Проблемы Эволюции

Проблемы Эволюции

Происхождение эукариот

Марков А. В.

Обзор 7

 

Происхождение эукариот

 

А. В. Марков, А. М. Куликов. Происхождение эукариот как результат интеграционных процессов в микробном сообществе (иллюстрированный доклад)

 

 

ЗАЧЕМ? Появление эукариотической клетки является вторым по значимости (после зарождения самой жизни) событием биологической эволюции. Важнейшее отличие эукариотических организмов от прокариотических состоит в более совершенной системе регуляции генома (именно в этом смысл появления клеточного ядра: область активного метаболизма – цитоплазма – отделилась от области хранения, считывания, репликации генетической информации и, главное, регуляции транскрипции и посттранскрипционных модификаций РНК). Благодаря этому резко возросла приспособляемость одноклеточных организмов, их способность адаптироваться к меняющимся условиям БЕЗ внесения наследственных изменений в геном, т.е. оставаясь "самими собой". Рост приспособляемости, устойчивости живых систем – основной закон биологической эволюции; в Фанерозое, например, он проявляется в закономерном и неуклонном росте средней продолжительности существования родов (см. об этом наш обзор и статью А.Маркова). Именно благодаря возможности адаптироваться, т.е. изменяться в зависимости от внешних условий, эукариоты смогли стать многоклеточными: ведь в многоклеточном организме клетки с одним и тем же геномом, в зависимости от условий, образуют совершенно разные как по морфологии, так и по функции ткани.

 

Фотоальбом "Прокариоты"

 

Фотоальбом "Одноклеточные эукариоты"

 

Марков А.В. Ядро земное и ядро клеточное: что между ними общего? (популярная статья)

 

В.В.Малахов. Основные этапы эволюции эукариотных организмов. 2003.

 

М. А. Федонкин. Сужение геохимического базиса жизни и эвкариотизация биосферы: причинная связь. 2003.

 

С. В. Шестаков. О ранних этапах биологической эволюции с позиции геномики. 2003.

 

Марков А.В. Проблема происхождения эукариот

 

А.В.Марков, А.М.Куликов. Происхождение эвкариот: выводы из анализа белковых гомологий в трех надцарствах живой природы

 

О происхождении эукариот. Из популярной книги А.Ю.Журавлева.

 

Г.А.Заварзин. Эволюция микробных сообществ.

 

Н.А.Колчанов. Эволюция регуляторных генетических систем.

 

Рассуждения А.С.Раутиана (из комментариев к кн. Тейяра де Шардена "Феномен человека") о разделении организма на герму (часть, в которой заключена наследственная информация) и сому (все остальное тело) помогают понять значение выделения клеточного ядра:

"Разделение организма на сому и герму обусловлено прежде всего тем, что задачи хранения наследственной информации и функционирования предъявляют к своей материальной основе противоположные требования. Любая динамика понижает устойчивость гермы и содержащейся в ней наследственной информации (книга лучше всего сохраняется, если ее не читают). Все живые системы принципиально динамичны. Находясь вдали от состояния термодинамического равновесия, они поддерживают свои существенные параметры благодаря постоянному обмену веществм и энергией с внешней средой. Иными словами, для поддержания сомы необходима динамика, а для сохранения гермы с ее наследственной информацией - покой. Компромисс между этими противоположными требованиями достигается путем пространственного разделения сомы и гермы внутри организма"

 

А.Ю.Розанов, М.А.Федонкин. Проблема первичного биотопа эвкариот. 1994.

 

Симбиоз. "Блочный" принцип сборки живых систем. См. об этом в нашем обзоре "Проблема эволюционных новообразований".

 

Тут есть о чем подумать и в философском плане. Мы свыклись с мыслью о том, что произошли от обезьяны. Обезьяна - зверь, нам близкий и понятный. Сложнее, но все-таки можно представить, что мы произошли от бактерии. Какой-никакой, а все же организм, клетка, что-то конкретное и осязаемое. Но нам становится жутковато, когда мы пытаемся осознать следующую истину в ее неприкрытой бесчеловечности. Наш предок - сообщество бактерий. Мы произошли от кишащей массы разных мельчайших тварей, постепенно сливавшихся в единый организм...

 

