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The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene transfers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.

ABC proteins, which include ABCG transporters, form one of the largest and most evolutionarily conserved protein families found in all systematic groups. Their function is associated with the active transport of several structurally and functionally unrelated compounds across cell membranes. All members of this protein family have a characteristic domain organization, which quantity and orientation determine their division and classification into subfamilies. ABCGs are recognized as being crucial for plant development as well as interactions with the environment. However, researchers have only just begun to discover the role of ABCG transporters as important modulators of symbioses.

Introns are non-coding sequences within the genes. They seemed to be just "junk" DNA, although currently are considered as important genetic elements influencing the genome functions, as they increase the diversity of transcriptome and proteome, perform regulatory activities in the cell, affect gene expression, mRNA processing, degradation and translation. Based on the mechanism of their excision, introns were classified into three main categories: spliceosomal, self-splicing and tRNA introns. Spliceosomal introns are unique for eukaryotic organisms. Sequence analyses of orthologous genes in different groups of eukaryotes revealed many cases of intron gains and losses due to the multiple mechanisms. Some of these events took place in the distant past, while others happened relatively recently. It is believed that these processes can act as one of the forces driving the evolution of eukaryotic genes.

Transposable elements (TEs) are the sequences that are able to „jump” across the genome. They are found in virtually all organisms including human. Although in human, the majority of TEs lost their ability to autonomous transposition, they make up almost half of our genome, and played important roles in genome evolution. Fast progress in deep sequencing and functional analysis has revealed the importance of domes­ticated copies of transposable elements, including their regulatory sequences, transcripts and proteins in normal cells functioning. However, a growing numer of evidence suggest the involvment of TEs in development and progression of autoimmune and neurodegenerative disaeses as well as in many types of cancer. In this review we summarize the current state of knowledge about the LTR retroelements: endogenous retroviruses (ERVs) and Ty3/Gypsy retrotransposons, and their role in human organism.

The proper functioning of mitochondria and consequently of eukaryotic cells requires protein import into mitochondria. The import proceeds due to the presence of different pathways formed by sophisticated complexes known as the import complexes. The complexes are located in all mitochondrial compartments including the both mitochondrial membranes. Here we collect data concerning the organization of the import complexes and available for representatives of currently distinguished eukaryotic lineages. Despite the lack of many data, the emerging picture indicates at differentiation of the complex organization, particularly observed for the TOM complex. This, in turn, implicates interesting issues for further discussion concerning mitochondria evolution and the knowledge practical application.

Hsp70 molecular chaperones function in variety of critical cellular processes, including protein folding, translocation of proteins across membranes and assembly/disassembly of protein complexes. Hsp70 systems consist of a core Hsp70 protein and its co-chaperones: J-protein and nucleotide release factor NRF. These co-chaperones regulate the cycle of interaction with protein substrate via stimulating the ATPase activity of Hsp70 (J-protein) and promoting nucleotide exchange (NRF). Compartments within the eukaryotic cell often contain multiple Hsp70s, J-proteins and NRFs. The capabilities of these systems to carry out diverse cellular functions results from either specialization of an Hsp70 or by interaction of multifunctional Hsp70 with an array of specialized J-proteins. The well-studied Hsp70 systems of yeast mitochondria provide an excellent example of functional divergence and evolution of Hsp70 machineries.

PPR proteins make up the most numerous family of RNA-binding proteins identified to date. They localize almost exclusively to plastids and mitochondria of eukaryotic organisms. The most striking feature of this family is the expansion of PPR protein-encoding genes in vascular plants, which likely coincided with plants colonizing land. PPR proteins participate in stabilizing, editing, splicing, degradation and processing of policistronic transcripts, as well as translation activation in mitochondria and plastids. Although the number of PPR proteins in non-plant organisms is significantly smaller than in plants, they still play a crucial role in regulating the expression of mtDNA. Disruptions of PPR protein-encoding genes usually result in severe phenotypic consequences. Plant PPR proteins bind RNA in a sequence-specific manner, where a single PPR motif recognizes an individual nucleotide in a given sequence. This opens up possibilities for engineering de novo synthetic protein sequences that would interact with precisely determined organellar sequences, thus enabling modulation of mtDNA and ctDNA expression.

Acyltransferases'participate in many metabolic pathways in plants, especially in secondary metabolism pathways. These enzymes catalyse transfer of an acyl group from energy-rich donor molecule to nucleophilic group of an acceptor molecule resulting in ester bond formation. Plant acyltransferases can be divided into two families: serine carboxypeptidase-like acyltransferases (SCPL) and BAHD acyltransferases (named after its first four characterized enzymes). Based on differences in substrate specificity and aminoacid sequence, BAHD acyltransferas-es have been classified into five clades. SCPL acyltransferases utilise energy-rich 1-O-β-D-glucose esters as donors of an acyl group, instead of coenzyme A thioesters, which are substrates for acyltransferases from more abundant BAHD family. SCPL acyliransferases are homologous to hydrolases from serine carboxypeptidases family. They share some structural elements, such as conserved catalitic triad or αβ hydrolase fold.

