Primitive Organisms Research Articles

Structure and function of photosystem I in Cyanidioschyzon merolae.

The evolution of photosynthesis from primitive photosynthetic bacteria to higher plants has been driven by the need to adapt to a wide range of environmental conditions. The red alga Cyanidioschyzon merolae is a primitive organism, which is capable of performing photosynthesis in extreme acidic and hot environments. The study of its photosynthetic machinery may provide new insight on the evolutionary path of photosynthesis and on light harvesting and its regulation in eukaryotes. With that aim, the structural and functional properties of the PSI complex were investigated by biochemical characterization, mass spectrometry, and X-ray crystallography. PSI was purified from cells grown at 25 and 42°C, crystallized and its crystal structure was solved at 4Å resolution. The structure of C. merolae reveals a core complex with a crescent-shaped structure, formed by antenna proteins. In addition, the structural model shows the position of PsaO and PsaM. PsaG and PsaH are present in plant complex and are missing from the C. merolae model as expected. This paper sheds new light onto the evolution of photosynthesis, which gives a strong indication for the chimerical properties of red algae PSI. The subunit composition of the PSI core from C. merolae and its associated light-harvesting antennae suggests that it is an evolutionary and functional intermediate between cyanobacteria and plants.

The use of algae in animal nutrition

In this review article the use of algae as feed in animal nutrition is being examined. The algae evolved on earth 3.5 billion years ago. They are primitive, generally aquatic and photosynthetic organisms, which range in size from 0,2-2,0 μιτι in diameter -microalgae (phytoplankton) up to 60 m length- macroalgae and may divide once or more per day. Algae are classified using a combination of characteristics in the chlorophyta, phaeophyta, chrysophyta, rhodophyta (all of them are macroalgae), pyrrhophyta and cyanophyta (they are microalgae). The chemical composition of algae varies over a wide range and depends on environmental conditions. Algae are necessary in the reduction of greenhouse gas emissions. They can be used as biodisel from their bio-lipid oil, as feed additives (alginates, carrageenans, agar, pigments), as therapeutic agents, as cosmetics, as organic fertilizer. Moreover, edible algae are considered sources of minerals and a complementary source of food protein for human -especially infunctional foods and animal nutrition, both in ruminants and monogastric animals. Algae in the rations of lactating cows increased milk production, the average milk protein, the amount of lactose, and prolonged the lactation period, while algae rich in (n-3) fatty acids effected positively on this fatty acid content of milk. In calves the dietary algae en-hanced immune function and improved carcass characteristics. Regarding the ewes, the algae nutrition affected milk fat composition and their dairy products. Researches on monogastric animals showed that the dietary supplementation of algae rich in docosqexaenoic acid increased its content in muscle tissue of rabbits, heavy pigs (live weight around 160 kg) and in the egg yolk of laying hens. In addition, algae in poultry diets can be used effectively as pigment sources both in egg yolk and in broiler skin and shanks. Algae have been found also to be a valuable food for fish farmed by acquaculture. However, further investigation is needed concerning the use of algae in human and animal nutrition.

Ancient Living Organisms Escaping from, or Imprisoned in, the Vents?

We have recently criticised the natural pH gradient hypothesis which purports to explain how the difference in pH between fluid issuing from ancient alkali vents and the more acidic Hadean ocean could have driven molecular machines that catalyse reactions that are useful in prebiotic and autotrophic chemistry. In this article, we temporarily suspend our earlier criticism while we consider difficulties for primitive organisms to have managed their energy supply and to have left the vents and become free-living. We point out that it may have been impossible for organisms to have acquired membrane-located proton (or sodium ion) pumps to replace the natural pH gradient, and independently to have driven essential molecular machines such as the ATP synthase. The volumes of the ocean and of the vent fluids were too large for a membrane-located pump to have generated a significant ion concentration gradient. Our arguments apply to three of the four concurrent models employed by the proponents of the natural pH gradient hypothesis. A fourth model is exempt from these arguments but has other intrinsic difficulties that we briefly consider. We conclude that ancient organisms utilising a natural pH gradient would have been imprisoned in the vents, unable to escape and become free-living.

Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles.

Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.