КОГДА И ПОЧЕМУ? Этот крупнейший ароморфоз произошел, по-видимому, не позднее, чем 2,6 – 2,7 млрд. лет назад, на рубеже Архея и Протерозоя (это определили по биомаркерам – остаткам хим. соединений, свойственных только эукариотам, см. наш обзор "древнейшие следы жизни"). Появление эукариот (точнее, тот момент, когда их присутствие становится заметным в летописи) совпадает по времени с самой крупной за всю историю Земли геофизической перестройкой. Первопричиной этой перестройки, по одной из последних моделей, стало выделение у Земли железного ядра, которое привело к целому комплексу последствий:  исключительно сильным конвективным течениям в мантии, образованию "Моногеи" (единого континента), максимуму тектонической активности, смене тектоники тонких базальтовых пластин тектоникой литосферных плит, резкому снижению CO2 в атмосфере и резкому похолоданию (кислород в атмосфере стал накапливаться гораздо позже). Такие катастрофические события могли способствовать развитию эукариот двумя способами. Во-первых, они не могли не привести к разрушению, хотя бы частичному, сложившихся ранее прокариотных сообществ, в частности, цианобактериальных "матов". В ходе кризиса и после стали складываться новые микробные сообщества, уже не чисто прокариотные, а смешанные – прокариотно-эукариотные. Такие сообщества были более устойчивыми. Таким образом, возможно, величайший в истории Земли кризис "помог" эукариотам занять прочное положение в биосфере точно так же, как "массовое вымирание" на рубеже Мезозоя и Кайнозоя помогло млекопитающим и птицам занять множество ниш, которые раньше были заняты рептилиями (пока Мезозойские динозавровые сообщества не были разрушены кризисом, млекопитающие и птицы были вынуждены оставаться второстепенными, подчиненными группами). Во-вторых, очевидно, что в эпоху чрезвычайно резких (катастрофических) колебаний внешних условий более приспособляемые формы должны были получить огромное адаптивное преимущество, должен был идти "отбор на приспособляемость".

КАК? Общепризнано, что эукариоты появились в результате симбиоза нескольких разновидностей прокариот (бактерий). По-видимому, митохондрии произошли от альфа-протеобактерий (аэробных эубактерий), пластиды – от цианобактерий, а основная клетка – цитоплазма – от какой-то архебактерии. Пока нет общепринятой теории возникновения ядра, цитоскелета, жгутиков. Приведенная ниже подборка рефератов показывает, как много различных гипотез и моделей сейчас обсуждается. Очевидно, имеющиеся фактические данные пока недостаточны для того, чтобы отдать предпочтение какой-то одной из гипотез или выработать новую, которая устроила бы большинство ученых.

Моя точка зрения, основанная на анализе белковых доменов архей, бактерий и эукариот, изложена здесь . Согласно предлагаемой модели, ядерно-цитоплазматический компонент будущих эукариот (перед приобретением митохондриальных симбионтов) представлял собой химерный организм, возникший в результате активного поглощения архебактерией чужеродного (в основном эубактериального) наследственного материала из внешней среды. Возможно, главным стимулом для возникновения такой стратегии у архебактерии стал кризис, вызванный переходом цианобактерий к кислородному фотосинтезу.

 

Весьма важен для эволюционной теории следующий вопрос: если эукариоты такие прогрессивные и приспособляемые, почему же они не вытеснили "отсталых", "примитивных" прокариот? Почему прокариотический мир продолжает процветать и по сей день? Этот вопрос можно задать и в более общей форме: почему "прогрессивные" новые формы продолжают сосуществовать с "примитивными" старыми, а не вытесняют их? Интересный ответ предложил в своем докладе академик Г.А.Заварзин: "Фокус заключается в том, что новый организм может установить себя только в том случае, если он соответствует существующему сообществу. Если он не соответствует этому сообществу, он в него вписаться не может. Отсюда следует, что старое должно быть сохранено как необходимое предварительное условие для устойчивого существования нового. По большой шкале эволюция происходит не путем замены, но аддитивно, поскольку новые члены выживают только в том случае, если они соответствуют существующим сообществам. Новое накладывается на старое, и старое должно быть сохранено как предварительное условие для существования нового. При этом функциональная структура не меняется, несмотря на частичные субституции... микробы остаются базисом планетарной системы поддержания жизни".

 

Подборка цитологической, генетической и биохимической литературы по происхождению эукариот

 

Молекулярные данные по эволюции мейоза

 

The Santa Barbara Basin is a symbiosis oasis.

Nature 2000 Jan 6;403(6765):77-80

Bernhard JM, Buck KR, Farmer MA, Bowser SS.

Department of Environmental Health Sciences, School of Public Health, University of South Carolina, Columbia 29208, USA. jmbernha@sph.sc.edu

 

It is generally agreed that the origin and initial diversification of Eucarya occurred in the late Archaean or Proterozoic Eons when atmospheric oxygen levels were low and the risk of DNA damage due to ultraviolet radiation was high. Because deep water provides refuge against ultraviolet radiation and early eukaryotes may have been aerotolerant anaerobes, deep-water dysoxic environments are likely settings for primeval eukaryotic diversification. Fossil evidence shows that deep-sea microbial mats, possibly of sulphur bacteria similar to Beggiatoa, existed during that time. Here we report on the eukaryotic community of a modern analogue, the Santa Barbara Basin (California, USA). The Beggiatoa mats of these severely dysoxic and sulphidic sediments support a surprisingly abundant protistan and metazoan meiofaunal community, most members of which harbour prokaryotic symbionts. Many of these taxa are new to science, and both microaerophilic and anaerobic taxa appear to be represented. Compared with nearby aerated sites, the Santa Barbara Basin is a 'symbiosis oasis' offering a new source of organisms for testing symbiosis hypotheses of eukaryogenesis.

PMID: 10638755

 

Это хорошо подтверждает идею о том, что эукариоты, как компоненты прокариотных сообществ, могли развиваться в анаэробных или почти анаэробных условиях; что симбиоз с прокариотами мог возникать легко и многократно.

