DOCSLIB.ORG

Analysis of Early Evolutionary Events During the Transition from Prokaryotes to Eukaryotes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Analysis of Early Evolutionary Events During the Transition from Prokaryotes to Eukaryotes Analysis of early evolutionary events during the transition from prokaryotes to eukaryotes INAUGURAL DISSERTATION For the attainment of the title of Doctor rerum naturalium (Dr. rer. nat.) in the Faculty of Mathematics and Natural Sciences at the Heinrich Heine University Düsseldorf presented by Julia Brückner, M.Sc. from Oldenburg (Oldb), Germany Düsseldorf, March 2021 From the Institute of Molecular Evolution at the Heinrich Heine University Düsseldorf Published by permission of the Faculty of Mathematics and Natural Sciences at the Heinrich Heine University Düsseldorf Supervisor: Prof Dr. William F. Martin Co-supervisor: Prof. Dr. Martin J. Lercher Date of oral examination: June 17th, 2021 Statement of declaration I hereby certify that this dissertation is the result of my own work. I confirm that no other person’s work has been used without due acknowledgement. This work was done wholly while in the candidature for a research degree at the Heinrich Heine University Düsseldorf and has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Düsseldorf, August 10th, 2021 Julia Brückner An meine Familie und Freunde. Danke, dass ihr mich durchgehend unterstützt und mir die wichtigen Dinge im Leben deutlich macht. Acknowledgements I never thought I would come this far in research. I didn’t even think of studying after school but only wanted to do my apprenticeship, get a good job as a biological laboratory assistant and that’s it. But as we all know: ‘Life happens to you while you’re busy making other plans’ (John Lennon). Almost all my experiences in my studies at the Heinrich Heine University were lined with lucky events. One of them being the attendance of the genome analysis Master course by Dr. Mayo Röttger from Prof. Dr. William F. Martin’s institute. I was lucky enough to get one of the last waiting list places of this course and found that I liked bioinformatics and the area of studying early evolution. And lucky as I was, there were enough free spaces in the institute at the time and I was able to do my Master thesis, which led to the PhD. Therefore, I want to especially thank Prof. Martin for giving me the opportunity to work in his group and always encouraging me and helping me out. Without him I would probably have quit early on. Additionally, I want to thank Prof. Lercher for his role as co-supervisor. Mayo was responsible for me finding joy in bioinformatics and without Nils and Michael in our office, I would not have felt as welcomed as I did. The banter and scientific discussions and especially the help with programming that I got from those two (mostly Michael, Nils was the emotional support) helped me out a lot in continuing to work hard. Thank you, Verena and Renate, for helping with questions regarding the bureaucratic side of the PhD process and being there for any and all important matters. I also want to thank all other members of the team and students that I got to know during my four years at the institute, for creating a welcoming and sociable work environment. Last but most importantly, I want to thank my mother, my brother and my best friends. You always support me, sometimes question me and my decisions (so I can make better ones), and most of all are always there if I need to talk. I feel special gratitude towards you for always believing in me and for believing that I could do it. Guess you were right. I really can do it after all. And I will never forget. Publications submitted in the course of this thesis: 1. Brueckner J, Martin WF. 2020. Bacterial genes outnumber archaeal genes in eukaryotic genomes. Genome Biol Evol; 12: 282–292. https://doi.org/10.1093/gbe/evaa047 2. Nagies FSP*, Brueckner J*, Tria FDK, Martin WF. 2020. A spectrum of verticality across genes. PLoS Genet; 16: e1009200. https://doi.org/10.1371/journal.pgen.1009200 3. Tria FDK*, Brueckner J*, Skejo J, Xavier JC, Kapust N, Knopp M, Wimmer JLE, Nagies FSP, Zimorski V, Gould SB, Garg SG, Martin WF. 2021. Gene duplications trace mitochondria to the onset of eukaryote complexity. Genome Biol Evol; 13: evab055. https://doi.org/10.1093/gbe/evab055 4. Xavier JC*, Gerhards R*, Wimmer JLE, Brueckner J, Tria FDK, Martin WF. 2021. The metabolic network of the last bacterial common ancestor. Commun Biol; 4: 413. https://doi.org/10.1038/s42003-021-01918-4 * These authors contributed equally to the publication. Abstract There are two forms of living cells on earth — prokaryotes and eukaryotes. Prokaryotic cells are very simple organisms while eukaryotes present more complex cells that can organize into multicellular forms. The most widely accepted theory of eukaryote evolution is the endosymbiotic theory, depicting eukaryotes as descendants of archaea through