A giant oil seep at a salt-induced escarpment of the São Paulo Plateau, Espírito Santo Basin, off Brazil: Host rock characteristics and geochemistry

An international research cruise named Iatá-Piuna took place on the São Paulo Plateau on May 2013 in the Campos and Espírito Santo basins, off Brazil. The cruise was carried ou on board the research vessel (R/V) Yokosuka that hosts the human operated vehicle (HOV) SHINKAI 6500. It aimed at finding chemosynthetic communities, composed of organisms capable of generating their own vital energy by metabolizing organic and inorganic compounds related to seeps. Identification of these organisms could provide information for understanding the origin of life, since they may resemble primitive organisms that existed in the initial stages of life on Earth. During Leg 2 (May 10–24, 2013), however, dives on the northern part of the São Paulo Plateau at the Espírito Santo Basin led to the discovery of a giant oil seep. The seep, ca. 3 nautical miles (ca. 5.6km) in length is located along an outcrop of Eocene rocks on a salt-induced escarpment of the plateau and at a water depth of ca. 2700m. The 200m relief of the seafloor suggests that the seep takes place along an active fault system driven by salt diapirism. The oil was analyzed and identified as a severely biodegraded marine oil, generated by carbonate rocks within a minibasin located to the east of the escarpment. This represents valuable exploratory information because it proves that an active petroleum system is present in the context of minibasins associated with salt diapirism in the area.

Discrimination of Self and Non-Self Ribonucleic Acids.

Most virus infections are controlled through the innate and adaptive immune system. A surprisingly limited number of so-called pattern recognition receptors (PRRs) have the ability to sense a large variety of virus infections. The reason for the broad activity of PRRs lies in the ability to recognize viral nucleic acids. These nucleic acids lack signatures that are present in cytoplasmic cellular nucleic acids and thereby marking them as pathogen-derived. Accumulating evidence suggests that these signatures, which are predominantly sensed by a class of PRRs called retinoic acid-inducible gene I (RIG-I)-like receptors and other proteins, are not unique to viruses but rather resemble immature forms of cellular ribonucleic acids generated by cellular polymerases. RIG-I-like receptors, and other cellular antiviral proteins, may therefore have mainly evolved to sense nonprocessed nucleic acids typically generated by primitive organisms and pathogens. This capability has not only implications on induction of antiviral immunity but also on the function of cellular proteins to handle self-derived RNA with stimulatory potential.

Cloning and Functional Characterization of a Lycopene β-Cyclase from Macrophytic Red Alga Bangia fuscopurpurea.

Lycopene cyclases cyclize the open ends of acyclic lycopene (ψ,ψ-carotene) into β- or ε-ionone rings in the crucial bifurcation step of carotenoid biosynthesis. Among all carotenoid constituents, β-carotene (β,β-carotene) is found in all photosynthetic organisms, except for purple bacteria and heliobacteria, suggesting a ubiquitous distribution of lycopene β-cyclase activity in these organisms. In this work, we isolated a gene (BfLCYB) encoding a lycopene β-cyclase from Bangia fuscopurpurea, a red alga that is considered to be one of the primitive multicellular eukaryotic photosynthetic organisms and accumulates carotenoid constituents with both β- and ε-rings, including β-carotene, zeaxanthin, α-carotene (β,ε-carotene) and lutein. Functional complementation in Escherichia coli demonstrated that BfLCYB is able to catalyze cyclization of lycopene into monocyclic γ-carotene (β,ψ-carotene) and bicyclic β-carotene, and cyclization of the open end of monocyclic δ-carotene (ε,ψ-carotene) to produce α-carotene. No ε-cyclization activity was identified for BfLCYB. Sequence comparison showed that BfLCYB shares conserved domains with other functionally characterized lycopene cyclases from different organisms and belongs to a group of ancient lycopene cyclases. Although B. fuscopurpurea also synthesizes α-carotene and lutein, its enzyme-catalyzing ε-cyclization is still unknown.

The Efficiency of PVA Based Nanofiber Textile PVA Doped Silver Particles against Mold

Mold and algae are primitive organisms that cause biological degradation of many type of construction materials. Subsequent remediation of damaged structures is very demanding and it is therefore necessary to take into consideration the high preventive protection against these microorganisms. In practice, as the prevention it is often use chemical products as a classical biocidal compounds. One of the modern methods of protection investigate the use of nanotechnology with biocidal ingredients, which is the main topic of this article. Silver ions and silver nanoparticles were selected as a biocide for the experiment. Research revealed that the silver in the form of nanoparticles and ions have biocidal effect against fungi and algae and it is conform to use theoretically possible them as a preventive protection against mold and algae.

The Nuclear Receptor HIZR-1 Uses Zinc as a Ligand to Mediate Homeostasis in Response to High Zinc.

