MICROBIOLOGY: PROKARYOTE BIOLOGY VOL. I - A. V. PINEVICH - 2006

CHAPTER 5. PROKARYOTES IN THE LIGHT OF CELL THEORY

Class="center">From an anatomical perspective, The Cell is the fundamental unit of life, wherein all manifestations of life must find their expression in the simplest and clearest form.

Yu. A. Filippenko. General Biology (Petrograd, 1923).

Living systems are so structurally and functionally diverse that providing a conceptual DEFINITION OF LIFE while avoiding reductionism—where the general is substituted by the particulars—remains an impossible task.

Nevertheless, one can single out the most characteristic attributes of life, an approach repeatedly undertaken from the Perspectives of Thermodynamics, information science, organic chemistry, and The Theory of competitive evolution.

In 1922, the Russian evolutionist and zoogeographer L. S. Berg defined life on The basis of teleology. In his view, living entities can be defined as physical bodies that adaptively and purposefully respond to external stimuli.

One of the founders of theoretical biology, the Russian physiologist E. S. Bauer, formulated a thermodynamic definition of life in 1935. According to him, the basis of life lies in nonequilibrium thermodynamic processes, whereby living systems create internal order by increasing disorder in the abiotic environment, thereby accumulating "negative" Entropy.

The information-theoretic definition of life was proposed by one of the creators of quantum theory, the Austrian physicist Erwin Schrödinger (E. Schrödinger, Nobel Prize in Physics, 1933). In his lectures delivered in 1943, he argued that the primary property of life is the linear anisotropy of organic macromolecules, enabling them to serve as carriers of hereditary information.

The renowned English chemist and philosopher John Bernal (J. Bernal), in his theoretical works of the 1960s, viewed life from the perspective of organic chemistry—as a self-sustaining network of coupled reactions occurring between organic molecules with the participation of endogenous organic catalysts.

In the 1984 NASA exobiology program, life is defined in light of the theory of competitive evolution as an autonomous physicochemical system governed by THE PRINCIPLE OF selectionism, i.e., Darwinian natural Selection.

All of the above Structure/97.html">Definitions fail to account for the fact that life represents a specific stage in the chemical Evolution of the Universe. The unique features of life include:

— existence based on Cells and aggregates of individuals;

— adaptive interaction with the environment;

— individual development, or ontogeny;

— historical development, or phylogeny.

A decisive contribution to understanding the informational foundations of life was made by the American virologist James Watson (J. Watson), the English molecular biologist Francis Crick (F. Crick), and the English biophysicist Maurice Wilkins (M. Wilkins), who established that heteropolynucleotides possess the capacity for template-directed copying (Nobel Prize in Physiology or Medicine, 1962). Further research led to the deciphering of the universal Genetic Code. They demonstrated that information-storing polynucleotides not only undergo self-copying (Replication), but in the interim also serve as a source of commands for the synthesis of Proteins and supramolecular systems, which, through a multi-step pathway, ensure that very same process of template copying.

The sequence of events comprises METABOLISM/31.html">Transcription (RNA Synthesis on a DNA template), Translation (Protein Synthesis on an RNA template), post-translational Processing, and, finally, the functional self-realization of the protein within subcellular systems.

The structure of polynucleotide templates is such that they not only replicate, but are also capable of:

— repair, i.e., the correction of damage;

— mutation, i.e., a heritable local alteration of structure resulting from inadequate repair;

— recombination, i.e., the relocation of endogenous blocks or the incorporation of exogenous blocks;

— Amplification, i.e., a manifold increase in the number of existing genetic elements.

All these transformations proceed on a competitive basis, with a general tendency toward increasing

template heterogeneity and expanding the volume of information they contain.

The chemical basis of this process is heteropolymerization. It is catalyzed by proteins, which are the products of template copying onto an alternative polypeptide carrier.

Template copying requires biosynthetic systems. These consist of enzyme-substrate complexes and depend on a supply of energy. Enzymes, substrates, and energy also serve to protect genomes from damage that could distort or block template copying. Specifically, DNA must be structurally stabilized and, when necessary, repaired.

Both types of polymerase reactions require a concentrated supply of organic matter and biologically available energy.

