DNA microarrays for studies of higher plants and other photosynthetic organisms

Iron chronically limits aquatic photosynthesis, especially in marine environments, and the correct perception and maintenance of iron homeostasis in photosynthetic bacteria, including cyanobacteria, is therefore of global significance. Multiple adaptive mechanisms, responsive promoters, and posttranscriptional regulators have been identified, which allow cyanobacteria to respond to changing iron concentrations. However, many factors remain unclear, in particular, how iron status is perceived within the cell. Here we describe a cyanobacterial ferredoxin (Fed2), with a unique C-terminal extension, that acts as a player in iron perception. Fed2 homologs are highly conserved in photosynthetic organisms from cyanobacteria to higher plants, and, although they belong to the plant type ferredoxin family of [2Fe-2S] photosynthetic electron carriers, they are not involved in photosynthetic electron transport. As deletion offed2appears lethal, we developed a C-terminal truncation system to attenuate protein function. Disturbed Fed2 function resulted in decreased chlorophyll accumulation, and this was exaggerated in iron-depleted medium, where different truncations led to either exaggerated or weaker responses to low iron. Despite this, iron concentrations remained the same, or were elevated in all truncation mutants. Further analysis established that, when Fed2 function was perturbed, the classical iron limitation marker IsiA failed to accumulate at transcript and protein levels. By contrast, abundance of IsiB, which shares an operon withisiA, was unaffected by loss of Fed2 function, pinpointing the site of Fed2 action in iron perception to the level of posttranscriptional regulation.

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Why don't plants have diabetes? Systems for scavenging reactive carbonyls in photosynthetic organisms

Biochemical Society Transactions ◽

10.1042/bst20130273 ◽

2014 ◽

Vol 42 (2) ◽

pp. 543-547 ◽

Cited By ~ 15

Author(s):

Ginga Shimakawa ◽

Mayumi Suzuki ◽

Eriko Yamamoto ◽

Ryota Saito ◽

Tatsuya Iwamoto ◽

...

Keyword(s):

Photosynthetic Activity ◽

Higher Plants ◽

Sugar Metabolism ◽

Toxic Effects ◽

Medium Chain ◽

Photosynthetic Organisms

In the present paper, we review the toxicity of sugar- and lipid-derived RCs (reactive carbonyls) and the RC-scavenging systems observed in photosynthetic organisms. Similar to heterotrophs, photosynthetic organisms are exposed to the danger of RCs produced in sugar metabolism during both respiration and photosynthesis. RCs such as methylglyoxal and acrolein have toxic effects on the photosynthetic activity of higher plants and cyanobacteria. These toxic effects are assumed to occur uniquely in photosynthetic organisms, suggesting that RC-scavenging systems are essential for their survival. The aldo–keto reductase and the glyoxalase systems mainly scavenge sugar-derived RCs in higher plants and cyanobacteria. 2-Alkenal reductase and alkenal/alkenone reductase catalyse the reduction of lipid-derived RCs in higher plants. In cyanobacteria, medium-chain dehydrogenases/reductases are the main scavengers of lipid-derived RCs.

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Exploration of Autophagy Families in Legumes and Dissection of the ATG18 Family with a Special Focus on Phaseolus vulgaris

Plants ◽

10.3390/plants10122619 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2619

Author(s):

Elsa-Herminia Quezada-Rodríguez ◽

Homero Gómez-Velasco ◽

Manoj-Kumar Arthikala ◽

Miguel Lara ◽

Antonio Hernández-López ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Higher Plants ◽