Симбиотический организм, сочетающий симбионтов с принципиально разным метаболизмом (они взаимодополняют друг друга, одни утилизируют "отходы" жизнедеятельности других) – это фактически маленькая компактная экосистема. Которую, к тому же, можно эффективно и слаженно регулировать через единый регуляторный механизм.

 

 

Hyperthermophiles in the history of life.

Ciba Found Symp 1996;202:1-10; discussion 11-8   

Stetter KO.
Lehrstuhl fur Mikrobiologie, Universitat Regensburg, Germany.

Prokaryotes requiring extremely high growth temperatures (optimum 80-110 degrees C) have recently been isolated from water-containing terrestrial, subterranean and submarine high temperature environments. These hyperthermophiles consist of primary producers and consumers of organic matter, forming unique high temperature ecosystems. Surprisingly, within the 16S rRNA-based phylogenetic tree, hyperthermophiles occupy all the shortest and deepest branches closest to the root. Therefore, they appear to be the most primitive extant organisms. Most of them (the primary producers) are able to grow chemolithoautotrophically, using CO2 as sole carbon source and inorganic energy sources, suggesting a hyperthermophilic autotrophic common ancestor. They gain energy from various kinds of respiration. Molecular hydrogen and reduced sulfur compounds serve as electron donors while CO2, oxidized sulfur compounds, NO3- and O2 (only rarely) serve as electron acceptors. Growth demands of hyperthermophiles fit the scenario of a hot volcanism-dominated primitive Earth. Similar anaerobic chemolithoautotrophic hyperthermophiles, completely independent of a sun, could even exist on other planets provided that active volcanism and liquid water were present.
PMID
: 9243007

Гипертермофилы – вроде самые древние (по кладограммам так получалось). Предварительные соображения об их роли в происхождении жизни. Это уже несколько устарело.

 

 

 

Bioelectrochemistry 2002 Nov;58(1):41-6 
Role of lipid membrane-nucleic acid interactions, DNA-membrane contacts and metal (II) cations in origination of initial cells and in evolution of prokaryotes to eukaryotes.
Zhdanov RI, Kuvichkin VV, Shmyrina AS, Jdanov AR, Tverdislov VA.
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10, Pogodinskaya Street, 119121, Moscow, Russia

The problems of the origin of primary cells and eukaryotic cells are discussed in terms of possible role of interactions between nucleic acids with lipid membrane according to corresponding original hypothesis. We propose that there are two main hypotheses of the origin of primary cells: (a) RNA appeared before proteins and DNA [Nature 213 (1967) 119]; (b) it is needed for the appearance of a primary cell, the volume closed by the lipid membrane. There was no information about the ways on how RNA appeared inside that volume for saving the reaction products around. Our hypothesis suggests that one of the starting points in the origination of primary cells was the interaction of nucleic acid and lipid membrane bubbles in the presence of metal (II) ions (which existed in high concentrations in prebiotic conditions), and this resulted in the enclosing of the pro-RNAs inside the lipid membrane. This hypothesis is formulated by us on the basis of experimental biochemical and biophysical studies of the DNA/RNA-phospholipid vesicles interactions in the presence of metal ions (II) fulfilled in the Institute of Biomedical Chemistry, RAMS, Moscow and Institute of Biophysics, RAS, Pushchino. Our belief is that DNA-membrane contacts (DNA-MCs) played an important role in the prokaryotes-to-eukaryotes transition. The model of the confluence of four prokaryotic cells may explain the prokaryotes-to-eukaryotes transition by the way of eukaryotic nuclear pore formation from prokaryotic Bayer' contacts. The main requirement for the following fusion of prokaryotic cells must be their mutual orientation. After possible association, the division of the formed cell is begun. The great advantage of the model of four prokaryotic cells is the profit in the metabolism and the possibility of the intensive growth of intercellular membrane structures.
PMID: 12401569 [PubMed - in process] ; 10664676

 

 

Anat Rec 2002 Nov 1;268(3):290-301                                                                                              
Motility proteins and the origin of the nucleus.
Dolan MF, Melnitsky H, Margulis L, Kolnicki R.
Department of Geosciences, University of Massachusetts, Morrill Science Center, Amherst 01003, USA. mdolan@geo.umass.edu

Hypotheses on the origin of eukaryotic cells must account for the origin of the microtubular cytoskeletal structures (including the mitotic spindle, undulipodium/cilium (so-called flagellum) and other structures underlain by the 9(2)+2 microtubular axoneme) in addition to the membrane-bounded nucleus. Whereas bacteria with membrane-bounded nucleoids have been described, no precedent for mitotic, cytoskeletal, or axonemal microtubular structures are known in prokaryotes. Molecular phylogenetic analyses indicate that the cells of the earliest-branching lineages of eukaryotes contain the karyomastigont cytoskeletal system. These protist cells divide via an extranuclear spindle and a persistent nuclear membrane. We suggest that this association between the centriole/kinetosome axoneme (undulipodium) and the nucleus existed from the earliest stage of eukaryotic cell evolution. We interpret the karyomastigont to be a legacy of the symbiosis between thermoacidophilic archaebacteria and motile eubacteria from which the first eukaryote evolved. Mutually inconsistent hypotheses for the origin of the nucleus are reviewed and sequenced proteins of cell motility are discussed because of their potential value in resolving this problem. A correlation of fossil evidence with modern cell and microbiological studies leads us to the karyomastigont theory of the origin of the nucleus. Copyright 2002 Wiley-Liss, Inc.
PMID: 12382325 [PubMed - in process]

