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Book ; Online: Autophagy in plants and algae

Crespo, Jose L. / Bassham, Diane C.

2015

Abstract: Autophagy (also known as macroautophagy) is an evolutionarily conserved process by which cytoplasmic components are nonselectively enclosed within a double-membrane vesicle known as the autophagosome and delivered to the vacuole for degradation of toxic ... ...

Abstract	Autophagy (also known as macroautophagy) is an evolutionarily conserved process by which cytoplasmic components are nonselectively enclosed within a double-membrane vesicle known as the autophagosome and delivered to the vacuole for degradation of toxic components and recycling of needed nutrients. This catabolic process is required for the adequate adaptation and response of the cell, and correspondingly the whole organism, to different types of stress including nutrient starvation or oxidative damage. Autophagy has been extensively investigated in yeasts and mammals but the identification of autophagy-related (ATG) genes in plant and algal genomes together with the characterization of autophagy-deficient mutants in plants have revealed that this process is structurally and functionally conserved in photosynthetic eukaryotes. Recent studies have demonstrated that autophagy is active at a basal level under normal growth in plants and is upregulated during senescence and in response to nutrient limitation, oxidative stress, salt and drought conditions and pathogen attack. Autophagy was initially considered as a non-selective pathway, but numerous observations mainly obtained in yeasts revealed that autophagy can also selectively eliminate specific proteins, protein complexes and organelles. Interestingly, several types of selective autophagy appear to be also conserved in plants, and the degradation of protein aggregates through specific adaptors or the delivery of chloroplast material to the vacuole via autophagy has been reported. This research topic aims to gather recent progress on different aspects of autophagy in plants and algae. We welcome all types of articles including original research, methods, opinions and reviews that provide new insights about the autophagy process and its regulation
Keywords	Botany ; Science (General)
Size	1 electronic resource (102 p.)
Publisher	Frontiers Media SA
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT020091046
ISBN	9782889194773 ; 2889194779
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Monitoring of ATG4 Protease Activity During Autophagy in the Model Microalga Chlamydomonas reinhardtii.

Crespo, José L / Pérez-Pérez, M Esther

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2447, Page(s) 205–220

Abstract: Deciphering the molecular mechanisms underlying the regulation of the ATG4 protease is essential to understand the regulation of ATG8 lipidation, a key step in the biogenesis of the autophagosome and hence in autophagy progression. Here, we describe two ... ...

Abstract	Deciphering the molecular mechanisms underlying the regulation of the ATG4 protease is essential to understand the regulation of ATG8 lipidation, a key step in the biogenesis of the autophagosome and hence in autophagy progression. Here, we describe two complementary approaches to monitor ATG4 proteolytic activity in the model green alga Chlamydomonas reinhardtii: an in vitro assay using recombinant ATG4 and recombinant ATG8 as substrate, and a cell-free assay using soluble total protein extract from Chlamydomonas and recombinant Chlamydomonas ATG8 as substrate. Both assays are followed by non-reducing SDS-PAGE and immuno-blot analysis. Given the high evolutionary conservation of the ATG8 maturation process, these assays have also been validated to monitor ATG4 activity in yeast using Chlamydomonas ATG8 as substrate.
MeSH term(s)	Autophagy/physiology ; Autophagy-Related Protein 8 Family/metabolism ; Autophagy-Related Proteins/metabolism ; Chlamydomonas ; Chlamydomonas reinhardtii/genetics ; Chlamydomonas reinhardtii/metabolism ; Microalgae/metabolism ; Microtubule-Associated Proteins/metabolism ; Peptide Hydrolases/metabolism ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Autophagy-Related Protein 8 Family ; Autophagy-Related Proteins ; Microtubule-Associated Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2022-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2079-3_17
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Monitoring Autophagic Flux in the Model Single-Celled Microalga Chlamydomonas reinhardtii.

Crespo, José L / Pérez-Pérez, María Esther

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2581, Page(s) 123–134

Abstract: Autophagy is a catabolic process by which eukaryotic cells degrade and recycle unnecessary or damaged intracellular components to maintain cellular homeostasis and to cope with stress. The development of specific tools to monitor autophagy in microalgae ... ...

