Archamoebea, Pelobiontida). PROTOPLASMA 2020; 257:1701-1708. [PMID: 32829470 DOI: 10.1007/s00709-020-01546-5] [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: 06/02/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The nature and features of organization of reserve polysaccharides in three species of the genus Pelomyxa-P. palustris, P. belevskii, and P. stagnalis-were studied using light and transmission electron microscopy. We applied the periodic acid-Schiff reaction that is a highly selective method for detecting glycogen. The fluorescent dye auramine-SO2 (Au-SO2) was used as a Schiff-type reagent. The densely packed aggregates of glycogen that form the morphologically differentiated organelle-like bodies are revealed in the cytoplasm in all studied species. The organization of these bodies is characterized by the species-specific features, while in most cases, their size and number in the cells vary depending on the season of the year. Although in all the cases we studied, these bodies do not have their own boundary membrane, in fact, they are surrounded by membranous structures. These structures differ in a variety of Pelomyxa species. We concluded that there are two groups of species in the genus Pelomyxa. The first one includes organisms containing glycogen structures in the cytoplasm (P. palustris, P. belevskii, P. stagnalis, P. binucleata, P. corona, P. secunda). No inclusions resembling glycogen bodies were found in P. flava, P. paradoxa, P. gruberi, and P. prima that form the second group.
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Affiliation(s)
- Ludmila Chistyakova
- Zoological Institute Russian Academy of Sciences, Universitetskaya Emb. 1, 199034, St. Petersburg, Russia.
| | - Natalia Bezborodkina
- Zoological Institute Russian Academy of Sciences, Universitetskaya Emb. 1, 199034, St. Petersburg, Russia
| | - Mariia Berdieva
- Institute of Cytology Russian Academy of Sciences, 194064, St. Petersburg, Russia
| | - Anton Radaev
- Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Andrew Goodkov
- Institute of Cytology Russian Academy of Sciences, 194064, St. Petersburg, Russia
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Stairs CW, Dharamshi JE, Tamarit D, Eme L, Jørgensen SL, Spang A, Ettema TJG. Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. SCIENCE ADVANCES 2020; 6:eabb7258. [PMID: 32923644 PMCID: PMC7449678 DOI: 10.1126/sciadv.abb7258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The origin of eukaryotes is a major open question in evolutionary biology. Multiple hypotheses posit that eukaryotes likely evolved from a syntrophic relationship between an archaeon and an alphaproteobacterium based on H2 exchange. However, there are no strong indications that modern eukaryotic H2 metabolism originated from archaea or alphaproteobacteria. Here, we present evidence for the origin of H2 metabolism genes in eukaryotes from an ancestor of the Anoxychlamydiales-a group of anaerobic chlamydiae, newly described here, from marine sediments. Among Chlamydiae, these bacteria uniquely encode genes for H2 metabolism and other anaerobiosis-associated pathways. Phylogenetic analyses of several components of H2 metabolism reveal that Anoxychlamydiales homologs are the closest relatives to eukaryotic sequences. We propose that an ancestor of the Anoxychlamydiales contributed these key genes during the evolution of eukaryotes, supporting a mosaic evolutionary origin of eukaryotic metabolism.