Nuclear receptors were originally defined as endocrine sensors in humans, leading to the identification of the nuclear receptor superfamily. Despite intensive efforts, most nuclear receptors have no known ligand, suggesting new ligand classes remain to be discovered. Furthermore, nuclear receptors are encoded in the genomes of primitive organisms that lack endocrine signaling, suggesting the primordial function may have been environmental sensing. Here we describe a novel Caenorhabditis elegans nuclear receptor, HIZR-1, that is a high zinc sensor in an animal and the master regulator of high zinc homeostasis. The essential micronutrient zinc acts as a HIZR-1 ligand, and activated HIZR-1 increases transcription of genes that promote zinc efflux and storage. The results identify zinc as the first inorganic molecule to function as a physiological ligand for a nuclear receptor and direct environmental sensing as a novel function of nuclear receptors.

What Nanobacteria and Nanovesicles May Tell Us about the Origin of Life?

In contemporary, established biology life is almost exclusively treated as a molecular phenomenon. Therefore, the mystery of the origin of life is sought in molecular terms and processes. But according to certain advanced researches and considerations, life has also other essential “ingredients”: active and diffused organized information and a specific physical as well as physicochemical state of matter characterized by long range order and coherent domains. These characteristics should also form the basis of the prebiotic evolution, the phase of more or less organized nano-and micro-vesicular systems that lead from abiotic to living systems. In this view, the complex molecular, physical and physicochemical order replaces the DNA molecule in its capability to maintain the stability of information complexity from generation to generation. Such systems were already found on the present day Earth and even within organisms and were also synthetically reproduced. They are called nanobacteria and in general nanovesicles or nanoparticles. They may represent an actual passage from non living forms to primitive organisms.

Evolutionary biosemiotics and multilevel construction networks.

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism (in a broad sense) to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components (i.e., agents, scaffolds, signs, and resources) that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents.

Exploring Extracellular Electron Transfer in Hyperthermophiles for Electrochemical Energy Conversion

Hyperthermophiles are microorganisms that thrive in extremely hot environment from 80 °C and upwards. They are the most primitive organisms evolved to survive in the early uninhabitable earth. We explored the extracellular electron transfer ability of a hyperthermophilic archaeon called Pyrococccus furiosus (Pf). Pf is an aquatic anaerobe that grows optimally at 100 °C using a wide range of substrates such as carbohydrates and peptides. Their ability to reduce the extracellular oxidants such as insoluble Fe(III) oxide and soluble Fe(III) citrate has been investigated. Pf reduced Fe(III) oxide during its growth at 90 °C and the Pf culture re-suspended in MOPS buffer (pH 7.5) was found to reduce Fe(III) citrate significantly using H2 as an electron donor. Further, Pf grown in two-chamber microbial fuel cell (MFC) at 90 °C was found to show a significant electrochemical response compared to the un-inoculated control MFC. The proof of concept study reported here reveals the potential of Pf to generate electricity in MFCs at high temperature locations such as hydrothermal vents.

Tangled evolutionary processes with commonality and diversity in plastidial glycolipid synthesis in photosynthetic organisms

In photosynthetic organisms, the photosynthetic membrane constitutes a scaffold for light-harvesting complexes and photosynthetic reaction centers. Three kinds of glycolipids, namely monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol, constitute approximately 80–90% of photosynthetic membrane lipids and are well conserved from tiny cyanobacteria to the leaves of huge trees. These glycolipids perform a wide variety of functions beyond biological membrane formation. In particular, the capability of adaptation to harsh environments through regulation of membrane glycolipid composition is essential for healthy growth and development of photosynthetic organisms. The genome analysis and functional genetics of the model seed plant Arabidopsis thaliana have yielded many new findings concerning the biosynthesis, regulation, and functions of glycolipids. Nevertheless, it remains to be clarified how the complex biosynthetic pathways and well-organized functions of glycolipids evolved in early and primitive photosynthetic organisms, such as cyanobacteria, to yield modern photosynthetic organisms like land plants. Recently, genome data for many photosynthetic organisms have been made available as the fruit of the rapid development of sequencing technology. We also have reported the draft genome sequence of the charophyte alga Klebsormidium flaccidum, which is an intermediate organism between green algae and land plants. Here, we performed a comprehensive phylogenic analysis of glycolipid biosynthesis genes in oxygenic photosynthetic organisms including K. flaccidum. Based on the results together with membrane lipid analysis of this alga, we discuss the evolution of glycolipid synthesis in photosynthetic organisms. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.