Abstract	Autophagy is a catabolic process by which eukaryotic cells degrade and recycle unnecessary or damaged intracellular components to maintain cellular homeostasis and to cope with stress. The development of specific tools to monitor autophagy in microalgae and plants has been fundamental to investigate this catabolic pathway in photosynthetic organisms. The protein ATG8 is a widely used molecular marker of autophagy in all eukaryotes, including the model microalga Chlamydomonas reinhardtii. The drug concanamycin A, a specific inhibitor of vacuolar ATPase, has also been extensively used to block autophagic flux in the green lineage. In Chlamydomonas, inhibition of autophagic flux by concanamycin A has been shown to prevent the degradation of ribosomal proteins and the formation of lipid bodies under nitrogen or phosphorous starvation. Here, we detail how the abundance and lipidation state of ATG8 can be used to monitor autophagic flux in Chlamydomonas by western blot analysis.
MeSH term(s)	Chlamydomonas reinhardtii/metabolism ; Microalgae ; Autophagy/physiology ; Macrolides/pharmacology ; Chlamydomonas
Chemical Substances	concanamycin A (80890-47-7) ; Macrolides
Language	English
Publishing date	2022-11-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2784-6_10
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Compartmentalization, a key mechanism controlling the multitasking role of the SnRK1 complex.

Gutierrez-Beltran, Emilio / Crespo, Jose L

Journal of experimental botany

2022 Volume 73, Issue 20, Page(s) 7055–7067

Abstract: SNF1-related protein kinase 1 (SnRK1), the plant ortholog of mammalian AMP-activated protein kinase/fungal (yeast) Sucrose Non-Fermenting 1 (AMPK/SNF1), plays a central role in metabolic responses to reduced energy levels in response to nutritional and ... ...

Abstract	SNF1-related protein kinase 1 (SnRK1), the plant ortholog of mammalian AMP-activated protein kinase/fungal (yeast) Sucrose Non-Fermenting 1 (AMPK/SNF1), plays a central role in metabolic responses to reduced energy levels in response to nutritional and environmental stresses. SnRK1 functions as a heterotrimeric complex composed of a catalytic α- and regulatory β- and βγ-subunits. SnRK1 is a multitasking protein involved in regulating various cellular functions, including growth, autophagy, stress response, stomatal development, pollen maturation, hormone signaling, and gene expression. However, little is known about the mechanism whereby SnRK1 ensures differential execution of downstream functions. Compartmentalization has been recently proposed as a new key mechanism for regulating SnRK1 signaling in response to stimuli. In this review, we discuss the multitasking role of SnRK1 signaling associated with different subcellular compartments.
MeSH term(s)	Animals ; AMP-Activated Protein Kinases/metabolism ; Stress, Physiological ; Signal Transduction ; Saccharomyces cerevisiae/metabolism ; Plants/genetics ; Plants/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Mammals/metabolism
Chemical Substances	AMP-Activated Protein Kinases (EC 2.7.11.31) ; Arabidopsis Proteins
Language	English
Publishing date	2022-07-21
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erac315
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deciphering the function and evolution of the target of rapamycin signaling pathway in microalgae.

Mallén-Ponce, Manuel J / Pérez-Pérez, María Esther / Crespo, José L

Journal of experimental botany

2022 Volume 73, Issue 20, Page(s) 6993–7005

Abstract: Microalgae constitute a highly diverse group of photosynthetic microorganisms that are widely distributed on Earth. The rich diversity of microalgae arose from endosymbiotic events that took place early in the evolution of eukaryotes and gave rise to ... ...

Abstract	Microalgae constitute a highly diverse group of photosynthetic microorganisms that are widely distributed on Earth. The rich diversity of microalgae arose from endosymbiotic events that took place early in the evolution of eukaryotes and gave rise to multiple lineages including green algae, the ancestors of land plants. In addition to their fundamental role as the primary source of marine and freshwater food chains, microalgae are essential producers of oxygen on the planet and a major biotechnological target for sustainable biofuel production and CO2 mitigation. Microalgae integrate light and nutrient signals to regulate cell growth. Recent studies identified the target of rapamycin (TOR) kinase as a central regulator of cell growth and a nutrient sensor in microalgae. TOR promotes protein synthesis and regulates processes that are induced under nutrient stress such as autophagy and the accumulation of triacylglycerol and starch. A detailed analysis of representative genomes from the entire microalgal lineage revealed that the highly conserved central components of the TOR pathway are likely to have been present in the last eukaryotic common ancestor, and the loss of specific TOR signaling elements at an early stage in the evolution of microalgae. Here we examine the evolutionary conservation of TOR signaling components in diverse microalgae and discuss recent progress of this signaling pathway in these organisms.
MeSH term(s)	Microalgae/metabolism ; Sirolimus/metabolism ; Signal Transduction ; Photosynthesis ; Eukaryota
Chemical Substances	Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2022-06-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erac264
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Photosynthetic assimilation of CO

Mallén-Ponce, Manuel J / Pérez-Pérez, María Esther / Crespo, José L

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 2

Abstract: The target of rapamycin (TOR) kinase is a master regulator that integrates nutrient signals to promote cell growth in all eukaryotes. It is well established that amino acids and glucose are major regulators of TOR signaling in yeast and metazoan, but ... ...