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Affiliation(s)
- Courtney W. Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jennah E. Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay, France
| | - Steffen L. Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, Netherlands
| | - Thijs J. G. Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, Netherlands
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Mandalasi M, Kim HW, Thieker D, Sheikh MO, Gas-Pascual E, Rahman K, Zhao P, Daniel NG, van der Wel H, Ichikawa HT, Glushka JN, Wells L, Woods RJ, Wood ZA, West CM. A terminal α3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii. J Biol Chem 2020; 295:9223-9243. [PMID: 32414843 PMCID: PMC7335778 DOI: 10.1074/jbc.ra120.013792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/14/2020] [Indexed: 12/29/2022] Open
Abstract
Skp1, a subunit of E3 Skp1/Cullin-1/F-box protein ubiquitin ligases, is modified by a prolyl hydroxylase that mediates O2 regulation of the social amoeba Dictyostelium and the parasite Toxoplasma gondii The full effect of hydroxylation requires modification of the hydroxyproline by a pentasaccharide that, in Dictyostelium, influences Skp1 structure to favor assembly of Skp1/F-box protein subcomplexes. In Toxoplasma, the presence of a contrasting penultimate sugar assembled by a different glycosyltransferase enables testing of the conformational control model. To define the final sugar and its linkage, here we identified the glycosyltransferase that completes the glycan and found that it is closely related to glycogenin, an enzyme that may prime glycogen synthesis in yeast and animals. However, the Toxoplasma enzyme catalyzes formation of a Galα1,3Glcα linkage rather than the Glcα1,4Glcα linkage formed by glycogenin. Kinetic and crystallographic experiments showed that the glycosyltransferase Gat1 is specific for Skp1 in Toxoplasma and also in another protist, the crop pathogen Pythium ultimum The fifth sugar is important for glycan function as indicated by the slow-growth phenotype of gat1Δ parasites. Computational analyses indicated that, despite the sequence difference, the Toxoplasma glycan still assumes an ordered conformation that controls Skp1 structure and revealed the importance of nonpolar packing interactions of the fifth sugar. The substitution of glycosyltransferases in Toxoplasma and Pythium by an unrelated bifunctional enzyme that assembles a distinct but structurally compatible glycan in Dictyostelium is a remarkable case of convergent evolution, which emphasizes the importance of the terminal α-galactose and establishes the phylogenetic breadth of Skp1 glycoregulation.
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Affiliation(s)
- Msano Mandalasi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Hyun W Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - David Thieker
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - M Osman Sheikh
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Elisabet Gas-Pascual
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Kazi Rahman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Nitin G Daniel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - H Travis Ichikawa
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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Zhu RM, Chai S, Zhang ZZ, Ma CL, Zhang Y, Li S. Arabidopsis Chloroplast protein for Growth and Fertility1 (CGF1) and CGF2 are essential for chloroplast development and female gametogenesis. BMC PLANT BIOLOGY 2020; 20:172. [PMID: 32306898 PMCID: PMC7168881 DOI: 10.1186/s12870-020-02393-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Chloroplasts are essential organelles of plant cells for not only being the energy factory but also making plant cells adaptable to different environmental stimuli. The nuclear genome encodes most of the chloroplast proteins, among which a large percentage of membrane proteins have yet to be functionally characterized. RESULTS We report here functional characterization of two nuclear-encoded chloroplast proteins, Chloroplast protein for Growth and Fertility (CGF1) and CGF2. CGF1 and CGF2 are expressed in diverse tissues and developmental stages. Proteins they encode are associated with chloroplasts through a N-terminal chloroplast-targeting signal in green tissues but also located at plastids in roots and seeds. Mutants of CGF1 and CGF2 generated by CRISPR/Cas9 exhibited vegetative defects, including reduced leaf size, dwarfism, and abnormal cell death. CGF1 and CGF2 redundantly mediate female gametogenesis, likely by securing local energy supply. Indeed, mutations of both genes impaired chloroplast integrity whereas exogenous sucrose rescued the growth defects of the CGF double mutant. CONCLUSION This study reports that two nuclear-encoded chloroplast proteins, Chloroplast protein for Growth and Fertility (CGF1) and CGF2, play important roles in vegetative growth, in female gametogenesis, and in embryogenesis likely by mediating chloroplast integrity and development.
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Affiliation(s)
- Rui-Min Zhu
- State Key laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Sen Chai
- State Key laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhuang-Zhuang Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Chang-Le Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Yan Zhang
- State Key laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Sha Li
- State Key laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
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Zayed A, Ulber R. Fucoidans: Downstream Processes and Recent Applications. Mar Drugs 2020; 18:E170. [PMID: 32197549 PMCID: PMC7142712 DOI: 10.3390/md18030170] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/14/2020] [Accepted: 03/15/2020] [Indexed: 02/06/2023] Open
Abstract
Fucoidans are multifunctional marine macromolecules that are subjected to numerous and various downstream processes during their production. These processes were considered the most important abiotic factors affecting fucoidan chemical skeletons, quality, physicochemical properties, biological properties and industrial applications. Since a universal protocol for fucoidans production has not been established yet, all the currently used processes were presented and justified. The current article complements our previous articles in the fucoidans field, provides an updated overview regarding the different downstream processes, including pre-treatment, extraction, purification and enzymatic modification processes, and shows the recent non-traditional applications of fucoidans in relation to their characters.