At the Cytology/cytology/16.html">Early stages of evolution, polymerase reactions took place in an environment enriched with the products of abiotic synthesis (the primordial "soup"). As these reserves were depleted, the environment became increasingly oligotrophic. Consequently, primitive living systems began to concentrate structural substrates and energy carriers, and subsequently to metabolize them actively. Under modern natural conditions, template copying can only occur within an isolated space—a compartment—whose internal environment exists in a state of stable non-equilibrium with the surrounding medium. For this condition to be sustained, the compartment must be quasi-stationary, meaning it must function as an open system. A cell, enclosed by a semipermeable membrane, satisfies this requirement. It acts as a chemical Reactor in which nucleotide-polymerase reactions take place. Both endogenous templates (the cellular genome) and exogenous templates (such as a plasmid or The Genome of a non-cellular parasitic Organism) can be copied.

Template copying is a potentially endless process, and in this sense, organic life is exceptionally "contagious"—capable of unlimited spatio-temporal expansion through the exploitation of all available energy and substrate resources.

Given the above, we can formulate another definition of organic life: organic life is the potentially unlimited expansion of polynucleotide templates that are copied within cells or self-replicating, multivariant membrane compartments.

This applies not only to living organisms with a cellular structure, but also to non-cellular life forms such as Viruses, which replicate within host cells. THE ORIGIN OF viruses remains unknown; they may represent a pre-cellular, secondarily simplified cellular, or independently evolved non-cellular form of life. The viral genome encodes only those systems required for its replication upon entering a cell, rather than the functional structures of the host cell itself. Unlike viruses, cells represent an autonomous form of life, although in a certain sense, viruses are more sophisticated.

In the definition of life given above, alongside the metabolic and genetic aspects, a leading role is assigned to the Spatial Organization of polynucleotide template copying. This is precisely why cytoarchitecture is considered the central aspect of cell biology.

Regarding cytoarchitecture, living organisms do not form a continuous spectrum, but rather a discrete set of morphotypes. By classifying these morphotypes, we construct a phenotypic megasystem, the objectivity of which is validated by MODERN CONCEPTS OF global phylogeny.

5.1. Modern Definition of the Cell. New Meanings of the Terms "Prokaryotes" and "Eukaryotes"

The Doctrine of the two morphotypes—eukaryotic and prokaryotic—is based primarily on whether a cell possesses a morphologically distinct nucleus. However, The Nucleus is not the only feature distinguishing prokaryotes from eukaryotes.

As early as the 1970s, Roger Stanier, Lynn Margulis, and Edward Dodson independently concluded that comparing prokaryotes with eukaryotes requires considering a multitude of criteria ranging from molecular to morphological. They attempted to rank cellular traits into Major and minor, universal and non-universal categories. However, this approach has a significant drawback: instead of providing an integral characterization of the morphotype, it yields a checklist of features corresponding to different levels of Cellular Organization. An alternative approach is to identify the most crucial characteristic from the totality of morphotype features.

In the early 1980s, Thomas Cavalier-Smith arrived at a fundamental Conclusion: eukaryotes differ fundamentally from prokaryotes in the overall plan of their membrane system, i.e., the mode of cellular compartmentalization.

Naturally, in nucleated cells, Mitochondria and Plastids are not taken into account. These Organelles, or "xenosomes" (from the Greek ksenos, meaning foreign, and soma, meaning body), originated from Bacteria. Structurally, they remain cells despite having largely lost their genetic, structural, and physiological autonomy.

The principal feature of The Introduction/5.html">Eukaryotic Cell—its "marker"—is the nuclear envelope. Some properties of this Membrane Structure are unique, and its functional role can hardly be overstated. Yet, viewed from a broader perspective, it turns out to be a specialized and functionally differentiated region of the endomembrane system. Put simply, the Specificity of eukaryotes is determined not by the nuclear envelope itself, but by the General Properties of their endomembrane system.

First and foremost, eukaryotes cannot exist without endomembranes, which are preserved in cells of this morphotype regardless of their evolutionary stage or ontogenetic features.

In addition, eukaryotes are characterized by a specific type of functional interaction between the endomembrane system and The Plasma Membrane: they are structurally disconnected and communicate via a Vesicular Transport apparatus.