Abstract	The target of rapamycin (TOR) kinase is a master regulator that integrates nutrient signals to promote cell growth in all eukaryotes. It is well established that amino acids and glucose are major regulators of TOR signaling in yeast and metazoan, but whether and how TOR responds to carbon availability in photosynthetic organisms is less understood. In this study, we showed that photosynthetic assimilation of CO
MeSH term(s)	Algal Proteins/metabolism ; Amino Acids/metabolism ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Chlamydomonas/metabolism ; Chlamydomonas reinhardtii/metabolism ; Photosynthesis/drug effects ; Photosynthesis/physiology ; Signal Transduction/drug effects ; Sirolimus/pharmacology ; Starch/metabolism ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	Algal Proteins ; Amino Acids ; Carbon Dioxide (142M471B3J) ; Carbon (7440-44-0) ; Starch (9005-25-8) ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2022-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2115261119
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analyzing the impact of autotrophic and heterotrophic metabolism on the nutrient regulation of TOR.

Mallén-Ponce, Manuel J / Pérez-Pérez, María Esther / Crespo, José L

The New phytologist

2022 Volume 236, Issue 4, Page(s) 1261–1266

Abstract: The target of rapamycin (TOR) protein kinase is a master regulator of cell growth in all eukaryotes, from unicellular yeast and algae to multicellular animals and plants. Target of rapamycin balances the synthesis and degradation of proteins, lipids, ... ...

Abstract	The target of rapamycin (TOR) protein kinase is a master regulator of cell growth in all eukaryotes, from unicellular yeast and algae to multicellular animals and plants. Target of rapamycin balances the synthesis and degradation of proteins, lipids, carbohydrates and nucleic acids in response to nutrients, growth factors and cellular energy to promote cell growth. Among nutrients, amino acids (AAs) and glucose are central regulators of TOR activity in evolutionary distant eukaryotes such as mammals, plants and algae. However, these organisms obtain the nutrients through totally different metabolic processes. Although photosynthetic eukaryotes can use atmospheric CO<sub>2</sub> as the sole carbon (C) source for all reactions in the cell, heterotrophic organisms get nutrients from other sources of organic C including glucose. Here, we discuss the impact of autotrophic and heterotrophic metabolism on the nutrient regulation of TOR, focusing on the role of AAs and C sources upstream of this signaling pathway.
MeSH term(s)	Animals ; Sirolimus ; Carbon Dioxide/metabolism ; TOR Serine-Threonine Kinases/metabolism ; Plants/metabolism ; Carbon/metabolism ; Glucose/metabolism ; Nutrients ; Amino Acids/metabolism ; Carbohydrates ; Nucleic Acids/metabolism ; Lipids ; Mammals
Chemical Substances	Sirolimus (W36ZG6FT64) ; Carbon Dioxide (142M471B3J) ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; Carbon (7440-44-0) ; Glucose (IY9XDZ35W2) ; Amino Acids ; Carbohydrates ; Nucleic Acids ; Lipids
Language	English
Publishing date	2022-09-16
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18450
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analyzing the impact of autotrophic and heterotrophic metabolism on the nutrient regulation of TOR

Mallén‐Ponce, Manuel J. / Pérez‐Pérez, María Esther / Crespo, José L.

New Phytologist. 2022 Nov., v. 236, no. 4 p.1261-1266

2022

Abstract	The target of rapamycin (TOR) protein kinase is a master regulator of cell growth in all eukaryotes, from unicellular yeast and algae to multicellular animals and plants. Target of rapamycin balances the synthesis and degradation of proteins, lipids, carbohydrates and nucleic acids in response to nutrients, growth factors and cellular energy to promote cell growth. Among nutrients, amino acids (AAs) and glucose are central regulators of TOR activity in evolutionary distant eukaryotes such as mammals, plants and algae. However, these organisms obtain the nutrients through totally different metabolic processes. Although photosynthetic eukaryotes can use atmospheric CO₂ as the sole carbon (C) source for all reactions in the cell, heterotrophic organisms get nutrients from other sources of organic C including glucose. Here, we discuss the impact of autotrophic and heterotrophic metabolism on the nutrient regulation of TOR, focusing on the role of AAs and C sources upstream of this signaling pathway.
Keywords	carbon ; carbon dioxide ; cell growth ; energy ; eukaryotic cells ; glucose ; photosynthesis ; protein kinases ; rapamycin ; yeasts
Language	English
Dates of publication	2022-11
Size	p. 1261-1266.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	REVIEW
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18450
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The ATG4 protease integrates redox and stress signals to regulate autophagy.