Exploring Extracellular Electron Transfer in Hyperthermophiles for Electrochemical Energy Conversion

Hyperthermophiles are microorganisms that thrive in extremely hot environment from 80 oC and upwards. They are the most primitive organisms evolved to survive in the early unhostile earth. The simplest and versatile respiratory electron transport chain of these hyperthermophiles made them suitable candidates for microbial fuel cells (MFC) anode catalysts to generate power at high temperatures. We explored the extracellular electron transfer ability of a hyperthermophilic archaeon called Pyrococccus furiosus (PF). PF is an aquatic anaerobe that grows optimally at 100 oC using a wide range of substrates such as carbohydrates and peptides1. The respiratory chain of PF is simple and unique that it does not require any terminal electron acceptor, rather reduces proton to H2 through membrane bound enzyme complex called hydrogenase2. Their ability to reduce the extracellular oxidants such as insoluble Fe(III) oxide and soluble Fe(III) citrate has been investigated. PF reduced Fe(III) oxide during its growth at 90 oC and the PF culture re-suspended in MOPS buffer (pH 7.5) was found to reduce Fe(III) citrate significantly using H2 as an electron donor. Further, low scan-rate cyclic voltammetry at 90 oC using potassium ferricyanide as a mediator showed greater mediated electron transfer by PF compared to the control without PF. The proof of concept study reported here reveals the potential of PF to generate electricity in MFCs at high temperature locations such as in solfataric fields or near hydrothermal vents. Moreover, such studies also help to advance our understanding in the field of biogeochemistry of the early hot environment and exobiology.

Transient Receptor Potential Melastatin-3 (TRPM3) Mediates Nociceptive-Like Responses in Hydra vulgaris.

The ability of mammals to feel noxious stimuli lies in a heterogeneous group of primary somatosensory neurons termed nociceptors, which express specific membrane receptors, such as the Transient Receptor Potential (TRP) family. Here, we show that one of the most important nociceptive-like pathways is conserved in the freshwater coelenterate Hydra vulgaris, the most primitive organism possessing a nervous system. In particular, we found that H. vulgaris expresses TRPM3, a nociceptor calcium channel involved in the detection of noxious heat in mammals. Furthermore, we detected that both heat shock and TRPM3 specific agonist (i.e., pregnenolone sulfate) induce the modulation of the heat shock protein 70 (HSP70) and the nitric oxide synthase (NOS), two genes activated by TRP-mediated heat painful stimuli in mammals. As expected, these effects are inhibited by a TRPM3 antagonist (i.e., mefenamic acid). Interestingly, the TRPM3 agonist and heat shock also induce the expression of nuclear transcription erythroid 2-related factor (Nrf2) and superoxide dismutase (SOD), known markers of oxidative stress; noteworthy gene expression was also inhibited by the TRPM3 antagonist. As a whole, our results demonstrate the presence of conserved molecular oxidative/nociceptive-like pathways at the primordial level of the animal kingdom.

Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology.

Na/K-ATPase is a key plasma membrane enzyme involved in cell signaling, volume regulation, and maintenance of electrochemical gradients. The α-subunit, central to these functions, belongs to a large family of P-type ATPases. Differences in transmembrane (TM) helix topology, sequence homology, helix–helix contacts, cell signaling, and protein domains of Na/K-ATPase α-subunit were compared in fungi (Beauveria), unicellular organisms (Paramecia), primitive multicellular organisms (Hydra), and vertebrates (Xenopus, Homo sapiens), and correlated with evolution of physiological functions in the α-subunit. All α-subunits are of similar length, with groupings of four and six helices in the N- and C-terminal regions, respectively. Minimal homology was seen for protein domain patterns in Paramecium and Hydra, with high correlation between Hydra and vertebrates. Paramecium α-subunits display extensive disorder, with minimal helix contacts. Increases in helix contacts in Hydra approached vertebrates. Protein motifs known to be associated with membrane lipid rafts and cell signaling reveal significant positional shifts between Paramecium and Hydra vulgaris, indicating that regional membrane fluidity changes occur during evolution. Putative steroid binding sites overlapping TM-3 occurred in all species. Sites associated with G-protein-receptor stimulation occur both in vertebrates and amphibia but not in Hydra or Paramecia. The C-terminus moiety “KETYY,” necessary for the Na+ activation of pump phosphorylation, is not present in unicellular species indicating the absence of classical Na+/K+-pumps. The basic protein topology evolved earliest, followed by increases in protein domains and ordered helical arrays, correlated with appearance of α-subunit regions known to involve cell signaling, membrane recycling, and ion channel formation.