the acquisition of a bacterial endosymbiont into its archaeal host. There has been more than one endosymbiotic event during eukaryote evolution with two major occurrences. The first gave rise to the mitochondrion from an archaeon incorporating a proteobacterium, generating the first eukaryote; the second resulted in the origin of the plant kingdom as a cyanobacterium was enveloped by an existing eukaryotic host. However, the mechanisms of how these events occurred are still mostly unknown and are the basis of many debates to date. Phylogenomic analyses have become the standard tool to investigate these early evolutionary events. Many studies focus on only a few genomes to represent a diverse spectrum of organisms from the three domains of life, some only examine a small number of genes. To obtain a more comprehensive view on how eukaryotes arose, the investigation of a broad spectrum of genomic data from a varied sample of lineages is desirable. Moreover, genome sequencing has become faster and simpler each year, enabling analyses containing a substantial number of organisms and genes. However, this is accompanied by extensively increased computational demands which can become a limiting factor that has to be addressed. This thesis reports the analysis of all protein coding genes from 5,655 prokaryotic and 150 eukaryotic genomes, the construction of their corresponding protein families, their alignments and phylogenetic trees in order to analyze evolutionary events at the border of prokaryotic and eukaryotic life. I Zusammenfassung Es gibt zwei unterschiedliche Formen von Leben auf der Erde — Prokaryoten und Eukaryoten. Prokaryotische Zellen sind sehr einfache Organismen während Eukaryoten komplexe Zellen darstellen, die sich in multizelluläre Formen organisieren können. Die am weitesten verbreitete Hypothese der Evolution von Eukaryoten ist die Endosymbiontentheorie: die Aufnahme eines bakteriellen Endosymbionten in seinen archaeellen Wirt. Im Laufe der Evolution von Eukaryoten gab es mehrere endosymbiontische Ereignisse — als erstes entstand das Mitochondrion durch Aufnahme eines Proteobakteriums in ein Archaeon und später ist das Pflanzenreich durch den Einschluss eines Cyanobakteriums in einen bestehenden Eukaryoten entstanden. Allerdings sind die Mechanismen, welche sich hinter diesen Vorgängen befinden, immer noch unzureichend untersucht und die Basis fortlaufender Debatten. Mittlerweile sind phylogenomische Analysen eine der Standardmethoden, um diese frühen Evolutionsvorgänge zu erforschen. Viele Untersuchungen verwenden nur wenige Genome, um die drei Domänen des Lebens zu repräsentieren, oder fokussieren sich auf eine geringe Anzahl an Genen. Um jedoch einen umfassenderen Überblick von der Entwicklung der Eukaryoten zu bekommen, sollte ein breites Spektrum von Sequenzdaten aus Genomen aller bekannten taxonomischen Gruppen herangezogen werden. Da die Sequenzierung von Genomen jedes Jahr einfacher und schneller wird, können nun auch Untersuchungen mit einer umfangreichen Anzahl an Organismen und Genen durchgeführt werden. Allerdings ist damit eine gesteigerte Nutzung von Rechenkapazitäten verbunden, welches schnell ein limitierender Faktor wird, der beachtet werden muss. Diese Arbeit stellt die Analyse aller proteinkodierenden Gene aus 5,655 prokaryotischen und 150 eukaryotischen Genomen dar. Die daraus rekonstruierten Proteinfamilien und phylogenetische Stammbäume wurden zur Untersuchung von evolutionären Ereignissen an der Grenze von prokaryotischem und eukaryotischem Leben verwendet. II Table of contents Abstract ..................................................................................................................................... I Zusammenfassung ................................................................................................................ II 1 Introduction ........................................................................................................................ 1 1.1 Protein sequences, gene sequences and genome sequences for phylogenetics ....... 4 1.2 Large-scale protein family reconstruction ................................................................................ 6 1.2.1 The importance of detecting orthologous proteins ................................................... 6 1.2.2 Influence of stringency on protein family properties ............................................ 10 1.2.3 Clustering of large protein sequence datasets .......................................................... 12 1.2.4 Applications for protein clusters ..................................................................................... 16 1.2.4.1 Available databases of protein clusters .............................................................. 16 1.2.4.2 Eukaryote-prokaryote
Load more

Recommended publications
  • Extremozymes of the Hot and Salty Halothermothrix Orenii
    Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry.