A portion of eukaryotic Ribosomes attaches to the membranes of The Endoplasmic reticulum, which grow through the incorporation of proteins and Lipids, whereas the growth of the plasma membrane occurs via the fusion of vesicles budding off from the Golgi apparatus. In contrast, in Prokaryotic Cells, ribosomes can attach directly to the plasma membrane.

Thus, the fundamental difference between eukaryotes and prokaryotes is that eukaryotes invariably contain endomembranes, whereas prokaryotes do not necessarily have them. When prokaryotes do possess endomembranes, these interact with the plasma membrane either constantly or temporarily, and always through direct contact, without the involvement of a vesicular transport apparatus.

Different Regions of the eukaryotic endomembrane system vary in Morphology and perform specific Functions related to transport and constructive metabolism. In contrast, prokaryotic endomembranes are uniform in structure and are dedicated to Energy Metabolism.

Thus, eukaryotes and prokaryotes differ in the organizational type of their membrane system, although it should be reiterated that eukaryotes are monophyletic, while prokaryotes are diphyletic, represented by two global domains: Bacteria and Archaea. The evolutionary distance between these two domains is roughly comparable to the distance that separates each of them from eukaryotes.

It turns out that the dichotomous Classification is obsolete. Does this mean that the terms "Prokaryotic Cell" and "eukaryotic cell" are also outdated? To answer this question, we need to clarify what we mean by a cell.

A cell is a microcompartment for storing and replicating Genetic information. Its most essential and indispensable components are:

— a limiting membrane;

— a genome encoding an individual protein-synthesizing system;

— a cloned population of ribosomes.

The elementary cell, or "monad", possesses all of the aforementioned attributes.

5.1.1. Monads and Chimeras

Because The concepts of "monad" and "chimera" are of fundamental importance to cytology, let us examine them in greater detail.

Since antiquity, the philosophical term "monad" (from the Greek monos — single, unit) has been used to denote the fundamental and indivisible element of being. The word "monad" and its derivatives have at various times been employed as biological terms. Most frequently, monads referred to a type of biological organization in which a cell constitutes a separate organism, which roughly corresponds to the meaning now attributed to the term "protist". In some cases, the word "monad" became part of taxonomic names, such as the bacteria Azomonas, Hyphomonas, and Pseudomonas, the archaeon Natronomonas, the green alga Chlamydomonas, etc. Hypothetical monads were assigned a pivotal role in evolution (Ernst Haeckel's "monera").

In 1982, F. Taylor used the term "monad" in a general cytological sense to distinguish between "monads" (cells proper) and "chimeras" (endosymbiotic systems).

The monad cell is the elementary unit of life. The attributes of a monad, or the set of structures necessary during ontogenesis and for reproduction, are as follows:

— a cytoplasmic membrane, or membrane barrier enclosing the cytoplasmic compartment;

— a genome, or an individual coding system based on compacted double-stranded DNA;

— a cloned population of ribosomes, or universal translation organelles.

The Cytoplasm serves as the fourth attribute of a monad, but it is amorphous and therefore not considered an element of cellular architecture. Finally, one could mention a fifth attribute of the monad: the Cytoskeleton. However, in different monads it performs various functions that are not necessarily related to cellular architecture or vital life processes.

Thus, based on the principle: "One cytoplasmic membrane — one genome — one cloned population of ribosomes," we can distinguish Two Types of monads: the prokaryotic monad and the eukaryotic monad.

Endosymbiotic organelles of bacterial origin — mitochondria and "simple" plastids — possess all the attributes of a prokaryotic monad. They feature a membrane surrounding the matrix (in mitochondria) or the stroma (in "simple" plastids), a chromosome, and a set of 70S ribosomes.

Monads possessing their own membrane barrier, an individual genome, and a cloned population of ribosomes can be of only two types: the prokaryotic monad and the eukaryotic monad.

Monads are capable of forming cell groups known as polymeric monad associations. To designate them, Taylor proposed the term "polymonad".

Polymonads may consist of monads with homologous genomes. An example of a "homologous" polymonad composed of phototrophic individuals is found in bacteria of the genus Pleurocapsa. An example of a "homologous" polymonad consisting of chemotrophic individuals is represented by bacteria of the genus Streptococcus (Fig. 3).