 

Первые эукариоты возникли в рез. симбиоза ацидотермофильной Археи с подвижной Бактерией. Это объясняет наличие у всех эукариот микротрубчатого цитоскелета – митотическое веретено, жгутики и др. – чего не бывает у прокариот. Древнейший митозбез разрушения ядерной мембраны.

 

Int J Syst Evol Microbiol 2002 Jan;52(Pt 1):7-76       
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.
Cavalier-Smith T.
Department of Zoology, University of Oxford, UK. tom.cavalier-smith@zoo.ox.ac.uk

Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein lob; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.
 PMID
: 11837318

"Переворот" в классификации жизни. Очень экстравагантная теория. Но здесь много важных фактов, напр., в чем состоит сходство Архей и Эукариот.

 

 

Proc Natl Acad Sci U S A 2002 Feb 5;99(3):1420-5                                                                         

Erratum in: Proc Natl Acad Sci U S A 2002 Apr 2;99(7):4752

 The origin of the eukaryotic cell: a genomic investigation.
Hartman H, Fedorov A.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. hhartman@mit.edu

We have collected a set of 347 proteins that are found in eukaryotic cells but have no significant homology to proteins in Archaea and Bacteria. We call these proteins eukaryotic signature proteins (ESPs). The dominant hypothesis for the formation of the eukaryotic cell is that it is a fusion of an archaeon with a bacterium. If this hypothesis is accepted then the three cellular domains, Eukarya, Archaea, and Bacteria, would collapse into two cellular domains. We have used the existence of this set of ESPs to test this hypothesis. The evidence of the ESPs implicates a third cell (chronocyte) in the formation of the eukaryotic cell. The chronocyte had a cytoskeleton that enabled it to engulf prokaryotic cells and a complex internal membrane system where lipids and proteins were synthesized. It also had a complex internal signaling system involving calcium ions, calmodulin, inositol phosphates, ubiquitin, cyclin, and GTP-binding proteins. The nucleus was formed when a number of archaea and bacteria were engulfed by a chronocyte. This formation of the nucleus would restore the three cellular domains as the Chronocyte was not a cell that belonged to the Archaea or to the Bacteria.

PMID
: 11805300

Еще одна забавная теория происхождения эукариот.

Кроме Архей и Бактерий был еще третий базовый тип ("царство") прокариот – хроноциты. Хроноцит проглотил много Архей и Бактерий и стал Эукариотом. У хроноцита был ЦИТОСКЕЛЕТ, позволявший ему ГЛОТАТЬ другие клетки; сложную внутреннюю с-му мембран, на кот. синтезировались липиды и белки; сложную внутреннюю сигнальную систему.

Однако некие зачатки цитоскелета все-таки найдены у прокариот:  van den Ent F, Amos L, Lowe J.  Bacterial ancestry of actin and tubulin. Curr Opin Microbiol. 2001 Dec;4(6):634-8. Review. PMID: 11731313, 11544518

 

 

BMC Evol Biol 2001;1(1):4                                                                                                                 
A genomic timescale for the origin of eukaryotes.
Hedges SB, Chen H, Kumar S, Wang DY, Thompson AS, Watanabe H.
Astrobiology Research Center and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. sbh1@psu.edu

BACKGROUND: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes. RESULTS: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (~4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events. CONCLUSIONS: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.
PMID: 11580860 [PubMed - as supplied by publisher]

Попытка определить время происхождения эукариот по генным часам. Ничего особо интересного и много явной чуши.

 

Symbiosis 1985;1:101-24      
Symbiosis as a mechanism of evolution: status of cell symbiosis theory.
Margulis L, Bermudes D.
Department of Biology, Boston University, MA 02215, USA.

Several theories for the origin of eukaryotic (nucleated) cells from prokaryotic (bacterial) ancestors have been published: the progenote, the direct filiation and the serial endosymbiotic theory (SET). Compelling evidence for two aspects of the SET is now available suggesting that both mitochondria and plastids originated by symbioses with a third type of microbe, probably a Thermoplasma-like archaebacterium ancestral to the nucleocytoplasm. We conclude that not enough information is available to negate or substantiate another SET hypothesis: that the undulipodia (cilia, eukaryotic flagella) evolved from spirochetes. Recognizing the power of symbiosis to recombine in single individual semes from widely differing partners, we develop the idea that symbiosis has been important in the origin of species and higher taxa. The abrupt origin of novel life forms through the formation of stable symbioses is consistent with certain patterns of evolution (e.g punctuated equilibria) described by some paleontologists.
PMID: 11543608

Маргулис. Обзор состояния теории симбиогенеза: пластиды и митохондриида, жгутикипод вопросом. Предок цитоплазмы с ядром – Thermoplasma–подобная Архея.

