DOCSLIB.ORG

Molecular Evidence for Origin, Diversification and Ancient Gene Duplication of Plant Subtilases (Sbts)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Molecular Evidence for Origin, Diversification and Ancient Gene Duplication of Plant Subtilases (Sbts) Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs) Xu, Yan; Wang, Sibo; Li, Linzhou; Sahu, Sunil Kumar; Petersen, Morten; Liu, Xin; Melkonian, Michael; Zhang, Gengyun; Liu, Huan Published in: Scientific Reports DOI: 10.1038/s41598-019-48664-6 Publication date: 2019 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Xu, Y., Wang, S., Li, L., Sahu, S. K., Petersen, M., Liu, X., ... Liu, H. (2019). Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs). Scientific Reports, 9, [12485]. https://doi.org/10.1038/s41598-019-48664-6 Download date: 09. apr.. 2020 www.nature.com/scientificreports OPEN Molecular evidence for origin, diversifcation and ancient gene duplication of plant subtilases Received: 22 January 2019 Accepted: 9 August 2019 (SBTs) Published: xx xx xxxx Yan Xu1,2,3, Sibo Wang2,4,5, Linzhou Li2,6, Sunil Kumar Sahu 2,4, Morten Petersen5, Xin Liu 2,4, Michael Melkonian7, Gengyun Zhang2,4 & Huan Liu 2,4,5 Plant subtilases (SBTs) are a widely distributed family of serine proteases which participates in plant developmental processes and immune responses. Although SBTs are divided into seven subgroups in plants, their origin and evolution, particularly in green algae remain elusive. Here, we present a comprehensive large-scale evolutionary analysis of all subtilases. The plant subtilases SBT1-5 were found to be monophyletic, nested within a larger radiation of bacteria suggesting that they originated from bacteria by a single horizontal gene transfer (HGT) event. A group of bacterial subtilases comprising representatives from four phyla was identifed as a sister group to SBT1-5. The phylogenetic analyses, based on evaluation of novel streptophyte algal genomes, suggested that the recipient of the HGT of bacterial subtilases was the common ancestor of Coleochaetophyceae, Zygnematophyceae and embryophytes. Following the HGT, the subtilase gene duplicated in the common ancestor and the two genes diversifed into SBT2 and SBT1, 3–5 respectively. Comparative structural analysis of homology-modeled SBT2 proteins also showed their conservation from bacteria to embryophytes. Our study provides the frst molecular evidence about the evolution of plant subtilases via HGT followed by a frst gene duplication in the common ancestor of Coleochaetophyceae, Zygnematophyceae, and embryophytes, and subsequent expansion in embryophytes. Serine proteases are a highly abundant and functionally diverse class of proteins which occupy a notable place in plants1,2. According to the MEROPS peptidase database, the clan SB is one of 13 clans of serine proteases that are widely distributed in Archaea, Bacteria, and eukaryotes2–4. Clan SB contains two families, family S8 (ofen called the subtilase family) and family S53 (the sedolisin family)4. Te catalytic mechanisms of the two families of clan SB are diferent. In family S8 the active site residues form a catalytic triad in the order Asp, His, Ser, whereas fam- ily S53 contains a catalytic tetrad in the order Glu, Asp, Asp, Ser. Family S8 is the second largest family of serine proteases and is divided into two subfamilies, S8A (type example subtilisin) and S8B (type example kexin)5. Plant subtilisin-like proteases (also known as plant subtilases, SBTs) belong to subfamiliy S8A. Te frst subtilase cloned from plants was cucumisin from melon fruit6. In the past 20 years, several SBT gene families have been revealed throughout the plant kingdom, in Vitis vinifera7,8, Arabidopsis thaliana9, Oryza sativa10, Solanum lycopersicum11,12, Solanum tuberosum13, and others. Te Arabidopsis proteome alone comprises 56 subtilases. Based on these fndings SBTs have been divided into six subgroups9, and recently one of the sub- groups (SBT6.1) was described as a seventh subgroup (SBT7)14. Schaller et al. have summarized most of the functions of plant subtilases, such as in embryogenesis, seed devel- opment and germination, cuticle formation and epidermal patterning, vascular development, programmed cell 1BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China. 2BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. 3China National GeneBank, Institute of New Agricultural Resources, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China. 4State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. 5Department of Biology, University of Copenhagen, Copenhagen, Denmark. 6School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China. 7Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, D-50674, Germany. Yan Xu, Sibo Wang and Linzhou Li contributed equally. Correspondence and requests for materials should be addressed to H.L. (email: [email protected]) SCIENTIFIC REPORTS | (2019) 9:12485 | https://doi.org/10.1038/s41598-019-48664-6 1 www.nature.com/scientificreports/ www.nature.com/scientificreports a. b. Embryophyta Alveolata Streptophyte algae Euglenozoa Chlorophyta Stramenopiles Glaucophyta Amoebozoa Rhodophyta Fungi Bacteria Archaea Chloroflexi Chloroflexi Firmicutes 100 Bacterial S8A genes 100 Caldiserica (S8 cluster 1) SBT1-5 97 Caldiserica 98 Coprothermobacterota 84 Actinobacteria Chloroflexi Chloroflexi 98 Gamma-proteobacteria 83 75 S8 cluster 1 86 100 Delta-proteobacteria Delta-proteobacteria Bacterial Subtilases 79 100 Actinobacteria 69 100 Chloroflexi Actinobacteria Actinobacteria 40 83 100 Bacterial Subtilases S8 cluster 2 100 100 Gamma-proteobacteria 98 59 Proteinase K 97 Chloroflexi 99 Beta-proteobacteria/Gamma-proteobacteria Beta-proteobacteria/Gamma-proteobacteria KP43 proteinase 93 100 Gamma-proteobacteria 70 Beta-proteobacteria 88 100 Firmicutes 83 Actinobacteria 56 57 SBT7 97 Chloroflexi 95 68 Actinobacteria Mesotaenium endlicherianum S8 cluster 4 99 Streptophyte algae Coleochaete scutata HGT 100 92 Streptophyte algae 100 “Spirotaenia sp.” Plant Subtilases 100 Streptophyte algae (SBT2) 73 Tree scale: 1 Embryophyta SBT6 100 S8 cluster 3 Figure 1. Phylogenetic relationship of the S8A protease gene subfamily. (a) Maximum likelihood unrooted phylogenetic tree of the S8A subfamily from representative Archaea, Bacteria and eukaryote species was constructed with IQ-TREE (model: LG + R10, predicted by Modelfnder) using an ultrafast bootstrap approximation (100,000 bootstrap replicates). Colored domains display eight diferent clusters in the S8A subfamily. Te domains with a continuous line indicate resolved clusters, while domains with dotted lines represent undefned clusters. Te colored circles at the top lef represent the species composition of individual clusters. Te plant subtilases (SBT1-5) apparently originated from bacterial subtilases (red branches in in paraphyletic divergences) through a single HGT. (b) Phylogenetic analysis of plant subtilases using an extended taxon sampling of bacterial subtilases to search for a bacterial sister group to the plant subtilases was constructed by Maximum Likelihood using 500 bootstrap replicates (model: WAG + F + R7, predicted by Modelfnder). Plant subtilases are monophyletic with a clade of bacterial sequences derived from four phyla (Proteobacteria (only Gammaproteobacteria and Betaproteobacteria), Chlorofexi, Actinobacteria and Firmicutes). Te streptophyte algal sequences from Mesotaenium endlicherianum, Coleochaete scutata and “Spirotaenia sp.” diverge paraphyletically from the common ancestor of the plant subtilases with “Spirotaenia sp.” in sister position to embryophytes (the detailed tree with all taxon and species names is shown as Supplementary Fig. S1). Some bacterial S8 genes from the phylogenetic tree of the S8 cluster 1 (a) were selected as an outgroup. death, organ abscission, and plant responses to their biotic and abiotic environments15–17. However, many specifc functions and physiological substrates of SBTs still need to be explored. Previous studies have found that land plant subtilases were derived from a single HGT (horizontal gene transfer) event18. Horizontal gene transfer is proposed relative to vertical gene transfer, which breaks down the boundaries of kinship and complicates the pos- sibility of gene fow. Many genes found in algae doesn’t have any homologs in higher plants were suggesting their possible bacterial origin. For instance, two alginate-specifc enzymes, MC5E and GDP-mannose dehydrogenase show high similarity with the bacterial genes, indicating that these genes might have undergone a non-canonical evolutionary history. Taylor and Qiu (2017) investigated the evolutionary history of plant subtilases through a phylogenetic analysis using 2,460 subtilase amino acid sequences of 341 species, and identifed 11 new gene lin- eages14. Meanwhile, the presence of plant subtilases in streptophyte algae, the grade of green algae most closely related to land plants (embryophytes), was also frst reported in their study, based on analysis of transcriptomes14. Plant subtilases seem to have experienced several gene duplications, which were accompanied by functional diversifcation7. Due to their multiple duplications and complex evolutionary history, it is important to explore the origin and diversifcation of SBTs among Viridiplantae including the streptophyte algae. We have recently sequenced the genomes of several streptophyte algal species (unpublished data) enabling us to explore the evo- lution of subtilases including all
Load more

Recommended publications
  • Unique Metabolic Strategies in Hadean Analogues Reveal Hints for Primordial Physiology