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Affiliation(s)
- Ahmed Zayed
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany;
- Department of Pharmacognosy, Tanta University, College of Pharmacy, El Guish Street, Tanta 31527, Egypt
| | - Roland Ulber
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany;
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Monroe JD. Involvement of five catalytically active Arabidopsis β-amylases in leaf starch metabolism and plant growth. PLANT DIRECT 2020; 4:e00199. [PMID: 32072133 PMCID: PMC7011640 DOI: 10.1002/pld3.199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/16/2019] [Accepted: 12/27/2019] [Indexed: 05/14/2023]
Abstract
Starch degradation in chloroplasts requires β-amylase (BAM) activity, but in Arabidopsis, there are nine BAM proteins, five of which are thought to be catalytic. Although single-gene knockouts revealed the necessity of BAM3 for starch degradation, contributions of other BAMs are poorly understood. Moreover, it is not possible to detect the contribution of individual BAMs in plants containing multiple active BAMs. Therefore, we constructed a set of five quadruple mutants each expressing only one catalytically active BAM, and a quintuple mutant missing all of these BAMs (B-Null). Using these mutants, we assessed the influence of each individual BAM on plant growth and on leaf starch degradation. Both BAM1 and BAM3 alone support wild-type (WT) levels of growth. BAM3 alone is sufficient to degrade leaf starch completely whereas BAM1 alone can only partially degrade leaf starch. In contrast, BAM2, BAM5, and BAM6 have no detectable effect on starch degradation or plant growth, being comparable with the B-Null plants. B-Null plant extracts contained no measurable amylase activity, whereas BAM3 and BAM1 contributed about 70% and 14% of the WT activity, respectively. BAM2 activity was low but detectable and BAM6 contributed no measurable activity. Interestingly, activity of BAM1 and BAM3 in the mutants varied little developmentally or diurnally, and did not increase appreciably in response to osmotic or cold stress. With these genetic lines, we now have new opportunities to investigate members of this diverse gene family.
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Gupta JK, Rai P, Jain KK, Srivastava S. Overexpression of bicarbonate transporters in the marine cyanobacterium Synechococcus sp. PCC 7002 increases growth rate and glycogen accumulation. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:17. [PMID: 32015756 PMCID: PMC6988372 DOI: 10.1186/s13068-020-1656-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/13/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Synechococcus sp. PCC 7002 is an attractive organism as a feedstock and for photoautotrophic production of biofuels and biochemicals due to its fast growth and ability to grow in marine/brackish medium. Previous studies suggest that the growth of this organism is limited by the HCO3 - transport across the cytoplasmic membrane. Tools for genetic engineering are well established for this cyanobacterium, which makes it possible to overexpress genes of interest. RESULTS In this work, we overexpressed two different native Na+-dependent carbon transporters viz., SbtA and BicA in Synechococcus sp. PCC 7002 cells under the influence of a strong light-inducible promoter and a strong RBS sequence. The overexpression of these transporters enhanced biomass by about 50%, increased intracellular glycogen about 50%, and increased extracellular carbohydrate up to threefold. Importantly, the biomass and glycogen productivity of the transformants with air bubbling was even higher than that of WT cells with 1% CO2 bubbling. The overexpression of these transporters was associated with an increased carotenoid content without altering the chl a content. CONCLUSIONS Our work shows the utility of increased carbon transport in improving the growth as well as product formation in a marine cyanobacterium and will serve to increase the utility of this organism as a potential cell factory.
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Affiliation(s)
- Jai Kumar Gupta
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Preeti Rai
- DBT-ICGEB Centre for Advanced Bioenergy Research, New Delhi, India
| | | | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, New Delhi, India
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Lawrence TJ, Amrine KCH, Swingley WD, Ardell DH. tRNA functional signatures classify plastids as late-branching cyanobacteria. BMC Evol Biol 2019; 19:224. [PMID: 31818253 PMCID: PMC6902448 DOI: 10.1186/s12862-019-1552-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/29/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. RESULTS Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. CONCLUSIONS Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.