The amplification of DNA is considered as a mechanism for rapid evolution of organisms. Duplication can be especially advantageous in the case of changing environmental conditions. Whole genome duplication maintains the proper balance between gene expression. This seems to be the main reason why WGD is more favorable than duplication of the fragments of DNA. The polyploidy status disappear as a result of the loss of the majority of duplicated genes. The preservation of duplicated genes is associated with the development of their new functions. Polyploidization is often noted for plants. However due to sequencing technique, the duplications episodes are more frequently reports also for the other systematic taxa, including animals. The occurrence of ancient genome duplication is also considered for yeast Saccharomyces cerevisiae. The existence of two active copies of ribosomal protein genes can be a confirmation of this process. Development of the fermentation process might be one of the probable causes of the yeast genome duplication.

Relaxin 2 is a polypeptide hormone structurally related to insulin and insulin-like growth factors (IGFs). However it does not interact with insulin receptors and has a decidedly different biological properties. Relaxin 2 activates LGR 7 and LGR 8 relaxin receptors, that belong to the leucine-rich repeat-containing (LRR), G protein-coupled receptors. The characteristic functions of relaxin are associated with female reproductive system, especially during pregnancy. However recent studies have shown that polypeptides with relaxin-like factor family (RLF) are involved in cell proliferation and differentiation, as well as invasion and angiogenesis of female and male reproductive cancers. This review provides information on the structure and function of relaxin and its receptors. Furthermore, we present evidence of the involvement of these elements in the process of cancerogenesis.

Staphylococcus aureus is one of the most important etiological factors of both nosocomial and community-acquired infections. Multidrug-resistant S. aureus is frequently isolated nowadays. Antibiotics used on the hospital ward exert a selective pressure on the strains and favor resistant strains. Multidrug-resistant and highly virulent strains can spread not only within the hospital but also between hospitals. Numerous studies show a predominance of one clone on a specific territory. The spread of such dangerous clones to neighboring countries and the entire continent is possible. Typing methods are very useful in infection control and prevention. Modern methods which are based on sequencing are necessary in rationalizing of infection control programs. Typing of Staphylococcus aureus includes methods that allow to determine the spread of drug-resistant pathogens. 'Gold standard' is pulsed-field gel electrophoresis (PFGE), which relies on separating the DNA fragments after restriction cutting. MLST (Multi Locus Sequence Typing) is based on a comparison of"housekeeping" gene sequences controlling the basic cell functions. With the MLST method, it is possible to demonstrate a broad, international spread of the specific clones. However, for epidemiological investigations, MLST seems to be too time-consuming and expensive to be used as a basic typing tool. The complementary method is spa typing, based on the sequencing of short repetitive sequences of the polymorphic X region from the gene encoding protein A. This method can be used for studying molecular evolution of S. aureus, as well as for testing for hospital outbreaks. It is faster and cheaper than MLST. It is also necessary to subtype the elements responsible for methycillin resistance (SCCmec), which allows to distinguish MRSA (Methicillin-resistant Staphylococcus aureus) clones with a common ancestor, but different epidemiological origin. All of those methods have their specific advantages and disadvantages and there is no single method efficient and suitable in any case.

Enterprises of whole genome sequencing together with information technology progress enable reconstruction of blood clotting evolution by bioinformatic methods. It together offers a base to conclude that the contact phase of vertebrate blood coagulation is evolutionary young and shaped merely before divergence of marsupial and placental mammals. Amphibians, birds and platypus own a single gene corresponding to the predecessor of factor XI and plasma prekallikrein. The opossum has both PK and FXI like eutherian mammals. FXII appears first in amphibians, it is present in platypus and opossum, but disappears in lineage leading to birds, probably by gene loss. The last findings brought to live the intrinsic coagulation pathway as it was discovered that FXII-knockout mice were protected from experimentally induced thrombosis, with no changes of proper clotting. The contact proteases may be a target for new antithrombotic therapies.

The information about features of the Eukaryotic cells is maintained not only in the nucleus, but also in the extranuclear genomes localized in mitochondria and chloroplasts. Comparison between plant and animal mitochondrial genomes allows to perceive two extremely distinct evolution strategies. Animals clearly tend to reduce the size of the mitochondrial genome to the minimum. In accordance with this, the simplification in decoding of genetic information present in the genome is observed. On the contrary, plant mitochondrial genomes tend to increase their size. Accumulation of extraordinary solutions for maintaining and expression of genetic information present in the genome is the second distinctive feature of plant mitochondria.