    Unique metabolic strategies in Hadean analogues reveal hints for primordial physiology - Supplementary Information - Masaru Konishi Nobu1†*, Ryosuke Nakai1,2†, Satoshi Tamazawa1,3, Hiroshi Mori4, Atsushi Toyoda4, Akira Ijiri5, Shino Suzuki6,7, Ken Kurokawa4, Yoichi Kamagata1, and Hideyuki Tamaki1* Affiliation: 1 Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan 2 Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Sapporo, 062-8517, Japan 3 Horonobe Research Institute for the Subsurface Environment (H-RISE), Northern Advancement Center for Science & Technology, 5-3 Sakaemachi, Horonobe, Teshio, Hokkaido, 098-3221, Japan 4 National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan 5 Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 200 Monobe Otsu, Nankoku, Kochi, Japan 6 Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Natsushima 2-15, Yokosuka, Kanagawa 237-0061, Japan 7 Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210, Japan † These authors contributed equally. * Corresponding author: [email protected] and [email protected] Table of Contents Supplementary Results ..................... 2 Supplementary Figures ..................... 3 Figure S1 3 Figure S2 4 Figure S3 5 Figure S4 6 Figure S5 7 Figure S6 8 Figure S7 9 References 10 Supplementary Tables ..................... 11 Table S1 11 Table S2 12 Table S3 13 Table S4 14 1 Supplementary Results H2 and formate metabolism Assuming that the hydrogenases and formate dehydrogenases in situ use NADP(H) or NAD(H)+ferredoxin (i.e., electron-bifurcating) (an assumption confirmed based on analysis of the metagenome-assembled genomes we recover; see below), H2 and formate are likely reductants.
    [Show full text]
  • An Extension of Shannon's Entropy to Explain Taxa Diversity and Human Diseases
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.233767; this version posted August 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title Page 2 Title: An extension of Shannon’s entropy to explain taxa diversity and human 3 diseases 4 Running title: A mathematical interpretation of life 5 6 Author list and full affiliations: 7 Farzin Kamari*1,2, MD, MPH; Sina Dadmand2,3, PharmD. 8 1Neurosciences Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran. 9 2Synaptic ProteoLab, Synaptic ApS, Skt Knuds Gade 20, 5000 Odense C, Denmark. 10 3Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. 11 *Corresponding author: Farzin Kamari 12 Email: [email protected] 13 14 Total character count (with spaces): 72,502 15 Keywords: origin of diseases/ protein-protein interaction/ Shannon’s entropy/ taxonomic 16 classification/ tree of life 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.233767; this version posted August 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 17 Abstract 18 In this study, with the use of the information theory, we have proposed and proved a 19 mathematical theorem by which we argue the reason for the existence of human diseases.
    [Show full text]
  • The Distribution of Microbiomes and Resistomes Across Farm Environments in Conventional and Organic Dairy Herds in Pennsylvania Dipti W
    Pitta et al. Environmental Microbiome (2020) 15:21 Environmental Microbiome https://doi.org/10.1186/s40793-020-00368-5 RESEARCH ARTICLE Open Access The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania Dipti W. Pitta* , Nagaraju Indugu, John D. Toth, Joseph S. Bender, Linda D. Baker, Meagan L. Hennessy, Bonnie Vecchiarelli, Helen Aceto and Zhengxia Dou Abstract Background: Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures. Results: Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol.
    [Show full text]
  • Mannitol Biosynthesis in Algae : More Widespread and Diverse Than Previously Thought
    This is a repository copy of Mannitol biosynthesis in algae : more widespread and diverse than previously thought. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/113250/ Version: Accepted Version Article: Tonon, Thierry orcid.org/0000-0002-1454-6018, McQueen Mason, Simon John orcid.org/0000-0002-6781-4768 and Li, Yi (2017) Mannitol biosynthesis in algae : more widespread and diverse than previously thought. New Phytologist. pp. 1573-1579. ISSN 1469-8137 https://doi.org/10.1111/nph.14358 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ 1 Mannitol biosynthesis in algae: more widespread and diverse than previously thought. Thierry Tonon1,*, Yi Li1 and Simon McQueen-Mason1 1 Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK. * Author for correspondence: tel +44 1904328785; email [email protected] Key words: Algae, primary metabolism, mannitol biosynthesis, mannitol-1-phosphate dehydrogenase, mannitol-1-phosphatase, haloacid dehalogenase, histidine phosphatase, evolution of metabolic pathways.