Large Family ◽

Lipid Binding ◽

Model Organisms ◽

Special Focus ◽

Scaling Analysis ◽

Protein Motifs ◽

Photosynthetic Organisms ◽

Atg Genes

Macroautophagy/autophagy is a fundamental catabolic pathway that maintains cellular homeostasis in eukaryotic cells by forming double-membrane-bound vesicles named autophagosomes. The autophagy family genes remain largely unexplored except in some model organisms. Legumes are a large family of economically important crops, and knowledge of their important cellular processes is essential. Here, to first address the knowledge gaps, we identified 17 ATG families in Phaseolus vulgaris, Medicago truncatula and Glycine max based on Arabidopsis sequences and elucidated their phylogenetic relationships. Second, we dissected ATG18 in subfamilies from early plant lineages, chlorophytes to higher plants, legumes, which included a total of 27 photosynthetic organisms. Third, we focused on the ATG18 family in P. vulgaris to understand the protein structure and developed a 3D model for PvATG18b. Our results identified ATG homologs in the chosen legumes and differential expression data revealed the nitrate-responsive nature of ATG genes. A multidimensional scaling analysis of 280 protein sequences from 27 photosynthetic organisms classified ATG18 homologs into three subfamilies that were not based on the BCAS3 domain alone. The domain structure, protein motifs (FRRG) and the stable folding conformation structure of PvATG18b revealing the possible lipid-binding sites and transmembrane helices led us to propose PvATG18b as the functional homolog of AtATG18b. The findings of this study contribute to an in-depth understanding of the autophagy process in legumes and improve our knowledge of ATG18 subfamilies.

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Biosynthesis Pathways of Vitamin E and Its Derivatives in Plants

10.5772/intechopen.97267 ◽

2021 ◽

Author(s):

Makhlouf Chaalal ◽

Siham Ydjedd

Keyword(s):

Vitamin E ◽

Higher Plants ◽

Aromatic Amino Acids ◽

Biosynthetic Pathways ◽

Edible Plant ◽

Methylerythritol Phosphate Pathway ◽

Methylerythritol Phosphate ◽

Photosynthetic Organisms ◽

And Function

Naturally occurring vitamin E, comprised of four forms each of tocopherols and tocotrienols, are synthesized solely by photosynthetic organisms and function primarily as antioxidants. The structural motifs of the vitamin E family and specifically the chroman moiety, are amenable to various modifications in order to improve their bioactivities towards numerous therapeutic targets. Tocopherols are lipophilic antioxidants and together with tocotrienols belong to the vitamin-E family. These lipid-soluble compounds are potent antioxidants that protect polyunsaturated fatty acids from lipid peroxidation. Biosynthetic pathways of plants producing a diverse array of natural products that are important for plant function, agriculture, and human nutrition. Edible plant-derived products, notably seed oils, are the main sources of vitamin E in the human diet. The biosynthesis of tocopherols takes place mainly in plastids of higher plants from precursors derived from two metabolic pathways: homogentisic acid, an intermediate of degradation of aromatic amino acids, and phytyldiphosphate, which arises from methylerythritol phosphate pathway. Tocopherols and tocotrienols play an important roles in the oxidative stability of vegetable oils and in the nutritional quality of crop plants for human and livestock diets. Here, we review major biosynthetic pathways, including common precursors and competitive pathways of the vitamin E and its derivatives in plants.

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The synthesis of acetylcholine by plants

Biochemical Journal ◽

10.1042/bj1940361 ◽

1981 ◽

Vol 194 (1) ◽

pp. 361-364 ◽

Cited By ~ 26

Author(s):

B N Smallman ◽

A Maneckjee

Keyword(s):

Pisum Sativum ◽

Green Algae ◽

Choline Acetyltransferase ◽

Spinacia Oleracea ◽

Higher Plants ◽

Urtica Dioica ◽

The Other ◽

Affinity Column ◽

Blue Green Algae ◽

Photosynthetic Organisms

Choline acetyltransferase was demonstrated in nettles (Urtica dioica), peas (Pisum sativum), spinach (Spinacia oleracea), sunflower (Helianthus annuus) and blue–green algae by using a Sepharose–CoASH affinity column. The column effected a 1500-fold purification of the enzyme from nettle homogenates and was required for demonstrating activity in the other higher plants. Demonstration of the enzyme in blue-green algae suggests that acetylcholine was a biochemical necessity in the earliest photosynthetic organisms.