    [Show full text]
  • The Life of Brine: Halophiles in 2001 Comment Mike Dyall-Smith* and Michael Danson†
    http://genomebiology.com/2001/2/12/reports/4033.1 Meeting report The life of brine: halophiles in 2001 comment Mike Dyall-Smith* and Michael Danson Addresses: *Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia. Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK. Correspondence: Mike Dyall-Smith. E-mail: [email protected] Published: 21 November 2001 reviews Genome Biology 2001, 2(12):reports4033.1–4033.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2001/2/12/reports/4033 © BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) reports haloarchaea found in salt ponds that have 8% salt (or A report on the International conference on Halophilic 2.3-fold concentrated seawater) but are not detectable at the Microorganisms, Sevilla, Spain, 23-27 September 2001. higher salinities usually associated with haloarchaea (20-35% salt). Discovered using 16S rRNA libraries, the new haloar- chaea are distantly related to Haloarcula. None has been cul- The 2001 halophiles meeting covered archaea, bacteria, tured but these results suggest an optimum salt concentration fungi and algae adapted to living hypersaline environments. for growth far lower than that of known haloarchaea. These deposited research Despite the absence of some American colleagues as a result represent an intermediate group of haloarchaea, not previ- of the recent terrorist attack, the meeting was full of exciting ously suspected, and offer insight into the evolution of advances (as well as pictures of salt lakes, salterns, brines extreme halophiles.
    [Show full text]
  • The Phagotrophic Origin of Eukaryotes and Phylogenetic Classification Of
    International Journal of Systematic and Evolutionary Microbiology (2002), 52, 297–354 DOI: 10.1099/ijs.0.02058-0 The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa Department of Zoology, T. Cavalier-Smith University of Oxford, South Parks Road, Oxford OX1 3PS, UK Tel: j44 1865 281065. Fax: j44 1865 281310. e-mail: tom.cavalier-smith!zoo.ox.ac.uk Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an α-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an α-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton.
