scholarly journals RSH enzyme diversity for (p)ppGpp metabolism in Phaeodactylum tricornutum and other diatoms

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Luisana Avilan ◽  
Carine Puppo ◽  
Adrien Villain ◽  
Emanuelle Bouveret ◽  
Benoit Menand ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Enzymatic Activity ◽  
Active Site ◽  
Red Algae ◽  
Phaeodactylum Tricornutum ◽  
Marine Diatom ◽  
Photosynthetic Eukaryote ◽  
Guanosine Tetraphosphate ◽  
The Third ◽  
Photosynthetic Eukaryotes

AbstractThe nucleotides guanosine tetraphosphate and pentaphosphate (together known as (p)ppGpp or magic spot) are produced in plant plastids from GDP/GTP and ATP by RelA-SpoT homologue (RSH) enzymes. In the model plant Arabidopsis (p)ppGpp regulates chloroplast transcription and translation to affect growth, and is also implicated in acclimation to stress. However, little is known about (p)ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here we studied (p)ppGpp metabolism in the marine diatom Phaeodactylum tricornutum. We identified three expressed RSH genes in the P. tricornutum genome, and determined the enzymatic activity of the corresponding enzymes by heterologous expression in bacteria. We showed that two P. tricornutum RSH are (p)ppGpp synthetases, despite substitution of a residue within the active site believed critical for activity, and that the third RSH is a bifunctional (p)ppGpp synthetase and hydrolase, the first of its kind demonstrated in a photosynthetic eukaryote. A broad phylogenetic analysis then showed that diatom RSH belong to novel algal RSH clades. Together our work significantly expands the horizons of (p)ppGpp signalling in the photosynthetic eukaryotes by demonstrating an unexpected functional, structural and evolutionary diversity in RSH enzymes from organisms with plastids derived from red algae.

scholarly journals Golden magic: RSH enzymes for (p)ppGpp metabolism in the diatom Phaeodactylum tricornutum

2018 ◽  
Author(s):  
L Avilan ◽  
C Puppo ◽  
A Villain ◽  
E Bouveret ◽  
B Menand ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Enzymatic Activity ◽  
Active Site ◽  
Phaeodactylum Tricornutum ◽  
Structural Features ◽  
Marine Diatom ◽  
Photosynthetic Eukaryote ◽  
Guanosine Tetraphosphate ◽  
The Third ◽  
Photosynthetic Eukaryotes

AbstractThe nucleotides guanosine tetraphosphate and pentaphosphate (together known as (p)ppGpp or magic spot) are produced in plant plastids from GDP/GTP and ATP by RelA-SpoT homologue (RSH) enzymes. In the model plant Arabidopsis (p)ppGpp regulates chloroplast transcription and translation to affect growth, and is also implicated in acclimation to stress. However, little is known about (p)ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here we studied (p)ppGpp metabolism in the golden-coloured marine diatom Phaeodactylum tricornutum. We identified three expressed RSH genes in the P. tricornutum genome, and determined the enzymatic activity of the corresponding enzymes by heterologous expression in bacteria. We showed that two P. tricornutum RSH are (p)ppGpp synthetases, despite substitution of a residue within the active site believed critical for activity, and that the third RSH is a bifunctional (p)ppGpp synthetase and hydrolase, the first of its kind demonstrated in a photosynthetic eukaryote. A broad phylogenetic analysis then showed that diatom RSH belong to novel algal RSH clades. Together our work significantly expands the horizons of (p)ppGpp signalling in the photosynthetic eukaryotes by demonstrating an unexpected functional, structural and evolutionary diversity in RSH enzymes from organisms with plastids derived from red algae.HighlightWe discover RSH enzymes for (p)ppGpp metabolism in the diatom Phaeodactylum tricornutum and show that they have surprising functional and structural features, and belong to novel red-plastid lineage RSH clades.

Reassessment of Tristan da Cunha Gelidium (Gelidiales, Rhodophyta) species

2020 ◽  
Vol 63 (5) ◽  
pp. 455-462
Author(s):  
D. Wilson Freshwater ◽  
Sue Scott ◽  
Enrico M. Tronchin ◽  
Gary W. Saunders
Keyword(s):  
Southern Africa ◽  
Endemic Species ◽  
Red Algae ◽  
Genetic Group ◽  
The Third ◽  
Tristan Da Cunha

AbstractThree endemic species of Gelidium have been described from the remote Tristan da Cunha archipelago. A recent barcode survey of Tristan da Cunha red algae in combination with the clarification of vouchers for previously sequenced specimens has prompted a molecular and morphological reassessment of these species. Analyses of rbcL and COI-5P data indicated that all sequenced Tristan da Cunha specimens represented a single taxon, and furthermore that this genetic group was conspecific with Gelidium micropterum from southern Africa. Morphologically the Tristan da Cunha specimens represented either Gelidium concinnum or Gelidium regulare, and there was a grade of character states between both of these species, as well as G. micropterum. Based on these results the synonymy of G. concinnum and G. regulare under G. micropterum is proposed and an expanded description of G. micropterum provided. None of the studied Tristan da Cunha specimens clearly fit the description of the third endemic species, Gelidium inflexum, and its status could not be determined.

