Molecular Phylogeny of Microorganisms

232 Pages·2010·5.311 MB·English

by  Aharon Oren (editor), R. Thane Papke (editor)

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A B C D
Molecular Phylogeny
of Microorganisms
Edited by
Aharon Oren and R. Th ane Papke
Caister Academic Press
Molecular Phylogeny of
Microorganisms
Aharon Oren
Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Israel
and
R. Thane Papke
Department of Molecular and Cell Biology
University of Connecticut
USA
Caister Academic Press
Copyright © 2010
Caister Academic Press
Norfolk, UK
www.caister.com
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library
ISBN:978-1-904455-67-7
Description or mention of instrumentation, software, or other products in this book does
not imply endorsement by the author or publisher. The author and publisher do not assume
responsibility for the validity of any products or procedures mentioned or described in this
book or for the consequences of their use.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval
system, or transmitted, in any form or by any means, electronic, mechanical, photocopying,
recording or otherwise, without the prior permission of the publisher. No claim to original
U.S. Government works.
Cover image: courtesy of Olga Zhaxybayeva
Printed and bound in Great Britain
Contents
List of Contributors v
Preface: From a ‘Protoplasmal Primordial Atomic Globule’ to a
Wealth of ‘Scientific Names of beings Animalculous’ vii
1 Concepts About Phylogeny of Microorganisms – an Historical Overview 1
Aharon Oren
2 Methods and Programs for Calculation of Phylogenetic
Relationships from Molecular Sequences 23
Jongsik Chun and Soon Gyu Hong
3 Multilocus Sequence Analysis and Bacterial Species Phylogeny Estimation 41
Pablo Vinuesa
4 Molecular Phylogeny of Microorganisms: Is rRNA Still a Useful Marker? 65
Wolfgang Ludwig
5 The Phyla of Prokaryotes – Cultured and Uncultured 85
Aharon Oren
6 Rooting the Tree of Life 109
Greg Fournier
7 Applications of Conserved Indels for Understanding Microbial Phylogeny 135
Radhey S. Gupta
8 Construction and Deconstruction: The Influence of Lateral Gene
Transfer on the Evolution of the Tree of Life 151
Maureen O’Malley
9 Horizontal Gene Transfer and the Formation of Groups of Microorganisms 167
David Williams, Cheryl P. Andam and J. Peter Gogarten
10 Endosymbiosis and the Evolution of Plastids 185
Christopher E. Lane and Dion G. Durnford
Index 217
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Contributors
Cheryl P. Andam Radhey S. Gupta
Department of Molecular and Cell Biology Department of Biochemistry
University of Connecticut McMaster University
Storrs, CT Hamilton, Canada
USA
[email protected]
cheryl@[email protected]
Soon Gyu Hong
Jongsik Chun Polar Biocenter
School of Biological Sciences and Institute of Korea Polar Research Institute
Microbiology KORDI
Seoul National University Songdo Techno Park
Gwanak-gu Yeonsu-gu
Seoul, Republic of Korea Incheon, Republic of Korea
[email protected] [email protected]
Dion G. Durnford Christopher E. Lane
Department of Biology Department of Biological Sciences
University of New Brunswick University of Rhode Island
Fredericton, NB Kingston, RI
Canada USA
[email protected] [email protected]
Gregory P. Fournier Wolfgang Ludwig
Department of Biological Engineering Lehrstuhl für Mikrobiologie
NASA Astrobiology Institute Technische Universität München
Massachusetts Institute of Technology Freising, Germany
Cambridge, MA
[email protected]
[email protected]
Maureen A. O’Malley
J. Peter Gogarten Egenis
Department of Molecular and Cell Biology University of Exeter
University of Connecticut Exeter, UK
Storrs, CT
M.A.O’[email protected]
USA
[email protected]
vi | Contributors
Aharon Oren Pablo Vinuesa
Department of Plant and Environmental Sciences Centro de Ciencias Genómicas
The Institute of Life Sciences and The Moshe Shilo Universidad Nacional Autónoma de México
Minerva Center for Marine Biogeochemistry Cuernavaca, Morelos
The Hebrew University of Jerusalem Mexico
Jerusalem
[email protected]
Israel
[email protected] David Williams
Department of Molecular and Cell Biology
R. Thane Papke University of Connecticut
Department of Molecular and Cell Biology, Storrs, CT
University of Connecticut USA
Storrs, CT
[email protected]
USA
[email protected]
Preface
From a ‘Protoplasmal Primordial Atomic
Globule’ to a Wealth of ‘Scientific Names of
Beings Animalculous’
Don’t mention it. I am, in point of fact, a par- etc., known since the days when Antonie van
ticularly haughty and exclusive person, of pre- Leeuwenhoek saw the first bacteria through the
Adamite ancestral descent. You will understand lens of this primitive microscope. The diversity
this when I tell you that I can trace my ancestry of protozoa was documented in detail in the first
back to a protoplasmal primordial atomic glob- decades of the nineteenth century by Christian
ule. Consequently, my family pride is something Ehrenberg and others. What Darwin did not
inconceivable. know was how genetic information was inherited,
though Mendel sent him a manuscript of his work