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Affiliation(s)
- Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831 USA
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
| | - Katherine CH Amrine
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
- Insight Data Science, 500 3rd St., San Francisco, CA, 94107 USA
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, 1425 Lincoln Hwy., DeKalb, IL, 60115 USA
| | - David H Ardell
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
- Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
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What Is in Store for EPS Microalgae in the Next Decade? Molecules 2019; 24:molecules24234296. [PMID: 31775355 PMCID: PMC6930497 DOI: 10.3390/molecules24234296] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 11/17/2022] Open
Abstract
Microalgae and their metabolites have been an El Dorado since the turn of the 21st century. Many scientific works and industrial exploitations have thus been set up. These developments have often highlighted the need to intensify the processes for biomass production in photo-autotrophy and exploit all the microalgae value including ExoPolySaccharides (EPS). Indeed, the bottlenecks limiting the development of low value products from microalgae are not only linked to biology but also to biological engineering problems including harvesting, recycling of culture media, photoproduction, and biorefinery. Even respecting the so-called "Biorefinery Concept", few applications had a chance to emerge and survive on the market. Thus, exploiting EPS from microalgae for industrial applications in some low-value markets such as food is probably not a mature proposition considering the competitiveness of polysaccharides from terrestrial plants, macroalgae, and bacteria. However, it does not imply drawing a line on their uses but rather "thinking them" differently. This review provides insights into microalgae, EPS, and their exploitation. Perspectives on issues affecting the future of EPS microalgae are also addressed with a critical point of view.
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Gruber A, Haferkamp I. Nucleotide Transport and Metabolism in Diatoms. Biomolecules 2019; 9:E761. [PMID: 31766535 PMCID: PMC6995639 DOI: 10.3390/biom9120761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 01/01/2023] Open
Abstract
Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology.
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Affiliation(s)
- Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Ilka Haferkamp
- Pflanzenphysiologie, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany;
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Slugina MA, Shchennikova AV, Kochieva EZ. The expression pattern of the Pho1a genes encoding plastidic starch phosphorylase correlates with the degradation of starch during fruit ripening in green-fruited and red-fruited tomato species. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:1146-1157. [PMID: 31615619 DOI: 10.1071/fp18317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Genes encoding plastidic starch phosphorylase Pho1a were identified in 10 tomato species (Solanum section Lycopersicon). Pho1a genes showed higher variability in green-fruited than in red-fruited tomato species, but had an extremely low polymorphism level compared with other carbohydrate metabolism genes and an unusually low ratio of intron to exon single nucleotide polymorphisms (SNPs). In red-fruited species, Pho1a was expressed in all analysed tissues, including fruit at different developmental stages, with the highest level in mature green fruit, which is strong sink organ importing sucrose and accumulating starch. In green-fruited species Solanum peruvianum and Solanum arcanum, the Pho1a expression level was similar in mature green and ripe fruit, whereas in Solanum chmielewskii, it was higher in ripe fruit, and in Solanum habrochaites, the dynamics of fruit-specific Pho1a expression was similar to that in red-fruited tomatoes. During fruit development, in red-fruited Solanum lycopersicum, sucrose level was low, the monosaccharide content increased; in green-fruited S. peruvianum, the sucrose concentration increased and those of monosaccharides decreased. In both species, the starch content and Pho1a expression were downregulated. The evolutionary topology based on Pho1a sequences was consistent with the current division of tomatoes into red-fruited and green-fruited species, except for S. habrochaites.
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Affiliation(s)
- Maria A Slugina
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky prospect. 33, bld. 2, Moscow 119071, Russia; and Corresponding author.