Fig. 3. Monad cells, endosymbiotic chimera systems, and polymeric associations of monads or chimeras. N — nucleus; n — nucleomorph (nuclear vestige).

In addition, polymonads may consist of monads with heterologous genomes. Such associations are called consortia (from the Latin consortium — fellowship). Examples include the consortium formed by sulfate-reducing heterotrophic bacteria and green phototrophic bacteria, as well as the consortium formed by the hyperthermophilic archaeon Igniococcus sp. and Nanoarchaeum equitans.

Endosymbiotic systems represent a fundamentally different type of intercellular association. In this case, a prokaryotic monad takes up residence inside a eukaryotic monad. As a result, they become so interdependent that they can no longer exist independently. This is precisely how mitochondria (descendants of chemotrophic prokaryotic monads) and "simple" plastids (descendants of phototrophic prokaryotic monads) evolved.

For the endosymbiotic association of prokaryotic monads with a eukaryotic monad, Taylor proposed the term "simple chimera" (from the Greek chimaira — Chimera, the mythological monstrous hybrid of a lion, goat, and serpent). Depending on the COMPOSITION OF THE partners, two types of simple chimeras are distinguished.

A simple chimera formed by a eukaryotic monad and a chemotrophic prokaryotic monad is called a "diad" (from the Greek dio — two). Conversely, a simple chimera formed by a eukaryotic monad, a chemotrophic monad, and a phototrophic monad is called a "triad" (from the Greek tris — three). Associations of diads and triads are termed "polydiads" and "polytriads", respectively.

Most Representatives of the kingdom Animalia possessing mitochondria are polydiads. In turn, most representatives of the kingdom Plantae that possess mitochondria alongside "simple" plastids are polytriads.

The quantitative foundation of modern biodiversity is formed by animals (1,032 thousand species, of which only 751 thousand are insects), vascular plants (248 thousand species), Fungi (69 thousand species), non-photosynthetic protists (30 thousand

species), and Algae (27 thousand species). These organisms are descendants of endosymbiotic associations between phagotrophic Eukaryotic cells (domain Eucarya) and representatives of two different phyla of the domain Bacteria — BXII Proteobacteria and BX Cyanobacteria. Here, the monads function as host cells, mitochondria, and "simple" plastids, respectively.

A more complex variant of an endosymbiotic association arises when one chimera takes up residence inside another. Such an endosymbiotic system is called a "complex chimera". Examples of complex chimeras include many phototrophic protists, specifically representatives of the classes Cryptophyceae and Chlorarachniophyceae, which have retained a nuclear remnant (nucleomorph). It has now been established that the "complex" plastids of these microorganisms originated not from bacteria, but from triad algae that possessed mitochondria and simple plastids. Through endocytosis, such triads were engulfed by phagotrophic dyads and, as a result of the evolution of intercellular association, transformed into phototrophic organelles.

Complex chimeras can also form polymeric associations. Examples include brown, golden-brown, and yellow-green algae, which have lost the nucleomorph but retained rudimentary "eukaryotic" membranes around a "simple" plastid.

Returning to monads, it must be emphasized that the recorded biodiversity of these organisms (5.2 thousand species of bacteria and archaea, as well as several dozen species of "amitochondriate" protists) is negligible compared to the biodiversity of chimeras (1,406 thousand species).

5.1.2. PROKARYOTES AND EUKARYOTES as Two Types of Monads

Based on Current Concepts of cell properties and phylogeny, prokaryotes can be defined as follows: prokaryotes are non-nuclear monads that make up the phylogenetic domains Bacteria and Archaea.

In turn, eukaryotes can be defined as follows: eukaryotes are nuclear monads that make up the phylogenetic domain Eucarya.

Representatives of the phylogenetic domain Eucarya possess the eukaryotic morphotype. Its characteristic feature is a unique membrane system, which is divided into two distinct parts: the plasma membrane and endomembranes.

Eukaryotic endomembranes represent a collection of compartments communicating with one another via a vesicular transport system. Endomembranes interact with the plasma membrane via a vesicular shuttle system that carries out cytosis, or "packaged transport". It occurs from the cytoplasm to the extracellular environment and in the opposite direction—from the extracellular environment to the cytoplasm. In addition, the material that makes up the plasma membrane is transported using the vesicular shuttle system.