This statement was made by Poo-Bah, the with peas. Despite the fact that Fredrick Griffith’s
‘Lord High Everything Else’ of the Town of Titipu 1928 experiments demonstrating DNA as the
in The Mikado, the comic opera with lyrics by molecule of genetic information was clearly a
William Schwenck Gilbert and music by Arthur case of lateral gene transfer, acceptance of this
Sullivan, first produced in 1885. It is a surpris- mode of inheritance as an import mechanism
ing statement, as in that period hardly anybody for the evolution of prokaryotes had to wait until
thought about the phylogeny of those ancient the creation of inexpensive DNA sequencing and
‘protoplasmal primordial atomic globules’ that computational power. Today, lateral gene transfer
may have had some resemblance to the microor- is acknowledged as a relevant source of genetic
ganisms found in nature today. Charles Darwin, variation in each domain of life, but the debate
who introduced the concepts of phylogeny and still rages as to whether phylogenetic reconstruc-
evolution to the scientific world, was indeed opti- tion of the ‘tree of life’, especially for prokaryotes,
mistic that some time in the future, the secrets of represents organism or gene evolution, which has
phylogeny will be revealed. ‘The time will come, an enormous impact on all facets of evolution and
I believe, though I shall not live to see it, when taxonomy. Here, we explore phylogeny and its
we shall have very fairly true genealogical trees usefulness with respect to microorganisms.
of each great kingdom of Nature’, thus Darwin The first chapter by Aharon Oren provides an
wrote in a letter to Thomas Henry Huxley (26 historical overview of how scientists looked at the
September 1859). It is also noteworthy that the phylogeny of microbes, and especially of prokary-
only illustration to appear in The Origin of Species otic microorganisms, in the past – from the
was a tree-like representation showing how life nineteenth century morphology-based schemes
may have diverged from one or more common to schemes based on physiological properties and
ancestors to result in the current diversity of liv- information on the cell wall, to the 16S rRNA
ing organisms on Earth. However, it is interesting gene-based phylogenetic trees used nowadays by
to note that Darwin did not often mention the nearly all workers in the field to establish order
microbial world in his writings. Darwin surely in the complex world of the prokaryotes. This
knew about the diversity of bacteria, protozoa, molecular approach, pioneered by Carl Woese
viii | Preface
in the 1970s, leading to the three-domain model heat shock and recA proteins. Although the
(Archaea–Bacteria–Eucarya), has revolutionized comparative analyses are hampered by the gen-
our thinking about evolution in the microbial erally low phylogenetic information content, a
world. domain and prokaryotic phyla concept is globally
The wealth of sequence information that is supported.
accumulating at an ever-increasing speed can only The result of the 16S rRNA sequence based
be used for phylogenetic reconstruction when phylogenetic tree reconstruction is summarized
appropriate computational tools are available to in Chapter 5, in which Aharon Oren presents the
use the information to reconstruct phylogenetic major phyla of prokaryotes, based on cultured
trees. Chapter 2 by Jongsik Chun and Soon Gyu and named species as well as on ‘environmental’
Hong provides an overview of the methods and sequences recovered from DNA isolated from
programs for the calculation of phylogenetic rela- different environments. To obtain the organisms
tionships and trees. Even though we may never harbouring these sequences and to study their
know the true phylogeny, phylogenetic analysis properties is a major challenge of microbiology
provides best assumptions, thereby providing a today. This type of classification, in which the
framework for various disciplines in microbiol- now over 8200 species of prokaryotes with validly
ogy. Due to the technologically innovative burst published names are classified in respectively 27
of modern molecular biology and the rapid phyla of Bacteria and two phyla of Archaea (as of
advancement in computational science, inferring November 2009), was adopted in the latest edi-
the true phylogeny of a gene or organism seems tion of Bergey’s Manual of Systematic Bacteriology.
possible in the near future. The chapter reviews It should, however, be stressed that there is no
major steps in phylogenetic analysis and introduc- official classification of prokaryotes. For the high-
es relevant computer software tools with respect er taxa there even is no official nomenclature: the
to their accuracy, efficiency and availability. rules of the International Code of Nomenclature
Chapter 3 by Pablo Vinuesa presents a review of Prokaryotes do not cover taxa above the rank
of the critical factors that have to be considered of class. Alternative classifications have been
and evaluated in multilocus sequence analysis, proposed, based, for example, on the structure of
a technique increasingly used in order to make the cell wall.