 

Speculations Sci Technol 1984;7(2):77-81     
The origin of the eukaryotic cell.
Hartman H.
Massachusetts Institute of Technology, Department of Earth, Atmospheric and Planetary Sciences, Cambridge 02139, USA.

The endosymbiotic hypothesis for the origin of the eukaryotic cell has been applied to the origin of the mitochondria and chloroplasts. However as has been pointed out by Mereschowsky in 1905, it should also be applied to the nucleus as well. If the nucleus, mitochondria and chloroplasts are endosymbionts, then it is likely that the organism that did the engulfing was not a DNA-based organism. In fact, it is useful to postulate that this organism was a primitive RNA-based organism. This hypothesis would explain the preponderance of RNA viruses found in eukaryotic cells. The centriole and basal body do not have a double membrane or DNA. Like all MTOCs (microtubule organising centres), they have a structural or morphic RNA implicated in their formation. This would argue for their origin in the early RNA-based organism rather than in an endosymbiotic event involving bacteria. Finally, the eukaryotic cell uses RNA in ways quite unlike bacteria, thus pointing to a greater emphasis of RNA in both control and structure in the cell. The origin of the eukaryotic cell may tell us why it rather than its prokaryotic relative evolved into the metazoans who are reading this paper.
PMID
: 11541973

Еще одна теория: клеткой-хозяином при происхождении эукариот был РНК-организм (из РНК-мира). Интересный факт: центриоли, и др. микротрубочные организующие центры содержат структурную РНК (или она участвует в их формировании).

 

J Mol Evol 2001 May;52(5):419-25  
Poxviruses and the origin of the eukaryotic nucleus.
Takemura M.
Laboratory of Cancer Cell Biology, Research Institute for Disease Mechanism and Control, Nagoya University School of Medicine, Tsurumai-cho 65, Showa-ku, Nagoya 466-8550 Japan. takemura@tsuru.med.nagoya-u.ac.jp

A number of molecular forms of DNA polymerases have been reported to be involved in eukaryotic nuclear DNA replication, with contributions from alpha-, delta-, and epsilon-polymerases. It has been reported that delta-polymerase possessed a central role in DNA replication in archaea, whose ancestry are thought to be closely related to the ancestor of eukaryotes. Indeed, in vitro experiment shown here suggests that delta-polymerase has the potential ability to start DNA synthesis immediately after RNA primer synthesis. Therefore, the question arises, where did the alpha-polymerase come from? Phylogenetic analysis based on the nucleotide sequence of several conserved regions reveals that two poxviruses, vaccinia and variola viruses, have polymerases similar to eukaryotic alpha-polymerase rather than delta-polymerase, while adenovirus, herpes family viruses, and archaeotes have eukaryotic delta-like polymerases, suggesting that the eukaryotic alpha-polymerase gene is derived from a poxvirus-like organism, which had some eukaryote-like characteristics. Furthermore, the poxvirus's proliferation independent from the host-cell nucleus suggests the possibility that this virus could infect non-nucleated cells, such as ancestral eukaryotes. I wish to propose here a new hypothesis for the origin of the eukaryotic nucleus, posing symbiotic contact of an orthopoxvirus ancestor with an archaebacterium, whose genome already had a delta-like polymerase gene.
PMID
: 11443345

Еще одна теория: ядро возникло в рез-те взаимодействия Археи с каким-то вирусом.

 

Am Nat 1999 Oct;154(S4):S146-S163
Reconstructing Early Events in Eukaryotic Evolution.
Roger AJ.

Resolving the order of events that occurred during the transition from prokaryotic to eukaryotic cells remains one of the greatest problems in cell evolution. One view, the Archezoa hypothesis, proposes that the endosymbiotic origin of mitochondria occurred relatively late in eukaryotic evolution and that several mitochondrion-lacking protist groups diverged before the establishment of the organelle. Phylogenies based on small subunit ribosomal RNA and several protein-coding genes supported this proposal, placing amitochondriate protists such as diplomonads, parabasalids, and Microsporidia as the earliest diverging eukaryotic lineages. However, trees of other molecules, such as tubulins, heat shock protein 70, TATA box-binding protein, and the largest subunit of RNA polymerase II, indicate that Microsporidia are not deeply branching eukaryotes but instead are close relatives of the Fungi. Furthermore, recent discoveries of mitochondrion-derived genes in the nuclear genomes of entamoebae, Microsporidia, parabasalids, and diplomonads suggest that these organisms likely descend from mitochondrion-bearing ancestors. Although several protist lineages formally remain as candidates for Archezoa, most evidence suggests that the mitochondrial endosymbiosis took place prior to the divergence of all extant eukaryotes. In addition, discoveries of proteobacterial-like nuclear genes coding for cytoplasmic proteins indicate that the mitochondrial symbiont may have contributed more to the eukaryotic lineage than previously thought. As genome sequence data from parabasalids and diplomonads accumulate, it is becoming clear that the last common ancestor of these protist taxa and other extant eukaryotic groups already possessed many of the complex features found in most eukaryotes but lacking in prokaryotes. However, our confidence in the deeply branching position of diplomonads and parabasalids among eukaryotes is weakened by conflicting phylogenies and potential sources of artifact. Our current picture of early eukaryotic evolution is in a state of flux.
PMID
: 10527924 [PubMed - as supplied by publisher]