    [Show full text]
  • Thermophilic Anaerobic Digestion of Second Cheese Whey: Microbial Community Response to H2 Addition in a Partially Immobilized Anaerobic Hybrid Reactor
    processes Article Thermophilic Anaerobic Digestion of Second Cheese Whey: Microbial Community Response to H2 Addition in a Partially Immobilized Anaerobic Hybrid Reactor Giuseppe Lembo 1,2, Silvia Rosa 1, Valentina Mazzurco Miritana 1,3 , Antonella Marone 4, Giulia Massini 1, Massimiliano Fenice 2 and Antonella Signorini 1,* 1 Department of Energy Technologies and Renewable Source, Casaccia Research Center, ENEA-Italian Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese 301, 00123 Rome, Italy; [email protected] (G.L.); [email protected] (S.R.); [email protected] (V.M.M.); [email protected] (G.M.) 2 Ecological and Biological Sciences Department, University of Tuscia, 01100 Viterbo, Italy; [email protected] 3 Water Research Institute, National Research Council (IRSA-CNR) Via Salaria km 29,300-C.P. 10, Monterotondo Street, 00015 Rome, Italy 4 Department of Energy Efficiency Unit, Casaccia Research Center, ENEA-Italian Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese 301, 00123 Rome, Italy; [email protected] * Correspondence: [email protected] Abstract: In this study, we investigated thermophilic (55 ◦C) anaerobic digestion (AD) performance and microbial community structure, before and after hydrogen addition, in a novel hybrid gas-stirred tank reactor (GSTR) implemented with a partial immobilization of the microbial community and fed with second cheese whey (SCW). The results showed that H2 addition led to a 25% increase in the methane production rate and to a decrease of 13% in the CH4 concentration as compared with the control. The recovery of methane content (56%) was reached by decreasing the H2 flow rate.
    [Show full text]
  • Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
    bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected].
    [Show full text]
  • New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
    bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments.
    [Show full text]
  • Sepf Is the Ftsz Anchor in Archaea, with Features of an Ancestral Cell Division System
    ARTICLE https://doi.org/10.1038/s41467-021-23099-8 OPEN SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system Nika Pende1,8, Adrià Sogues2,8, Daniela Megrian1,3, Anna Sartori-Rupp4, Patrick England 5, Hayk Palabikyan6, ✉ Simon K.-M. R. Rittmann 6, Martín Graña 7, Anne Marie Wehenkel 2 , Pedro M. Alzari 2 & ✉ Simonetta Gribaldo 1 Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, 1234567890():,; but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.
    [Show full text]
  • Downloaded in FASTA Format
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.233767; this version posted August 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title Page 2 Title: An extension of Shannon’s entropy to explain taxa diversity and human 3 diseases 4 5 Author list and full affiliations: 6 Farzin Kamari*1,2, MD, MPH; Sina Dadmand2,3, PharmD. 7 1Neurosciences Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran. 8 2Synaptic ProteoLab, Synaptic ApS, Skt Knuds Gade 20, 5000 Odense C, Denmark. 9 3Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. *Corresponding author: Farzin Kamari 10 11 Email: [email protected] 12 13 Number of words in the main text (excluding Abstract, Methods, References, and 14 Figure/Table Legends): 3,934 15 Number of words in the Abstract: 148 16 17 Keywords: origin of diseases/ protein-protein interaction/ Shannon’s entropy/ taxonomic 18 classification/ tree of life 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.233767; this version posted August 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 19 Abstract 20 In this study, with the use of the information theory, we have proposed and proved a 21 mathematical theorem by which we argue the reason for the existence of human diseases.
    [Show full text]
  • Plant Evolution and Diversity B. Importance of Plants C. Where Do Plants Fit, Evolutionarily? What Are the Defining Traits of Pl
    Plant Evolution and Diversity Reading: Chap. 30 A. Plants: fundamentals I. What is a plant? What does it do? A. Basic structure and function B. Why are plants important? - Photosynthesize C. What are plants, evolutionarily? -CO2 uptake D. Problems of living on land -O2 release II. Overview of major plant taxa - Water loss A. Bryophytes (seedless, nonvascular) - Water and nutrient uptake B. Pterophytes (seedless, vascular) C. Gymnosperms (seeds, vascular) -Grow D. Angiosperms (seeds, vascular, and flowers+fruits) Where? Which directions? II. Major evolutionary trends - Reproduce A. Vascular tissue, leaves, & roots B. Fertilization without water: pollen C. Dispersal: from spores to bare seeds to seeds in fruits D. Life cycles Æ reduction of gametophyte, dominance of sporophyte Fig. 1.10, Raven et al. B. Importance of plants C. Where do plants fit, evolutionarily? 1. Food – agriculture, ecosystems 2. Habitat 3. Fuel and fiber 4. Medicines 5. Ecosystem services How are protists related to higher plants? Algae are eukaryotic photosynthetic organisms that are not plants. Relationship to the protists What are the defining traits of plants? - Multicellular, eukaryotic, photosynthetic autotrophs - Cell chemistry: - Chlorophyll a and b - Cell walls of cellulose (plus other polymers) - Starch as a storage polymer - Most similar to some Chlorophyta: Charophyceans Fig. 29.8 Points 1. Photosynthetic protists are spread throughout many groups. 2. Plants are most closely related to the green algae, in particular, to the Charophyceans. Coleochaete 3.