robust estimates of bacterial species phylogenies The approaches towards the rooting of the
when the 16S rRNA alone does not provide the universal tree of life are discussed in Chapter 6
full information. The chapter presents a number by Greg Fournier. Identifying the location of the
of case studies, reviews criteria for marker selec- root of the tree corresponding to the most recent
tion and provides practical advice on the compu- common ancestor is a challenging and distinct
tational aspects, potential pitfalls, and software problem that has yet to be completely solved. To
choices available for each step in multilocus date, many investigations have proposed various
sequence analysis, emphasizing the importance of roots, using a wide diversity of biological data
using multiple isolates per species/lineage, proper and techniques. A survey of the most promising
model selection and thorough tree searches to get of these models illustrates the difficulty faced in
a good estimate of a multispecies phylogeny. reaching a scientific consensus on the issue, as
In Chapter 4, Wolfgang Ludwig asks whether well as the additional philosophical complications
the small subunit RNA sequence is still a useful posed by our emerging understanding of the role
marker to reconstruct the molecular phylogeny of horizontal gene transfer in genome evolution.
of microorganisms. The current taxonomy of Comparative analysis of genome sequences
prokaryotes as well as modern probe and chip is leading to discovery of large numbers of novel
based identification methods are mainly based molecular markers that are proving very helpful
upon rRNA derived phylogenetic conclusions. in understanding many important aspects of
The significance of single gene based phylogenetic microbial phylogeny. Of these molecular markers,
inference was evaluated by including alternative conserved inserts or deletions (indels) in protein
global markers such as elongation and initiation sequences provide a means for identifying differ-
factors, RNA polymerase subunits, DNA gyrases, ent groups of microbes in molecular terms and for
Preface | ix
understanding how they have may have evolved cells by non-photosynthetic eukaryotic hetero-
from a putative common ancestor. Chapter 7 by trophs. The result of this process is clear, but the
Radhey Gupta discusses the applications of con- mode and tempo of plastid movement among
served indels for analysing microbial phylogeny, eukaryotes, particularly plastids of red algal
and shows how genetic and biochemical studies derivation, are largely unknown. Recent changes
of these markers should also lead to identification in our understanding of the relationships between
of novel properties that are unique to different eukaryotic supergroups have only served to com-
groups of microbes. plicate the picture further.
Elucidation of an ever increasing number The different approaches applied today to elu-
of genome sequences of Bacteria and Archaea cidate the molecular phylogeny of the prokaryotes
shows how important lateral gene transfer has (and of eukaryotic protists as well) have taken us
been in the evolution of the prokaryotic world. a long way toward illuminating the complex world
Realization of the significance of lateral gene of the microbes that Linnaeus described under
transfer and other non-vertical processes has a single taxon, ‘Chaos infusorium’. The methods
reconceptualized and reoriented attempts to available to the microbiologist today will rapidly
construct the universal phylogeny. Chapter 8 by place a newly isolated strain or an environmental
Maureen O’Malley discusses the occurrence of small subunit rRNA gene sequence within the
paradigm shifts as construction, deconstruction existing framework of the universal tree, even if
and reconstruction of the tree of life changed, some details of the exact topology of the tree may
based on our increasing understanding of lateral still be unknown.
gene transfer phenomena. The number of isolated, characterized, and
The impact of gene transfer on the formation named species of prokaryotic and eukaryotic
of groups of organisms is described in further microorganisms – presumably all descendants of
depth in Chapter 9 by David Williams, Cheryl the above-mentioned ‘protoplasmal primordial
Andam and Peter Gogarten. Gene transfer can atomic globule’ that supposedly was the begin-
make it more difficult to define and determine ning of all life of Earth – is ever increasing. A
relationships. In those cases where many genes proper understanding of the diversity, systematics
have been transferred between partners, the and nomenclature of the microbes is important
majority of genes in a genome may reflect biased in many branches of biological science. Having
gene acquisition, and as a consequence, if a coher- opened this preface with a quote from a Gilbert &
ent signal is detected, one nevertheless might not Sullivan comic opera, we close with another quo-
be sure that the signal is due to shared organismal tation from their work, this time from The Pirates
ancestry. Lateral gene transfer may have posi- of Penzance (1879), that shows that knowledge of
tive aspects as well when trying to reconstruct microbial systematics, nomenclature and phylog-
phylogenetic trees. The presence of a particular eny can be of importance to many professionals,
transferred gene was shown, in several cases, to even to a Major-General:
constitute a shared derived character useful in
classification. Gene transfer can put together new I’m very good at integral and differential
metabolic pathways that open up new ecological calculus;
niches, and consequently, the transfer of an adap- I know the scientific names of beings animalcu-
tive gene might create a new group of organisms lous:
In Chapter 10, finally, Christopher Lane and In short, in matters vegetable, animal, and
Dion Durnford discuss the role of endosymbiosis mineral,
and the evolution of plastids. Photosynthesis is I am the very model of a modern
one of the most successful energy production Major-General.
strategies on the planet and has been co-opted
numerous times throughout evolutionary history Aharon Oren and R. Thane Papke
via the uptake and retention of photosynthetic