    [Show full text]
  • Diagnosis and Differentiation of the Order Primates
    YEARBOOK OF PHYSICAL ANTHROPOLOGY 30:75-105 (1987) Diagnosis and Differentiation of the Order Primates FREDERICK S. SZALAY, ALFRED L. ROSENBERGER, AND MARIAN DAGOSTO Department of Anthropolog* Hunter College, City University of New York, New York, New York 10021 (F.S.S.); University of Illinois, Urbanq Illinois 61801 (A.L. R.1; School of Medicine, Johns Hopkins University/ Baltimore, h4D 21218 (M.B.) KEY WORDS Semiorders Paromomyiformes and Euprimates, Suborders Strepsirhini and Haplorhini, Semisuborder Anthropoidea, Cranioskeletal morphology, Adapidae, Omomyidae, Grades vs. monophyletic (paraphyletic or holophyletic) taxa ABSTRACT We contrast our approach to a phylogenetic diagnosis of the order Primates, and its various supraspecific taxa, with definitional proce- dures. The order, which we divide into the semiorders Paromomyiformes and Euprimates, is clearly diagnosable on the basis of well-corroborated informa- tion from the fossil record. Lists of derived features which we hypothesize to have been fixed in the first representative species of the Primates, Eupri- mates, Strepsirhini, Haplorhini, and Anthropoidea, are presented. Our clas- sification of the order includes both holophyletic and paraphyletic groups, depending on the nature of the available evidence. We discuss in detail the problematic evidence of the basicranium in Paleo- gene primates and present new evidence for the resolution of previously controversial interpretations. We renew and expand our emphasis on postcra- nial analysis of fossil and living primates to show the importance of under- standing their evolutionary morphology and subsequent to this their use for understanding taxon phylogeny. We reject the much advocated %ladograms first, phylogeny next, and scenario third” approach which maintains that biologically founded character analysis, i.e., functional-adaptive analysis and paleontology, is irrelevant to genealogy hypotheses.
    [Show full text]
  • Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*
    J. Microbiol. Biotechnol. (2013), 23(12), 1645–1653 http://dx.doi.org/10.4014/jmb.1308.08015 Research Article Minireview jmb Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2* 1Department of Bio-Food Materials, College of Medical and Life Sciences, Silla University, Busan 617-736, Republic of Korea 2Research Center for Extremophiles, Silla University, Busan 617-736, Republic of Korea Received: August 8, 2013 Revised: September 6, 2013 Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular Accepted: September 9, 2013 biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are First published online being isolated and identified from high salt-fermented foods consumed by humans, and it has September 10, 2013 been found that various types of halophilic archaea exist in food products by culture- *Corresponding author independent molecular biological methods. In addition, even if the numbers are not quite Phone: +82-51-999-6308; high, DNAs of various halophilic archaea are being detected in human intestines and much Fax: +82-51-999-5458; interest is given to their possible roles. This review aims to summarize the types and E-mail: [email protected] characteristics of halophilic archaea reported to be present in foods and human intestines and pISSN 1017-7825, eISSN 1738-8872 to discuss their application as well. Copyright© 2013 by The Korean Society for Microbiology Keywords: Halophilic archaea, fermented foods, microbiome, human intestine, Halorubrum and Biotechnology Introduction Depending on the optimal salt concentration needed for the growth of strains, halophilic microorganisms can be Archaea refer to prokaryotes that used to be categorized classified as halotolerant (~0.3 M), halophilic (0.2~2.0 M), as archaeabacteria, a type of bacteria, in the past.
    [Show full text]
  • The Synaptic Vesicle Cycle
    The Synaptic Vesicle Cycle 1 Satyajit Mayor, National Centre for Biological Sciences KITP Evo Cell, Feb 3, 2010 The Eukaryotic Commandments: T. Cavalier-Smith (i)origin of the endomembrane system (ER, Golgi and lysosomes) and coated- vesicle budding and fusion, including endocytosis and exocytosis; (ii) origin of the cytoskeleton, centrioles, cilia and associated molecular motors; (iii) origin of the nucleus, nuclear pore complex and trans-envelope protein and RNA transport; (iv) origin of linear chromosomes with plural replicons, centromeres and telomeres; (v) origin of novel cell-cycle controls and mitotic segregation; (vi) origin of sex (syngamy, nuclear fusion and meiosis); (vii) origin of peroxisomes; (ix) origin of mitochondria; (viii) novel patterns of rRNAprocessing using small nucleolar-ribonucleoproteins (snoRNPs); (x) origin of spliceosomal introns. 2 EM of Chemical synapse mitochondria Active Zone Figure 5.3, Bear, 2001 3 T. Cavalier-Smith International Journal of Systematic and Evolutionary Microbiology (2002), 52, 297–354 Fig. 1. The bacterial origins of eukaryotes as a two-stage process. I phase: The ancestors of eukaryotes, the stem neomura, are shared with archaebacteria and evolved during the neomuran revolution, in which N-linked glycoproteins replaced murein peptidoglycan and 18 other suites of characters changed radically through adaptation of an ancestral actinobacterium to thermophily, as discussed in detail by Cavalier- Smith (2002a). 4 T. Cavalier-Smith International Journal of Systematic and Evolutionary Microbiology (2002), 52, 297–354 Fig. 1. The bacterial origins of eukaryotes as a two-stage process. II phase: In the next phase, archaebacteria and eukaryotes diverged dramatically. Archaebacteria retained the wall and therefore their general bacterial cell and genetic organization, but became adapted to even hotter and more acidic environments by substituting prenyl ether lipids for the ancestral acyl esters and making new acid- resistant flagellar shafts (Cavalier-Smith, 2002a).