Eukaryotic endomembranes have a second name, the "vacuome" (from Latin vacuola, a small bubble, and omnis, total). It was introduced in the 1980s by the Belgian biochemist Christian de Duve (C. de Duve, Nobel Prize in Physiology or Medicine, 1974). This term designates a system of topologically closed membrane microcompartments, or vacuoles in the broad sense of the word.

The vacuome includes the nuclear envelope, Golgi apparatus, transport vesicles, endoplasmic reticulum, microsomes, etc. The Functions of the vacuome are:

— storage, copying, and expression of genetic information;

— Intracellular Transport;

— import of nutrient substrates;

— constructive metabolism, i.e., the totality of substrate assimilation and metabolic waste dissimilation processes;

— Biosynthesis and targeting of material for The formation of cellular structures;

— accumulation of reserve substances and their utilization;

— export of exometabolites and metabolic wastes.

However, vacuome membranes are incapable of energy assimilation via the generation of a proton gradient. In nuclear cells, this role is performed by mitochondrial cristae and plastid thylakoids.

The nuclear envelope isolates the sites of genetic material processing from the sites of its expression. Recall that replication and transcription (along with post-transcriptional processing, which includes splicing, mRNA capping, etc.) take place in the nucleoplasm, whereas translation is carried out in the cytoplasm.

Unlike prokaryotes, prokaryotes lack spatiotemporal isolation of transcription and translation, and their ribosomes attach to the 5' end of the forming mRNA molecule without waiting for the completion of the transcript. This happens because in prokaryotes, the total rate of initiation, transcription, and elongation is higher than the reading speed of the DNA template by the RNA polymerase complex.

The subunits of the eukaryotic 80S ribosome are exported through nuclear pores into the cytoplasm, and only there is the translation-competent ribosome-mRNA complex formed. However, translation can also occur inside the nucleus—in 2001, F. J. Iborra demonstrated using immunocytochemical Methods that mammalian nuclei utilize aminoacyl-tRNA in small amounts. The purpose of intranuclear translation may lie in testing mRNA for the presence of nonsense codons to ensure their nonsense-mediated decay (NMD).

5.2. Evolutionary Origin of Eukaryotes

A special place in theoretical biology is occupied by the reconstruction of the scenario of eukaryotic cell origin. The difficulty lies in the fact that the question of the Water/144.html">Origin of the nucleus stands apart from the question of the origin of the eukaryotic cell as a distinct evolutionary Lineage.

Currently, two hypotheses regarding the origin of eukaryotes are being considered.

In the mid-1980s, the prevailing idea was the independent origin of eukaryotes, bacteria, and archaea from a hypothetical common ancestor. However, dendrograms reflecting the results of sequencing conservative proteins (elongation factors EF-G and EF-Tu, proton-translocating F0F1-ATPases and V-ATPases, molecular chaperone Hsp70, Glutamate dehydrogenase, etc.) do not coincide with dendrograms constructed based on rRNA comparisons. Therefore, a consensus on what the Base of the evolutionary tree looks like does not yet exist.

According to the most widely accepted scenario, bacteria diverged from a common ancestor shared by archaea and eukaryotes (see Fig. 2). Carl Woese, Naoyuki Iwabe, J. Peter Gogarten, and other leading authorities in evolutionary cytology suggest that eukaryotic ancestors, or "proto-eukaryotes," shared a structural organization similar to that of archaea. Later on, they

acquired a vacuole, a cytoskeleton, and ultimately a nucleus. In this framework, the Homology between eukaryotic and prokayotic elongation factors, proton ATPases, and other key proteins is attributed to "horizontal" Gene transfer. The chimeric Nature of the nuclear genome may stem from genetic information exchange that occurred either among free-living members of the three domains, or after bacteria became obligate endosymbionts and evolved into mitochondria and plastids.