Pérez-Pérez, María Esther / Lemaire, Stéphane D / Crespo, José L

Journal of experimental botany

2021 Volume 72, Issue 9, Page(s) 3340–3351

Abstract: Autophagy is a highly conserved degradative pathway that ensures cellular homeostasis through the removal of damaged or useless intracellular components including proteins, membranes, or even entire organelles. A main hallmark of autophagy is the ... ...

Abstract	Autophagy is a highly conserved degradative pathway that ensures cellular homeostasis through the removal of damaged or useless intracellular components including proteins, membranes, or even entire organelles. A main hallmark of autophagy is the biogenesis of autophagosomes, double-membrane vesicles that engulf and transport to the vacuole the material to be degraded and recycled. The formation of autophagosomes responds to integrated signals produced as a consequence of metabolic reactions or different types of stress and is mediated by the coordinated action of core autophagy-related (ATG) proteins. ATG4 is a key Cys-protease with a dual function in both ATG8 lipidation and free ATG8 recycling whose balance is crucial for proper biogenesis of the autophagosome. ATG4 is conserved in the green lineage, and its regulation by different post-translational modifications has been reported in the model systems Chlamydomonas reinhardtii and Arabidopsis. In this review, we discuss the major role of ATG4 in the integration of stress and redox signals that regulate autophagy in algae and plants.
MeSH term(s)	Arabidopsis ; Autophagy ; Autophagy-Related Proteins/genetics ; Autophagy-Related Proteins/metabolism ; Chlamydomonas reinhardtii ; Microtubule-Associated Proteins/metabolism ; Oxidation-Reduction ; Peptide Hydrolases
Chemical Substances	Autophagy-Related Proteins ; Microtubule-Associated Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-02-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erab063
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BiP links TOR signaling to ER stress in Chlamydomonas.

Crespo, José L

Plant signaling & behavior

2012 Volume 7, Issue 2, Page(s) 273–275

Abstract: The highly conserved target of rapamycin (TOR) Ser/Thr kinase promotes protein synthesis under favorable growth conditions in all eukaryotes. Downregulation of TOR signaling in the model unicellular green alga Chlamydomonas reinhardtii has recently ... ...

Abstract	The highly conserved target of rapamycin (TOR) Ser/Thr kinase promotes protein synthesis under favorable growth conditions in all eukaryotes. Downregulation of TOR signaling in the model unicellular green alga Chlamydomonas reinhardtii has recently revealed a link between control of protein synthesis, endoplasmic reticulum (ER) stress and the reversible modification of the BiP chaperone by phosphorylation. Inhibition of protein synthesis by rapamycin or cycloheximide resulted in the phosphorylation of BiP on threonine residues while ER stress induced by tunicamycin or heat shock caused the fast dephosphorylation of the protein. Regulation of BiP function by phosphorylation/dephosphorylation events was proposed in early studies in mammalian cells although no connection to TOR signaling has been established so far. Here I will discuss about the coordinated regulation of BiP modification by TOR and ER stress signals in Chlamydomonas.
MeSH term(s)	Chlamydomonas reinhardtii/metabolism ; Chlamydomonas reinhardtii/physiology ; Endoplasmic Reticulum Stress/physiology ; Heat-Shock Proteins/metabolism ; Phosphorylation ; Plant Proteins/metabolism ; Protein Biosynthesis ; Signal Transduction ; Stress, Physiological ; TOR Serine-Threonine Kinases/metabolism ; Threonine/metabolism
Chemical Substances	Heat-Shock Proteins ; Plant Proteins ; Threonine (2ZD004190S) ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; molecular chaperone GRP78 (YCYIS6GADR)
Language	English
Publishing date	2012-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1559-2324
ISSN (online)	1559-2324
DOI	10.4161/psb.18767
Database	MEDical Literature Analysis and Retrieval System OnLINE

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