    [Show full text]
  • Different Fates of the Chloroplast Tufa Gene Following Its Transfer to the Nucleus in Green Algae
    Proc. Nail. Acad. Sci. USA Vol. 87, pp. 5317-5321, July 1990 Evolution Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae (elongation factor Tu/gene transfer/organelle genomes/gene duplication/multigene family) SANDRA L. BALDAUF*, JAMES R. MANHARTt, AND JEFFREY D. PALMER* *Department of Biology, Indiana University, Bloomington, IN 47405; and tDepartment of Biology, Texas A&M University, College Station, TX 77843 Communicated by David L. Dilcher, May 8, 1990 (receivedfor review March 23, 1990) ABSTRACT Previous work suggested that the tufA gene, by a combination offilter hybridization and gene sequencing. encoding protein synthesis elongation factor Tu, was trans- Among the Charophyceae, an unusual chloroplast tufAl was ferred from the chloroplast to the nucleus within the green algal found in the genus Coleochaete, the proposed sister group to lineage giving rise to land plants. In this report we investigate land plants (10, 11). the timing and mode of transfer by examining chloroplast and nuclear DNA from the three major classes of green algae, with MATERIALS AND METHODS emphasis on the class Charophyceae, the proposed sister group Filaments of Spirogyra maxima and Sirogonium melanospo- to land plants. Filter hybridizations reveal a chloroplast tufA rum were obtained from unialgal cultures grown in soil/water gene in all Ulvophyceae and Chlorophyceae and in some but not medium (12) on a 16:8 hr light: dark cycle at 200C ± 20C under all Charophyceae. One charophycean alga, Coleochaete orbic- fluorescent light at an illumination of 50 gmol m-2'so1. Ni- ularis, is shown to contain an intact but highly divergent tella translucens and Chara connivens were grown in aquaria chloroplast tufA gene, whose product is predicted to be non- in a soil/water solution in a greenhouse.
    [Show full text]
  • Diversity and Evolution of Algae: Primary Endosymbiosis
    CHAPTER TWO Diversity and Evolution of Algae: Primary Endosymbiosis Olivier De Clerck1, Kenny A. Bogaert, Frederik Leliaert Phycology Research Group, Biology Department, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium 1Corresponding author: E-mail: [email protected] Contents 1. Introduction 56 1.1. Early Evolution of Oxygenic Photosynthesis 56 1.2. Origin of Plastids: Primary Endosymbiosis 58 2. Red Algae 61 2.1. Red Algae Defined 61 2.2. Cyanidiophytes 63 2.3. Of Nori and Red Seaweed 64 3. Green Plants (Viridiplantae) 66 3.1. Green Plants Defined 66 3.2. Evolutionary History of Green Plants 67 3.3. Chlorophyta 68 3.4. Streptophyta and the Origin of Land Plants 72 4. Glaucophytes 74 5. Archaeplastida Genome Studies 75 Acknowledgements 76 References 76 Abstract Oxygenic photosynthesis, the chemical process whereby light energy powers the conversion of carbon dioxide into organic compounds and oxygen is released as a waste product, evolved in the anoxygenic ancestors of Cyanobacteria. Although there is still uncertainty about when precisely and how this came about, the gradual oxygenation of the Proterozoic oceans and atmosphere opened the path for aerobic organisms and ultimately eukaryotic cells to evolve. There is a general consensus that photosynthesis was acquired by eukaryotes through endosymbiosis, resulting in the enslavement of a cyanobacterium to become a plastid. Here, we give an update of the current understanding of the primary endosymbiotic event that gave rise to the Archaeplastida. In addition, we provide an overview of the diversity in the Rhodophyta, Glaucophyta and the Viridiplantae (excluding the Embryophyta) and highlight how genomic data are enabling us to understand the relationships and characteristics of algae emerging from this primary endosymbiotic event.
    [Show full text]