An alternative scenario was proposed in 1989 by Werner Zillig, attributing the chimeric nature of the nuclear genome to the symbiotic fusion of two prokaryotic lineages. In the early 1990s, James Lake, T. Horiike, and Radhey Gupta hypothesized that the nucleus originated from an archaeal cell that was engulfed by a bacterium via phagocytosis. Another proponent of the archaeal origin of the nucleus, American molecular biologist Mitchell Sogin, suggests that the precursor to the eukaryotic cell was not a bacterium, but rather a hypothetical protocell. It was envisioned as a self-replicating membrane vesicle containing a primitive RNA genome, replicated with the aid of RNA replicase.

Have direct descendants of the primary nuclear organisms survived in the modern biosphere? Some hypothesize that anaerobic protists belonging to the group Archezoa could be such descendants, as they lack mitochondria, hydrogenosomes, plastids, dictyosomes, and Peroxisomes (see Chapter 6).

Conversely, an opposing view holds that amitochondriate protists are not direct descendants of archaic eukaryotes (implying their ancestors originally possessed mitochondria but lost them through secondary adaptation to an anaerobic environment). As an argument, researchers point out that the nuclear genomes of amitochondriate protists contain homologs of bacterial genes. However, this can be explained just as plausibly by "horizontal" gene transfer between free-living organisms during the early stages of biological evolution.

5.3. The Protocell

A distinct type of monad is the hypothetical protocell. It occupies the ROOT of the Phylogenetic Tree and serves as the common ancestor of all three primary domains. Woese named it the "progenote" (from the English progenitor).

Reconstructing The properties of the progenote—lately referred to as the Last Universal Common Ancestor (LUCA)—remains a distinct challenge in theoretical biology. Researchers face the dual task of localizing LUCA on the global dendrogram and providing a retrospective description of its biological traits.

Several prominent biologists, most notably Christian de Duve, lean toward the idea that the world of protocytes eventually superseded the world of evolving molecular entities. In 1986, Walter Gilbert termed it the "RNA world." It is believed that proteins did not yet exist during that epoch, with RNA functioning simultaneously as a carrier of genetic information and a biocatalyst.

According to Otto Kandler, cellular life was initially colonial and undifferentiated. At the dawn of evolution, "horizontal" gene transfer may have been

a strictly regular phenomenon rather than an episodic one as it is today. Modern biota maintains its diversity through the trophic interdependence of individuals alongside relative genomic stability enforced by genetic barriers. In contrast, the biological strategy of the protocell world relied on the free exchange of rapidly mutating genes utilizing trophic reserves accumulated abiotically. Most likely, LUCA was not a discrete species, but rather a polyvariant product of "horizontal" gene transfer among diverse life forms. According to Canadian molecular biologist W. Ford Doolittle, we may never be able to reconstruct the base of the tree of life, as The rate of "horizontal" gene transfer could have outpaced the rate of lineage divergence.

Unlike Otto Kandler, W. Ford Doolittle, and American molecular geneticist Russell W. Doolittle, the majority of researchers believe that although LUCA was relatively primitive, it possessed all the hallmarks of a true cell, such as:

— a DNA-based genome;

— a set of enzymes and other protein factors required for DNA and RNA biosynthesis;

— ribosomes, i.e., ribonucleoprotein systems for RNA Transcript Processing;

— post-translational protein processing systems, including molecular chaperones;

— recombination, Genetic regulation, and DNA Repair machineries;

— mechanisms for controlling Cell Division;

— ATP regeneration systems and a membrane-bound electron-proton-motive chain.

Any attempt to reconstruct LUCA's phenotype inevitably raises questions about how these protocells adapted to the physicochemical conditions prevailing on Earth 3.5 billion years ago. Geological data indicate that our planet condensed around its metallic core 4.5 billion years ago, while the primordial ocean formed 4.2 billion years ago. Over the subsequent 500 million years, the Earth's crust underwent the Late Heavy Meteorite Bombardment (LHB) several times, driving water temperatures up to boiling point and thereby favoring the selection of a hyperthermophilic biota, which explains why LUCA was a thermophile.

The exact position of LUCA on the global dendrogram remains a subject of debate. According to the consensus view, the root of cellular life lies somewhere between the bacterial lineage and another major branch that subsequently split into the archaeal and eukaryotic lineages (see Fig. 2). Most likely, LUCA resembled a bacterium, and its phenotype can be reconstructed by analyzing fully sequenced bacterial genomes.