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Photoprotection and triplet energy transfer in higher plants: the role of electronic and nuclear fluctuations

Physical Chemistry Chemical Physics ◽

10.1039/c6cp01437b ◽

2016 ◽

Vol 18 (16) ◽

pp. 11288-11296 ◽

Cited By ~ 9

Author(s):

Lorenzo Cupellini ◽

Sandro Jurinovich ◽

Ingrid G. Prandi ◽

Stefano Caprasecca ◽

Benedetta Mennucci

Keyword(s):

Energy Transfer ◽

Higher Plants ◽

Excess Energy ◽

High Light ◽

Light Conditions ◽

Triplet Energy ◽

Photosynthetic Organisms ◽

Triplet Energy Transfer

Photosynthetic organisms employ several photoprotection strategies to avoid damage due to the excess energy in high light conditions.

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Photometabolism of Glycollate by Euglena Gracilis

Australian Journal of Biological Sciences ◽

10.1071/bi9710023 ◽

1971 ◽

Vol 24 (1) ◽

pp. 23 ◽

Cited By ~ 16

Author(s):

David R Murray ◽

J Grovanelli ◽

Robert M Smillie

Keyword(s):

Carbon Source ◽

Euglena Gracilis ◽

Higher Plants ◽

Serine Hydroxymethyltransferase ◽

Single Source ◽

Photosynthetic Organisms ◽

Inhibition Of Growth ◽

Glycollate Oxidase ◽

Isonicotinyl Hydrazide ◽

Glyoxylate Reductase

The photometabolism of glycollate was investigated in E. gracilis, strain Z, an organism which can utilize glycollate as a single source of carbon in the light but not in the dark. The nature of the labelled products of the photometabolism of [1-14CJglycollate, [2_14CJglycollate, and [l-14CJglycine and the inhibition of growth on glycollate by isonicotinyl hydrazide and by ex-hydroxy-2-pyridine methane sul-phonate were consistent with the operation of a glycollate pathway of the type found in the leaves of higher plants. In addition, several enzymes associated with gly-collate metabolism in other photosynthetic organisms were demonstrated in cell-free extracts of E. gracilis grown with glycollate as the only carbon source. These included glycollate oxidase, NADPH: glyoxylate reductase, NADH: glyoxylate reductase (E.C.1.1.1.26), glycine transaminase (E.C.2.6.1.4), formyltetrahydro-folate synthetase (E.C. 6.3.4.3), and serine hydroxymethyltransferase (E.C. 2.1.2.1).

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Evolutionary insights into PtdIns3P signaling through FYVE and PHOX effector proteins from the moss Physcomitrella patens

10.1101/765594 ◽

2019 ◽

Author(s):

Patricia Agudelo-Romero ◽

Ana Margarida Fortes ◽

Trinidad Suárez ◽

Hernán Ramiro Lascano ◽

Laura Saavedra

Keyword(s):

Stress Responses ◽

Growth And Development ◽

Physcomitrella Patens ◽

Higher Plants ◽

Regulatory Elements ◽

Plant Evolution ◽

Effector Proteins ◽

Promoter Regions ◽

Photosynthetic Organisms ◽

Binding Domains

ABSTRACTPhosphatidylinositol 3-phosphate (PtdIns3P) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through PtdIns3P-binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest diverging group of terrestrial flora.In this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution.

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Microbial primary production and phototrophy

10.1093/oso/9780198789406.003.0006 ◽

2018 ◽

Author(s):

David L. Kirchman

Keyword(s):