| | - Anna V Shchennikova
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky prospect. 33, bld. 2, Moscow 119071, Russia
| | - Elena Z Kochieva
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky prospect. 33, bld. 2, Moscow 119071, Russia; and Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russia
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47
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Mock M, Schmid A, Bühler K. Photoautotrophic production of succinate via the oxidative branch of the tricarboxylic acid cycle influences glycogen accumulation in Synechocystis sp. PCC 6803. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Brewer MK, Uittenbogaard A, Austin GL, Segvich DM, DePaoli-Roach A, Roach PJ, McCarthy JJ, Simmons ZR, Brandon JA, Zhou Z, Zeller J, Young LEA, Sun RC, Pauly JR, Aziz NM, Hodges BL, McKnight TR, Armstrong DD, Gentry MS. Targeting Pathogenic Lafora Bodies in Lafora Disease Using an Antibody-Enzyme Fusion. Cell Metab 2019; 30:689-705.e6. [PMID: 31353261 PMCID: PMC6774808 DOI: 10.1016/j.cmet.2019.07.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022]
Abstract
Lafora disease (LD) is a fatal childhood epilepsy caused by recessive mutations in either the EPM2A or EPM2B gene. A hallmark of LD is the intracellular accumulation of insoluble polysaccharide deposits known as Lafora bodies (LBs) in the brain and other tissues. In LD mouse models, genetic reduction of glycogen synthesis eliminates LB formation and rescues the neurological phenotype. Therefore, LBs have become a therapeutic target for ameliorating LD. Herein, we demonstrate that human pancreatic α-amylase degrades LBs. We fused this amylase to a cell-penetrating antibody fragment, and this antibody-enzyme fusion (VAL-0417) degrades LBs in vitro and dramatically reduces LB loads in vivo in Epm2a-/- mice. Using metabolomics and multivariate analysis, we demonstrate that VAL-0417 treatment of Epm2a-/- mice reverses the metabolic phenotype to a wild-type profile. VAL-0417 is a promising drug for the treatment of LD and a putative precision therapy platform for intractable epilepsy.
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Affiliation(s)
- M Kathryn Brewer
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Annette Uittenbogaard
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Grant L Austin
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Dyann M Segvich
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anna DePaoli-Roach
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Peter J Roach
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - John J McCarthy
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Zoe R Simmons
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jason A Brandon
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Zhengqiu Zhou
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jill Zeller
- Northern Biomedical Research, Spring Lake, MI 49456, USA
| | - Lyndsay E A Young
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Ramon C Sun
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - James R Pauly
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | | | | | | | | | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, USA; University of Kentucky Epilepsy & Brain Metabolism Alliance, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
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Han SR, Kim DW, Kim B, Chi YM, Kang S, Park H, Jung SH, Lee JH, Oh TJ. Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation. Microb Pathog 2019; 137:103759. [PMID: 31560973 DOI: 10.1016/j.micpath.2019.103759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022]
Abstract
Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.
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Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Do Wan Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Young Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea; Genome-based BioIT Convergence Institute, Asan, South Korea; Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea.
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50
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Structural basis of glycogen metabolism in bacteria. Biochem J 2019; 476:2059-2092. [PMID: 31366571 DOI: 10.1042/bcj20170558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The evolution of metabolic pathways is a major force behind natural selection. In the spotlight of such process lies the structural evolution of the enzymatic machinery responsible for the central energy metabolism. Specifically, glycogen metabolism has emerged to allow organisms to save available environmental surplus of carbon and energy, using dedicated glucose polymers as a storage compartment that can be mobilized at future demand. The origins of such adaptive advantage rely on the acquisition of an enzymatic system for the biosynthesis and degradation of glycogen, along with mechanisms to balance the assembly and disassembly rate of this polysaccharide, in order to store and recover glucose according to cell energy needs. The first step in the classical bacterial glycogen biosynthetic pathway is carried out by the adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase. This allosteric enzyme synthesizes ADP-glucose and acts as a point of regulation. The second step is carried out by the glycogen synthase, an enzyme that generates linear α-(1→4)-linked glucose chains, whereas the third step catalyzed by the branching enzyme produces α-(1→6)-linked glucan branches in the polymer. Two enzymes facilitate glycogen degradation: glycogen phosphorylase, which functions as an α-(1→4)-depolymerizing enzyme, and the debranching enzyme that catalyzes the removal of α-(1→6)-linked ramifications. In this work, we rationalize the structural basis of glycogen metabolism in bacteria to the light of the current knowledge. We describe and discuss the remarkable progress made in the understanding of the molecular mechanisms of substrate recognition and product release, allosteric regulation and catalysis of all those enzymes.
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