scholarly journals Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

2021 ◽  
Author(s):  
Minoru Kumazawa ◽  
Hiroyo Nishide ◽  
Ryo Nagao ◽  
Natsuko Inoue-Kashino ◽  
Jian-Ren Shen ◽  
...  
Keyword(s):  
Light Harvesting ◽  
Phylogenetic Analyses ◽  
Distinct Type ◽  
Secondary Endosymbiosis ◽  
Light Harvesting Complex ◽  
Genome Data ◽  
Chaetoceros Gracilis ◽  
Red Algal ◽  
History Of ◽  
Species Specific

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e., fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identified 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggested that these FCPs could be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, had orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seemed to be diversified in each diatom species, and the number of Lhcqs differed among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs was common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provided insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

scholarly journals The complex evolution of the HSP70 gene family

2020 ◽  
Author(s):  
Er-meng Yu ◽  
Tatsuki Yoshinaga ◽  
Frank L. Jalufka ◽  
Hashimul Ehsan ◽  
David B. Mark Welch ◽  
...  
Keyword(s):  
Heat Shock ◽  
Evolutionary History ◽  
Brachionus Plicatilis ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Evolutionary Genetics ◽  
Purifying Selection ◽  
Hsp70 Family ◽  
History Of ◽  
Species Specific

AbstractThe 70-kDa heat shock protein (HSP70) family contains several isoforms localized in different subcellular compartments. The cytosolic isoforms have been classified into stress-inducible HSP70s and constitutive heat shock cognates (HSC70s), but occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons have been a source of confusion in the evolution of the metazoan HSP70 family. Here we provide novel insights into the evolutionary history of this important molecular chaperone. We first cloned two HSP70 genes from the rotifer Brachionus plicatilis, an emerging model in evolutionary genetics, and confirmed their stress inducibility. Subsequent phylogenetic analyses of 100 full-length HSP70 family member genes revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage contains a relatively small number of Lophotrochozoan and Ecdysozoan genes, none of which have been shown to be constitutively expressed. The second included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and in the second there are well-supported phylum-specific clades for Rotifera, Nematoda, and Chordata. Some genes in this lineage have likely independently acquired stress inducibility, which may explain the sporadic distribution of genes designated as “HSP70” or “HSC70” in previous analyses. Consistent with the history of diversification within each group, stress-inducible members of the second lineage show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family independent from their expression patterns, encouraging the development of new nomenclature based on evolutionary history.

scholarly journals The complex evolution of the metazoan HSP70 gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Er-meng Yu ◽  
Tatsuki Yoshinaga ◽  
Frank L. Jalufka ◽  
Hashimul Ehsan ◽  
David B. Mark Welch ◽  
...  
Keyword(s):  
Heat Shock ◽  
Molecular Chaperones ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Purifying Selection ◽  
Hsp70 Family ◽  
Number Of Genes ◽  
History Of ◽  
Species Specific

AbstractThe metazoan 70-kDa heat shock protein (HSP70) family contains several members localized in different subcellular compartments. The cytosolic members have been classified into inducible HSP70s and constitutive heat shock cognates (HSC70s), but their distinction and evolutionary relationship remain unclear because of occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons. Here we provide novel insights into the evolution of these important molecular chaperones. Phylogenetic analyses of 125 full-length HSP70s from a broad range of phyla revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage (A) contains a relatively small number of genes from many invertebrate phyla, none of which have been shown to be constitutively expressed (i.e., either inducible or unknown). The other lineage (B) included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and Lineage B contains well-supported phylum-specific clades for Platyhelminthes, Rotifera, Nematoda, Porifera/Cnidaria, and Chordata. Some genes in Lineage B have likely independently acquired inducibility, which may explain the sporadic distribution of “HSP70” or “HSC70” in previous phylogenetic analyses. Consistent with the diversification history within each group, inducible members show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family, encouraging us to propose a new nomenclature: “HSP70 + subcellular localization + linage + copy number in the organism + inducible or constitutive, if known.” e.g., HSP70cA1i for cytosolic Lineage A, copy 1, inducible.

scholarly journals Single, Ancient Origin of a Plastid Metabolite Translocator Family in Plantae from an Endomembrane-Derived Ancestor

2006 ◽  
Vol 5 (3) ◽  
pp. 609-612 ◽  
Author(s):  
Andreas P. M. Weber ◽  
Marc Linka ◽  
Debashish Bhattacharya
Keyword(s):  
Phylogenetic Analyses ◽  
Secondary Endosymbiosis ◽  
Gene Encoding ◽  
Single Origin ◽  
Red Algal