Важно: многие думают, что от появления ядра до появления митохондрий прошло долгое время. Но вроде на самом деле все-таки мтх появились очень рано, и общий предок всех современных эукариот имел мтх (а совр. безмитохондриальные эукариоты просто утратили их). Многие гены цитоплазматических белков у безмитохондриальных простейших имеют митохондриальное происхождение.

 

J Mol Evol 1998 May;46(5):499-507
Comment in:   
J Mol Evol. 2001 Sep;53(3):251-6.

A new aspect to the origin and evolution of eukaryotes.
Vellai T, Takacs K, Vida G.
Department of Genetics, Eotvos Lorand University, Muzeum krt. 4/A., Budapest, H-1088, Hungary. vellai@falco.elte.hu

One of the most important omissions in recent evolutionary theory concerns how eukaryotes could emerge and evolve. According to the currently accepted views, the first eukaryotic cell possessed a nucleus, an endomembrane system, and a cytoskeleton but had an inefficient prokaryotic-like metabolism. In contrast, one of the most ancient eukaryotes, the metamonada Giardia lamblia, was found to have formerly possessed mitochondria. In sharp contrast with the traditional views, this paper suggests, based on the energetic aspect of genome organization, that the emergence of eukaryotes was promoted by the establishment of an efficient energy-converting organelle, such as the mitochondrion. Mitochondria were acquired by the endosymbiosis of ancient alpha-purple photosynthetic Gram-negative eubacteria that reorganized the prokaryotic metabolism of the archaebacterial-like ancestral host cells. The presence of an ATP pool in the cytoplasm provided by this cell organelle allowed a major increase in genome size. This evolutionary change, the remarkable increase both in genome size and complexity, explains the origin of the eukaryotic cell itself. The loss of cell wall and the appearance of multicellularity can also be explained by the acquisition of mitochondria. All bacteria use chemiosmotic mechanisms to harness energy; therefore the periplasm bounded by the cell wall is an essential part of prokaryotic cells. Following the establishment of mitochondria, the original plasma membrane-bound metabolism of prokaryotes, as well as the funcion of the periplasm providing a compartment for the formation of different ion gradients, has been transferred into the inner mitochondrial membrane and intermembrane space. After the loss of the essential function of periplasm, the bacterial cell wall could also be lost, which enabled the naked cells to establish direct connections among themselves. The relatively late emergence of mitochondria may be the reason why multicellularity evolved so slowly.
PMID: 9545461 [PubMed - indexed for MEDLINE]

Хорошая статья, логичная. Опять мысль о том, что не было "этапа безмитохондриальных эукариот", что начальным событием было приобретение митохондрий, и это обусловило все последующие преобразования (в т.ч. генома) . Только на этот раз митохондрии выводятся из фотосинтезирующих бактерий!!!

 

Proc R Soc Lond B Biol Sci 1999 Aug 7;266(1428):1571-7  
The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells.
Vellai T, Vida G.
Institute for Advanced Study, Collegium Budapest, Hungary.

Eukaryotes have long been thought to have arisen by evolving a nucleus, endomembrane, and cytoskeleton. In contrast, it was recently proposed that the first complex cells, which were actually proto-eukaryotes, arose simultaneously with the acquisition of mitochondria. This so-called symbiotic association hypothesis states that eukaryotes emerged when some ancient anaerobic archaebacteria (hosts) engulfed respiring alpha-proteobacteria (symbionts), which evolved into the first energy-producing organelles. Therefore, the intracellular compartmentalization of the energy-converting metabolism that was bound originally to the plasma membrane appears to be the key innovation towards eukaryotic genome and cellular organization. The novel energy metabolism made it possible for the nucleotide synthetic apparatus of cells to be no longer limited by subsaturation with substrates and catalytic components. As a consequence, a considerable increase has occurred in the size and complexity of eukaryotic genomes, providing the genetic basis for most of the further evolutionary changes in cellular complexity. On the other hand, the active uptake of exogenous DNA, which is general in bacteria, was no longer essential in the genome organization of eukaryotes. The mitochondrion-driven scenario for the first eukaryotes explains the chimera-like composition of eukaryotic genomes as well as the metabolic and cellular organization of eukaryotes.

 PMID: 10467746 [PubMed - indexed for MEDLINE]

 

 

J Mol Evol 1998 Nov;47(5):517-30  
Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis
Moreira D, Lopez-Garcia P.
Laboratoire de Biologie Cellulaire (BC4), Batiment 444, URA CNRS 2227, Universite Paris-Sud, 91405 Orsay Cedex, France.