Protein Immobilization in Metal–Organic Frameworks by Covalent Binding

2014 ◽  
Vol 67 (11) ◽  
pp. 1629 ◽  
Author(s):  
Xuan Wang ◽  
Trevor A. Makal ◽  
Hong-Cai Zhou
Keyword(s):  
Enzymatic Activity ◽  
Enzyme Immobilization ◽  
Working Conditions ◽  
Active Site ◽  
Covalent Binding ◽  
Metal Organic Frameworks ◽  
Protein Immobilization ◽  
Immobilization Of Enzymes ◽  
Metal Organic ◽  
Biological Catalysis

Metal–organic frameworks (MOFs), possessing a well defined system of pores, demonstrate extensive potential serving as a platform in biological catalysis. Successful immobilization of enzymes in a MOF system retains the enzymatic activity, renders the active site more accessible to the substrate, and promises recyclability for reuse, and solvent adaptability in a broad range of working conditions. This highlight describes enzyme immobilization on MOFs via covalent binding and its significance.

scholarly journals The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jan Pyrih ◽  
Vojtěch Žárský ◽  
Justin D. Fellows ◽  
Christopher Grosche ◽  
Dorota Wloga ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Complex I ◽  
Phaeodactylum Tricornutum ◽  
Tetrahymena Thermophila ◽  
Thalassiosira Pseudonana ◽  
Cellular Distribution ◽  
Iron Sulfur Cluster ◽  
Iron Sulfur ◽  
Secondary Plastids ◽  
Respiratory Complex I

Abstract Background Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions. Results We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either α-proteobacterial or cyanobacterial endosymbionts. Conclusion Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans).

scholarly journals Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function

2017 ◽  
Vol 91 (23) ◽  
Author(s):  
Wenhua Kuang ◽  
Huanyu Zhang ◽  
Manli Wang ◽  
Ning-Yi Zhou ◽  
Fei Deng ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Active Site ◽  
Salt Bridge ◽  
Sulfhydryl Oxidase ◽  
Dimer Interface ◽  
Conserved Regions ◽  
Occlusion Bodies ◽  
Budded Virus ◽  
And Function ◽  
Substrate Proteins

ABSTRACT Baculoviruses encode a conserved sulfhydryl oxidase, P33, which is necessary for budded virus (BV) production and multinucleocapsid occlusion-derived virus (ODV) formation. Here, the structural and functional relationship of P33 was revealed by X-ray crystallography, site-directed mutagenesis, and functional analysis. Based on crystallographic characterization and structural analysis, a series of P33 mutants within three conserved regions, i.e., the active site, the dimer interface, and the R127-E183 salt bridge, were constructed. In vitro experiments showed that mutations within the active site and dimer interface severely impaired the sulfhydryl oxidase activity of P33, while the mutations in the salt bridge had a relatively minor influence. Recombinant viruses containing mutated P33 were constructed and assayed in vivo. Except for the active-site mutant AXXA, all other mutants produced infectious BVs, although certain mutants had a decreased BV production. The active-site mutant H114A, the dimer interface mutant H227D, and the salt bridge mutant R127A-E183A were further analyzed by electron microscopy and bioassays. The occlusion bodies (OBs) of mutants H114A and R127A-E183A had a ragged surface and contained mostly ODVs with a single nucleocapsid. The OBs of all three mutants contained lower numbers of ODVs and had a significantly reduced oral infectivity in comparison to control virus. Crystallographic analyses further revealed that all three regions may coordinate with one another to achieve optimal function of P33. Taken together, our data revealed that all the three conserved regions are involved in P33 activity and are crucial for virus morphogenesis and peroral infectivity. IMPORTANCE Sulfhydryl oxidase catalyzes disulfide bond formation of substrate proteins. P33, a baculovirus-encoded sulfhydryl oxidase, is different from other cellular and viral sulfhydryl oxidases, bearing unique features in tertiary and quaternary structure organizations. In this study, we found that three conserved regions, i.e., the active site, dimer interface, and the R127-E183 salt bridge, play important roles in the enzymatic activity and function of P33. Previous observations showed that deletion of p33 results in a total loss of budded virus (BV) production and in morphological changes in occlusion-derived virus (ODV). Our study revealed that certain P33 mutants lead to occlusion bodies (OBs) with a ragged surface, decreased embedded ODVs, and reduced oral infectivity. Interestingly, some P33 mutants with impaired ODV/OB still retained BV productivity, indicating that the impacts on BV and on ODV/OB are two distinctly different functions of P33, which are likely to be performed via different substrate proteins.

scholarly journals A new species of Pilarella (Copepoda, Calanoida, Arietellidae) from the hyperbenthic layer of Japan, with a molecular phylogenetic analysis of some representative genera of the Arietellidae

ZooKeys ◽  
2021 ◽  
Vol 1038 ◽  
pp. 179-194
Author(s):  
Sota Komeda ◽  
Kenta Adachi ◽  
Susumu Ohtsuka
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Phylogenetic Analysis ◽  
Posterior Border ◽  
The Third ◽  
The Family ◽  
Molecular Phylogenetic ◽  
New Diagnosis ◽  
Caudal Rami ◽  
A New Species

A new species of the continental shelf hyperbenthic genus Pilarella is described, the first from the Indo-Pacific. This is the second species of Pilarella known, and the first description of a male in the genus. The new species is easily distinguished from other species of Pilarella (P. longicornis) based on: (1) short caudal rami, approximately 1.5 times longer than wide; (2) 2 setae on the mandibular endopod; (3) 6 setae on the maxillular coxal epipodite; and (4) in the female, a short left antennule reaching the posterior border of the genital double-somite. The new diagnosis of Pilarella differs from Metacalanus in the separation of ancestral segments IX–XII and XIV–XV of the antennule, and the presence of 5–6 setae on the maxillular praecoxal arthrite. Pilarella is also separated from Metacalanalis based on the absence of a seta on the third ancestral segment of the antennary exopod, the symmetry of legs 1–3, the presence of a medial basal seta on the female leg 5, and 2 lateral exopodal spines on the female leg 5. A molecular phylogenetic analysis of some representative genera of the family Arietellidae, including the present new species, recovers two arietellid clades (Metacalanus- and Arietellus-clades) as in previous studies. Dichotomous keys for the genera of Arietellidae and the species of Pilarella are included.

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