    [Show full text]
  • A Revised Taxonomy of the Iguanodont Dinosaur Genera and Species
    ARTICLE IN PRESS + MODEL Cretaceous Research xx (2007) 1e25 www.elsevier.com/locate/CretRes A revised taxonomy of the iguanodont dinosaur genera and species Gregory S. Paul 3109 North Calvert Station, Side Apartment, Baltimore, MD 21218-3807, USA Received 20 April 2006; accepted in revised form 27 April 2007 Abstract Criteria for designating dinosaur genera are inconsistent; some very similar species are highly split at the generic level, other anatomically disparate species are united at the same rank. Since the mid-1800s the classic genus Iguanodon has become a taxonomic grab-bag containing species spanning most of the Early Cretaceous of the northern hemisphere. Recently the genus was radically redesignated when the type was shifted from nondiagnostic English Valanginian teeth to a complete skull and skeleton of the heavily built, semi-quadrupedal I. bernissartensis from much younger Belgian sediments, even though the latter is very different in form from the gracile skeletal remains described by Mantell. Currently, iguanodont remains from Europe are usually assigned to either robust I. bernissartensis or gracile I. atherfieldensis, regardless of lo- cation or stage. A stratigraphic analysis is combined with a character census that shows the European iguanodonts are markedly more morpho- logically divergent than other dinosaur genera, and some appear phylogenetically more derived than others. Two new genera and a new species have been or are named for the gracile iguanodonts of the Wealden Supergroup; strongly bipedal Mantellisaurus atherfieldensis Paul (2006. Turning the old into the new: a separate genus for the gracile iguanodont from the Wealden of England. In: Carpenter, K. (Ed.), Horns and Beaks: Ceratopsian and Ornithopod Dinosaurs.
    [Show full text]
  • Halophilic Microorganisms Springer-Verlag Berlin Heidelberg Gmbh Antonio Ventosa (Ed.)
    Halophilic Microorganisms Springer-Verlag Berlin Heidelberg GmbH Antonio Ventosa (Ed.) Halophilic Microorganisms With 58 Figures Springer Dr.ANTONIO VENTOSA Department of Microbiology and Parasitology Faculty of Pharmacy University of Sevilla 41012 Sevilla Spain e-mail: [email protected] ISBN 978-3-642-05664-2 ISBN 978-3-662-07656-9 (eBook) DOI 10.1007/978-3-662-07656-9 Library of Congress Cataloging-in-Publication Data applied for A catalog record for this book is available from the Library of Congress. Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publicati an in the Deutsche Nationalbibliographie; detailed bibliographic data is available in the Internet at http://dnb.ddb.de This work is subject ta copyright. AII rights are reservod, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of iIIustrations, recitation, broadcasting, reproduction an microfilm ar in any other way, and storage in data banks. Duplication of this publication ar parts thereofis permit­ ted only under the provisions of the German Copyright Law of September 9, 1965, in ils current version, and per­ missions for use must always be obtained from Springcr-Vcrlag Berlin Heiddhcrg GmbH. Violations are liable for prosecution under the German Copyright Law. http://www.springer.de © Springer-Verlag Berlin Heidelberg 2004 Originally published by Springer-Vcrlag lkrlin Hcidclbcrg New York in 2004 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
    [Show full text]
  • Life at Low Water Activity