We present a novel hypothesis for the origin of the eukaryotic cell, or eukaryogenesis, based on a metabolic symbiosis (syntrophy) between a methanogenic archaeon (methanobacterial-like) and a delta-proteobacterium (an ancestral sulfate-reducing myxobacterium). This syntrophic symbiosis was originally mediated by interspecies H2 transfer in anaerobic, possibly moderately thermophilic, environments. During eukaryogenesis, progressive cellular and genomic cointegration of both types of prokaryotic partners occurred. Initially, the establishment of permanent consortia, accompanied by extensive membrane development and close cell-cell interactions, led to a highly evolved symbiotic structure already endowed with some primitive eukaryotic features, such as a complex membrane system defining a protonuclear space (corresponding to the archaeal cytoplasm), and a protoplasmic region (derived from fusion of the surrounding bacterial cells). Simultaneously, bacterial-to-archaeal preferential gene transfer and eventual replacement took place. Bacterial genome extinction was thus accomplished by gradual transfer to the archaeal host, where genes adapted to a new genetic environment. Emerging eukaryotes would have inherited archaeal genome organization and dynamics and, consequently, most DNA-processing information systems. Conversely, primordial genes for social and developmental behavior would have been provided by the ancient myxobacterial symbiont. Metabolism would have been issued mainly from the versatile bacterial organotrophy, and progressively, methanogenesis was lost.
PMID: 9797402 [PubMed - as supplied by publisher]

еще одна эктравагантная теория симбиогенеза (с участием метанобразующих бактерий)

 

Antonie Van Leeuwenhoek 1997 Jul;72(1):49-61                                                                               
Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes.
Gupta RS.
Department of Biochemistry McMaster University Hamilton, Ontario, Canada.

The evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes is examined based on protein sequence data. Phylogenies and common signature sequences in some of the most conserved proteins point to a close evolutionary relationship between Archaebacteria and Gram-positive bacteria. The monophyletic nature and distinctness of the Archaebacterial domain is not supported by many of the phylogenies. Within Gram-negative bacteria, cyanobacteria are indicated as the deepest branching lineage, and a clade consisting of Archaebacteria, Gram-positive bacteria and cyanobacteria is supported by signature sequences in many proteins. However, the division within the prokaryotic species, viz. ArchaebacteriaGram-positive bacteria-->Cyanobacteria-->other groups of Gram-negative bacteria, is indicated to be not very rigid but, instead is an evolutionary continuum. It is expected that certain species will be found which represent intermediates in the above transitions. By contrast to the evolutionary relationships within prokaryotes, the eukaryotic species, which are structurally very different, appear to have originated by a very different mechanism. Protein phylogenies and signature sequences provide evidence that the eukaryotic nuclear genome is a chimera which has received major contributions from both an Archaebacterium and a Gram-negative bacterium. To explain these observations, it is suggested that the ancestral eukaryotic cell arose by a symbiotic fusion event between the above parents and that this fusion event led to the origin of both nucleus and endoplasmic reticulum. The monophyletic nature of all extant eukaryotic species further suggests that a 'successful primary fusion' between the prokaryotic species that gave rise to the ancestral eukaryotic cell took place only once in the history of this planet.
PMID: 9296263 [PubMed - indexed for MEDLINE]

Все нынешние эукариоты – монофилетичны, происходят от одного предка. Симбиоз Археи с грам-отрицательной бактерией. Ядерный геном – химерный.

 

Comp Biochem Physiol A 1988;90(2):209-23
The evolutionary origin of eukaryotic transmembrane signal transduction.
Janssens PM.
Cell Biology and Genetics Unit, University of Leiden, The Netherlands.

1. A comparison was made of transmembrane signal transduction mechanisms in different eukaryotes and prokaryotes. 2. Much attention was given to eukaryotic microbes and their signal transduction mechanisms, since these organisms are intermediate in complexity between animals, plants and bacteria. 3. Signal transduction mechanisms in eukaryotic microbes, however, do not appear to be intermediate between those in animals, plants and bacteria, but show features characteristic of the higher eukaryotes. 4. These similarities include the regulation of receptor function, adenylate cyclase activity, the presence of a phosphatidylinositol cycle and of GTP-binding regulatory proteins. 5. It is proposed that the signal transduction systems known to operate in present-day eukaryotes evolved in the earliest eukaryotic cells.
PMID
: 2900114 [PubMed - indexed for MEDLINE]

Подтверждается важная идея: что более сложный и совершенный механизм клеточной РЕГУЛЯЦИИ возник уже у самых первых эукариот. И, возможно, в этом их основное преимущество по сравн. с прокариотами.

 

[On bacterial origin of mitochondria in eukaryotes in the light of current ideas of evolution of the organic world]

Izv Akad Nauk Ser Biol 2002 Jul-Aug;(4):501-7

 [Article in Russian]

Kuznetsov AP, Lebkova NP.

Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovskii pr. 36, Moscow, 117851 Russia.