Carbon Dioxide ◽

Primary Production ◽

Microbial Mats ◽

Higher Plants ◽

Net Primary Production ◽

Terrestrial Plants ◽

Anoxygenic Photosynthesis ◽

Photosynthetic Organisms ◽

Anoxic Environments ◽

Large Numbers

This chapter is focused on the most important process in the biosphere, primary production, the turning of carbon dioxide into organic material by higher plants, algae, and cyanobacteria. Photosynthetic microbes account for roughly 50% of global primary production while the other half is by large, terrestrial plants. After reviewing the basic physiology of photosynthesis, the chapter discusses approaches to measuring gross and net primary production and how these processes affect fluxes of oxygen and carbon dioxide into and out of aquatic ecosystems. It then points out that terrestrial plants have high biomass but relatively low growth, while the opposite is the case for aquatic algae and cyanobacteria. Primary production varies greatly with the seasons in temperate ecosystems, punctuated by the spring bloom when the biomass of one algal type, diatoms, reaches a maximum. Other abundant algal types include coccolithophorids in the oceans and filamentous cyanobacteria in freshwaters. After the bloom, small algae take over and out-compete larger forms for limiting nutrients because of superior uptake kinetics. Abundant types of small algae include two coccoid cyanobacteria, Synechococcus and Prochlorococcus, the latter said to be the most abundant photoautotroph on the planet because of its large numbers in oligotrophic oceans. Other algae, often dinoflagellates, are toxic. Many algae can also graze on other microbes, probably to obtain limiting nitrogen or phosphorus. Still other microbes are mainly heterotrophic but are capable of harvesting light energy. Primary production in oxic environments is carried out by oxygenic photosynthetic organisms, whereas in anoxic environments with sufficient light, it is anaerobic anoxygenic photosynthesis in which oxygen is not produced. Although its contribution to global primary production is small, anoxygenic photosynthesis helps us understand the biophysics and biochemistry of photosynthesis and its evolution on early Earth. These microbes as well as aerobic phototrophic and heterotrophic microbes make up microbial mats. These mats can provide insights into early life on the planet when a type of mat, “stromatolites,” covered vast areas of primordial seas in the Proterozoic.

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Mass Spectrometry-based Footprinting Reveals Structural Dynamics of Loop E of the Chlorophyll-binding Protein CP43 during Photosystem II Assembly in the Cyanobacterium Synechocystis 6803

Journal of Biological Chemistry ◽

10.1074/jbc.m113.467613 ◽

2013 ◽

Vol 288 (20) ◽

pp. 14212-14220 ◽

Cited By ~ 22

Author(s):

Haijun Liu ◽

Jiawei Chen ◽

Richard Y.-C. Huang ◽

Daniel Weisz ◽

Michael L. Gross ◽

...

Keyword(s):

Mass Spectrometry ◽

Water Oxidation ◽

Higher Plants ◽

Protein A ◽

D1 Protein ◽

Cluster Assembly ◽

Conformational Rearrangement ◽

Photosynthetic Organisms ◽

Binding Interface ◽

Extrinsic Proteins

The PSII repair cycle is required for sustainable photosynthesis in oxygenic photosynthetic organisms. In cyanobacteria and higher plants, proteolysis of the precursor D1 protein (pD1) to expose a C-terminal carboxylate group is an essential step leading to coordination of the Mn4CaO5 cluster, the site of water oxidation. Psb27 appears to associate with both pD1- and D1-containing PSII assembly intermediates by closely interacting with CP43. Here, we report that reduced binding affinity between CP43 and Psb27 is triggered by the removal of the C-terminal extension of the pD1 protein. A mass spectrometry-based footprinting strategy was adopted to probe solvent-exposed aspartic and glutamic acid residues on the CP43 protein. By comparing the extent of footprinting between HT3ΔctpAΔ27PSII and HT3ΔctpAPSII, two genetically modified PSII assembly complexes, we found that Psb27 binds to CP43 on the side of Loop E distal to the pseudo-symmetrical D1-D2 axis. By comparing a second pair of PSII assembly complexes, we discovered that Loop E of CP43 undergoes a significant conformational rearrangement due to the removal of the pD1 C-terminal extension, altering the Psb27-CP43 binding interface. The significance of this conformational rearrangement is discussed in the context of recruitment of the PSII lumenal extrinsic proteins and Mn4CaO5 cluster assembly. In addition to CP43's previously known function as one of the core PSII antenna proteins, this work demonstrates that Loop E of CP43 plays an important role in the functional assembly of the Water Oxidizing Center (WOC) during PSII biogenesis.

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