Mitochondrial Fission in Human Diseases.

Mitochondria are an essential component of multicellular life - from primitive organisms, to highly complex entities like mammals. The importance of mitochondria is underlined by their plethora of well-characterized essential functions such as energy production through oxidative phosphorylation (OX-PHOS), calcium and reactive oxygen species (ROS) signaling, and regulation of apoptosis. In addition, novel roles and attributes of mitochondria are coming into focus through the recent years of mitochondrial research. In particular, over the past decade the study of mitochondrial shape and dynamics has achieved special significance, as they are found to impact mitochondrial function. Recent advances indicate that mitochondrial function and dynamics are inter-connected, and maintain the balance between health and disease at a cellular and an organismal level. For example, excessive mitochondrial division (fission) is associated with functional defects, and is implicated in multiple human diseases from neurodegenerative diseases to cancer. In this chapter we examine the recent literature on the mitochondrial dynamics-function relationship, and explore how it impacts on the development and progression of human diseases. We will also highlight the implications of therapeutic manipulation of mitochondrial dynamics in treating various human pathologies.

Applications of Microscopy in Bacteriology

Bacteria are smallest primitive, simple, unicellular, prokaryotic and microscopic organisms. But these organisms cannot be studied with naked eyes because of their minute structure. Therefore in search for the information about the structure and composition of bacterial cells, cell biologist used light microscopes with a numerical aperture of 1.4 and using wavelength of 0.4 μm separation. But there are still certain cellular structures that cannot be seen through naked eyes, and for them electron microscope is used. There are certain improved types of light microscope which can be incorporated to improve their resolving power. Hence microscopy is playing a crucial role in the field of bacteriology.

The structure of the muscular and nervous systems of the female Intoshia linei (Orthonectida)

The systematic position of the Orthonectida remains enigmatic. According to a classical point of view, they are placed together with Dicyemida in the phylum Mesozoa. Traditionally, orthonectids are regarded as rather primitive organisms, lacking digestive, muscular, and nervous systems. Here, using confocal laser scanning microscopy (CLSM) and immunohistochemical methods, we describe the musculature and serotoninergic nervous system of female adults of Intoshia linei (Orthonectida). The whole muscular system consists of 4 longitudinal and 9–11 circular muscle cells. The general muscular topography corresponds to the typical pattern for small-sized annelids or flatworms. Immunohistochemistry reveals six serotonin-like cells, which form part of a small nervous system comprising only 10–12 total cells based on nuclear counts. This is the first finding of a serotoninergic nervous system in orthonectids. Our analysis of muscular and neural organization in Orthonectida reveals significant differences from Diciemyda and aligns it more closely with the Lophotrochozoa.

Origin of Life in the Ocean: Direct Derivation of Mitochondria from Primitive Organisms Based on Complete Genomes

The origin of life has long been of interest to humans. However, despite the continuous increase in new data regarding complete genomes, the “origin of life” is still unclear. To evaluate this subject, the normalization of genome figures such as nucleotide or amino acid contents, which were predicted from the complete genome, was carried out, because this process excludes experimental errors and is independent of genome size and type (reviewed in). We can speculate about past and future evolutionary phenomena based on the rules that govern the evolution of present day organisms. Animals were classified into two groups; aquatic and terrestrial, based on nucleotide contents, GC skews and the ratio of methionine to valine predicted from complete mitochondrial genomes. This classification was linked to ammonia (which is fatally toxic to organisms), urea and uric acid excretion. The cytosine contents of primate and bird complete mitochondrial genomes are the highest among organisms examined, while that of the aquatic single-celled choanoflagellate (Monosiga brevicollis) are the lowest. Thus, the former two groups are ranked most highly evolved organisms, because more highly evolved organisms seem to have greater levels of cytosine. In non-animal mitochondrial genomes, the cytosine content of Fungi (Smittium culisetae) is the lowest, while that of land plants is the highest. As the cytosine contents of M. brevicollis and S. culisetae mitochondria are close to the closing point of all extended nucleotide content regression lines obtained from mitochondrial, chloroplast and chromosomal genomes, we conclude that the mitochondrial ancestor might be derived directly from primitive organisms, and that all organisms and cellular organelles might be derived from the single origin of life. Keywords: Amino acid composition, cellular organelles, chargaff’s parity rules, eukaryotes, evolution, genome, normalization, nucleotide content, origin of life, prokaryotes.