 

The hypothesis of bacterial origin of mitochondria, which existed until the end of the 20th century, has been confirmed on the basis of the current concepts of organic world evolution in the open sea hydrosphere and original data on the entry of bacteria (prokaryotes) in the cells of eukaryotes and their transformation into the mitochondrial mechanism of aerobic energy metabolism. This hypothesis can now be considered as a factually substantiated theory. The process of endocytosis of bacteria in the tissues of eukaryotes, which began at the onset of transition of the anaerobic state of open sea hydrosphere and land atmosphere (Early Proterozoic), is considered as the beginning of symbiotic mode of life of organisms of the Proterozoic and Postproterozoic organic world.

PMID: 12180017

 

Orig Life Evol Biosph 1995 Jun;25(1-3):251-64
The effects of heavy meteorite bombardment on the early evolution--the emergence of the three domains of life.
Gogarten-Boekels M, Hilario E, Gogarten JP.
Dept. Molecular and Cell Biology, University of Connecticut, Storrs 06269-3044.

A characteristic of many molecular phylogenies is that the three domains of life (Bacteria, Archaea, Eucarya) are clearly separated from each other. The analyses of ancient duplicated genes suggest that the last common ancestor of all presently known life forms already had been a sophisticated cellular prokaryote. These findings are in conflict with theories that have been proposed to explain the absence of deep branching lineages. In this paper we propose an alternative scenario, namely, a large meteorite impact that wiped out almost all life forms present on the early Earth. Following this nearly complete frustation of life on Earth, two surviving extreme thermophilic species gave rise to the now existing major groups of living organisms, the Bacteria and Archaea. [The latter also contributed the major portion to the nucleo-cytoplasmic component of the Eucarya]. An exact calibration of the molecular record with regard to time is not yet possible. The emergence of Eucarya in fossil and molecular records suggests that the proposed late impact should have occurred before 2100 million years before present (BP). If the 3500 million year old microfossils [Schopf, J. W. 1993: Science 260: 640-646] are interpreted as representatives of present day existing groups of bacteria (i.e., as cyanobacteria), then the impact is dated to around 3700 million years BP. The analysis of molecular sequences suggests that the separation between the Eucarya and the two prokaryotic domains is less deep then the separation between Bacteria and Archaea. The fundamental cell biological differences between Archaea and Eucarya were obtained over a comparatively short evolutionary distance (as measured in number of substitution events in biological macromolecules). Our interpretation of the molecular record suggests that life emerged early in Earth's history even before the time of the heavy bombardment was over. Early life forms already had colonized extreme habitats which allowed at least two prokaryotic species to survive a late nearly ocean boiling impact. The distribution of ecotypes on the rooted universal tree of life should not be interpreted as evidence that life originated in extremely hot environments.
PMID: 7708385 [PubMed - indexed for MEDLINE]

Еще одна теория, не очень обоснованная

 

 

Symbiosis 1995;18:181-210
The microbial community of Ophrydium versatile colonies: endosymbionts, residents, and tenants.
Duval B, Margulis L.
Department of Biology, University of Massachusetts, Amherst 01003, USA.

Ophrydium versatile is a sessile peritrichous ciliate (Kingdom Protoctista, class Oligohymenophora, order Peritrichida, suborder Sessilina) that forms green, gelatinous colonies. Chlorophyll a and b impart a green color to Ophrydium masses due to 400-500 Chlorella-like endosymbionts in each peritrich. Ophrydium colonies, collected from two bog wetlands (Hawley and Leverett, Massachusetts) were analyzed for their gel inhabitants. Other protists include ciliates, mastigotes, euglenids, chlorophytes, and heliozoa. Routine constituents include from 50-100,000 Nitzschia per ml of gel and at least four other diatom genera (Navicula, Pinnularia, Gyrosigma, Cymbella) that may participate in synthesis of the gel matrix. Among the prokaryotes are filamentous and coccoid cyanobacteria, large rod-shaped bacteria, at least three types of spirochetes and one unidentified Saprospira-like organism. Endosymbiotic methanogenic bacteria, observed using fluorescence microscopy, were present in unidentified hypotrichous ciliates. Animals found inside the gel include rotifers, nematodes, and occasional copepods. The latter were observed in the water reservoir of larger Ophrydium masses. From 30-46% of incident visible radiation could be attenuated by Ophrydium green jelly masses in laboratory observations. Protargol staining was used to visualize the elongate macronuclei and small micronucleus of O. versatile zooids and symbiotic algal nuclei. Electron microscopic analysis of the wall of the Chlorella-like symbiont suggests that although the Ophrydium zooids from British Columbia harbor Chlorella vulgaris, those from Hawley Bog contain Graesiella sp. The growth habit in the photic zone and loose level of individuation of macroscopic Ophrydium masses are interpretable as extant analogs of certain Ediacaran biota: colonial protists in the Vendian fossil record.
PMID: 11539474 [PubMed - indexed for MEDLINE]

Описано сообщество (типа мата) с эукариотной основой. У ИНФУЗОРИЙ (перитриха и др.) бывают эндосимбионты – эукариотические водоросли (хлорелла) и МЕТАНОБРАЗУЮЩИЕ бактерии!

Опять видим легкость возникновения симбиотических ансамблей (роль основного хозяина играют эукариоты, естественно).

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