ABSTRACT Phylogenetic analyses show the single origin of a plastid metabolite translocator family in the Plantae from a gene encoding an existing endomembrane-derived protein. Red algal secondary endosymbiosis has spread a translocator gene into the ancestor of the “chromalveolate” protists, where it has diversified into a novel clade of proteins.

scholarly journals Unique organization of photosystem I–light-harvesting supercomplex revealed by cryo-EM from a red alga

2018 ◽  
Vol 115 (17) ◽  
pp. 4423-4428 ◽  
Author(s):  
Xiong Pi ◽  
Lirong Tian ◽  
Huai-En Dai ◽  
Xiaochun Qin ◽  
Lingpeng Cheng ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Photosystem I ◽  
Light Harvesting ◽  
Higher Plants ◽  
Red Alga ◽  
Cyanidioschyzon Merolae ◽  
Higher Plant ◽  
Light Harvesting Complex ◽  
Red Algal ◽  
Eukaryotic Organisms

Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga Cyanidioschyzon merolae in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls a and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls a and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.

Macroorganisation and flexibility of thylakoid membranes

2019 ◽  
Vol 476 (20) ◽  
pp. 2981-3018 ◽  
Author(s):  
Petar H. Lambrev ◽  
Parveen Akhtar
Keyword(s):  
Light Harvesting ◽  
Current Knowledge ◽  
Three Dimensional ◽  
Photosynthetic Apparatus ◽  
Dynamic Responses ◽  
State Transitions ◽  
Photochemical Quenching ◽  
Light Harvesting Complex ◽  
Complex Ii ◽  
Light Harvesting Complex Ii

Abstract The light reactions of photosynthesis are hosted and regulated by the chloroplast thylakoid membrane (TM) — the central structural component of the photosynthetic apparatus of plants and algae. The two-dimensional and three-dimensional arrangement of the lipid–protein assemblies, aka macroorganisation, and its dynamic responses to the fluctuating physiological environment, aka flexibility, are the subject of this review. An emphasis is given on the information obtainable by spectroscopic approaches, especially circular dichroism (CD). We briefly summarise the current knowledge of the composition and three-dimensional architecture of the granal TMs in plants and the supramolecular organisation of Photosystem II and light-harvesting complex II therein. We next acquaint the non-specialist reader with the fundamentals of CD spectroscopy, recent advances such as anisotropic CD, and applications for studying the structure and macroorganisation of photosynthetic complexes and membranes. Special attention is given to the structural and functional flexibility of light-harvesting complex II in vitro as revealed by CD and fluorescence spectroscopy. We give an account of the dynamic changes in membrane macroorganisation associated with the light-adaptation of the photosynthetic apparatus and the regulation of the excitation energy flow by state transitions and non-photochemical quenching.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals Molecular Analysis of Targeted Insecticide Resistance Gene Mutations in Field-Caught Mosquitos of Medical Importance From Saudi Arabia

2021 ◽  
Author(s):  
Yuan Fang ◽  
Ernest Tambo ◽  
Jing-Bo Xue ◽  
Yi Zhang ◽  
Xiao-Nong Zhou ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Insecticide Resistance ◽  
Resistance Gene ◽  
Phylogenetic Analyses ◽  
Gene Mutations ◽  
Mosquito Vector ◽  
Dengue Disease ◽  
The Status ◽  
History Of ◽  
Exon 20

Abstract Gene mutations on target sites can be a valuable indicator of the status of insecticide resistance. Jeddah, a global commercial and major port-of-entry city, is bearing the brunt of dengue disease burden in Saudi Arabia. In the current study, six genotypes of three codon combinations (989, 1016, and 1534) were observed on voltage-gated sodium channel (VGSC) gene in Jeddah’s Aedes aegypti population, with PGF/PGC as the dominant one. Two types of introns between exon 20 and 21 on VGSC have been identified for the first time in Ae. aegypti in Saudi Arabia. Statistical and phylogenetic analyses showed that the intron type was significantly associated with the 1016 allele and may reflect the history of insecticide treatment in different continents. In addition, fixation of the L1014F allele on VGSC and G119S on acetylcholinesterase 1 gene was detected in local Culex quinquefasciatus populations, with frequencies of 95.24 and 100%, respectively. To the best of our knowledge, this is the first report of resistant-associated mutations in field-caught Cx. quinquefasciatus in Saudi Arabia. The high prevalence of insecticide resistance gene mutations in local primary mosquito vector species highlights the urgent need to carry out comprehensive insecticide resistance surveillance in Saudi Arabia.

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