    Published online 12 July 2004 Life at low water activity W. D. Grant Department of Infection, Immunity and Inflammation, University of Leicester, Maurice Shock Building, University Road, Leicester LE1 9HN, UK ([email protected]) Two major types of environment provide habitats for the most xerophilic organisms known: foods pre- served by some form of dehydration or enhanced sugar levels, and hypersaline sites where water availability is limited by a high concentration of salts (usually NaCl). These environments are essentially microbial habitats, with high-sugar foods being dominated by xerophilic (sometimes called osmophilic) filamentous fungi and yeasts, some of which are capable of growth at a water activity (aw) of 0.61, the lowest aw value for growth recorded to date. By contrast, high-salt environments are almost exclusively populated by prokaryotes, notably the haloarchaea, capable of growing in saturated NaCl (aw 0.75). Different strategies are employed for combating the osmotic stress imposed by high levels of solutes in the environment. Eukaryotes and most prokaryotes synthesize or accumulate organic so-called ‘compatible solutes’ (osmolytes) that have counterbalancing osmotic potential. A restricted range of bacteria and the haloar- chaea counterbalance osmotic stress imposed by NaCl by accumulating equivalent amounts of KCl. Haloarchaea become entrapped and survive for long periods inside halite (NaCl) crystals. They are also found in ancient subterranean halite (NaCl) deposits, leading to speculation about survival over geological time periods. Keywords: xerophiles; halophiles; haloarchaea; hypersaline lakes; osmoadaptation; microbial longevity 1. INTRODUCTION aw = P/P0 = n1/n1 ϩ n2, There are two major types of environment in which water where n is moles of solvent (water); n is moles of solute; availability can become limiting for an organism.
    [Show full text]
  • Extracellular Hydrolases Producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India
    Int.J.Curr.Microbiol.App.Sci (2016) 5(11): 51-64 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 5 Number 11 (2016) pp. 51-64 Journal homepage: http://www.ijcmas.com Original Research Article http://dx.doi.org/10.20546/ijcmas.2016.511.006 Extracellular Hydrolases producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India Bhavini N. Rathod1, Harshil H. Bhatt2 and Vivek N. Upasani1* 1Department of Microbiology, M.G. Science Institute, Ahmedabad- 380009, India 2Kadi Sarva Vishwavidyalay Gandhinagar-23, India *Corresponding author ABSTRACT Haloarchaea thrive in hypersaline environments such as marine salterns, saline soils, soda lakes, salted foods, etc. The lysis of marine phyto- and zoo-planktons such as algae, diatoms, shrimps, purple and green bacteria, fish, etc. releases K e yw or ds biopolymers namely cellulose, starch, chitin, proteins, lipids, etc. in the saline Extremozymes , ecosystems. The chemorganotrophic haloarchaea therefore, need to produce haloarchaea, hydrolytic enzymes to utilize these substrates. However, the raw solar salt used for hydrolases, preservation can cause spoilage of foods due to the growth of halobacteria leading Halobacterium, to economic loss. We report here the isolation and identification of extracellular Haloferax, hydrolases (substrates casein, gelatin, starch, and Tweens: 20, 60, 40, 80) Halopetinus, producing haloarchaea isolated from the salt and brine samples collected from Okhamadhi marine salterns at Okhamadhi, Gujarat, India. Morphological,
    [Show full text]
  • The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
    biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations.
    [Show full text]
  • Origin of the Cell Nucleus, Mitosis and Sex: Roles of Intracellular Coevolution Thomas Cavalier-Smith*
    Cavalier-Smith Biology Direct 2010, 5:7 http://www.biology-direct.com/content/5/1/7 RESEARCH Open Access Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution Thomas Cavalier-Smith* Abstract Background: The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long- standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. Results: I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange.
    [Show full text]