One of the key feature of prions is the ability to be stable in two alternative conformations. Besides the intensively studied mammalian prions, there are also prion proteins present in the yeast Saccharomyces cerevisiae. Research in this field has lead to opposite hypotheses that explain the sense of presence of [PSI+] prion in yeast cells. Some authors postulate e of role of the prions in the evolution of S. cerevisiae, whereas other investigators point out the negative influence of these particles upon the yeast physiology. In recent years, yeast prions are used for anti-prion drug screening, because of common features with mammalian prions. This work presents the most intensively studied fields of the research carried out on [PSI+] prion in yeast.

The mini-review series presented in this issue of Postepy Biochemii is focussed on some aspects of biology of calcium- and membrane-binding proteins, annexins, ubiquitous in all eucaryotic organisms (excluding yeasts), from Arabidopsis thaliana to Homo sapiens. Annexins are encoded by twelve genes in verterbrates and by eight in higher plants. Their physiological significance is underlined by two facts: the numer of the annexin genes seems to grow during evolution and in some cell types they comprise up to 2% of total protein. In the present review the hypothesis is discussed suggesting that multiplication of annexin genes in evolution represents mechanism of organism adaptation to changes in environment. In addition, the experimental data are presented suggestive of annexins playing a crucial role in functioning of plasma membrane, such as signal transduction, ion and vesicular transport and membrane repair. The review is then followed by articlesdealing in details with participation of annexins in plant response to abiotic stress (Arabidopsis thaliana), in tissue mineralization (Gallus gallus), in exocytosis of catecholamines by PC12 cells (mammals) and in Niemann-Pick type C disease related to abnormal transport and intracellular storage of cholesterol (Homo sapiens).

Retroviruses-derived elements in the human genome constitute 90% of non-coding mobile sequences. Reverse transcriptase (RT) plays an essential role in their transposition as do long terminal repeats (LTRs), which contain promotors, enhancers, and regulatory sequences. Some retroelements (pseudogens and retrogenes, e.g. SINE) are non-autonomic and do not possess their own RT. These elements are dependent on autonomic elements (retroposons, e.g. LINE, retrotransposons, exo- and endogenous retroviruses). The genome of retroviruses is composed of gag, pol, and env genes flanked by long terminal repeats. Endogenous retroviruses are probably the remnants of ancient germ cell infection by exogenous retroviruses and are transmissible to the next generation in a Mendelian way. Most of them are defective (because of mutation accumulation), but some are still active and their expression is regulated by different factors (UV radiation, inflammatory cytokines, steroid hormones, and exogenous virus products). Retroelements as well as their gene products exert influence on the organism's functions. They influence the plasticity and evolution of genomes, are a source of promotors and regulatory sequences, but they also supply additional signals of transcription initiation, mRNA splicing, and STOP codons. One of the positive aspects of human endogenous retroviruses (HERVs) is the participation of their products in normal syncytiotrophoblast formation. They also block exogenous retrovirus replication by receptor interference or antisense mRNA. Their presence is considered to be connected with a number of autoimmunological diseases (multiple sclerosis, insulin-dependent diabetes mellitus, systemic lupus erythematosus), cancer, or even psychiatric disorders (schizophrenia). There are also other problems connected with the potential role of ERVs in genomic therapy (with retroviruses vectors) and transplantology (xenotransplantation).

Ribosomal RNA (rRNA) is a component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5,8S, 28S and 5S rRNA. rRNA is the most conserved (least variable) gene in all cells. For this reason, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate related groups, and estimate rates of species divergence. Especially the internal transcribed spacers (ITS) are very useful for molecular diagnostic of parasite. They are noncoding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. These ribosomal RNA (rRNA) genes are highly conserved across taxa while the spacers between them may be species-specific. In this paper authors describe practical using of rRNA gene to parasite diagnostic.

This is an outline of the history of research on cytochrome c. Cytochromes were first discovered by Charles A. MacMunn (1886) and re-discovered by David Keilin (1925) who also identified their function in cell respiration. The role of cytochrome c in the mitochondrial electron transport chain has been well established, thus pointing to a vital role of this haemoprotein in cell function. Yet, towards the end of the last century, a novel role of cytochrome c, namely as a signal molecule for the programmed cell death (apoptosis), has been described. Differences in aminoacid composition of cytochrome c have also been used as markers of biochemical evolution. The article ends with a short biographic note on David Keilin.

Riboswitches are RNA structures able to bind small molecules and regulate gene expression at both, transcriptional and translational level. They are present in a wide variety of bacterial species. In Bacillus subtilis more than 2% of the genome is regulated by riboswitches. Metabolite binding is highly specific and can be provided in cooperative manner. Several riboswitches has been identified and characterized to be specific for flavin mononucleotide, thiamine, thiamine pyrophosphate, adenosylcobalamin, S-adenosylmethionine, lysine, glycine, adenine, guanine and glucosamine-6-phosphate. Some of them have been found also in fungi (Neurospora crassa) and plants (Oryza sativa, Arabidopsis thaliana). In human only one riboswitch with binding capacity for 2-aminopurine, has been found. Occurrence of riboswitches in all of the phylogenetic groups suggests that they are one of the oldest regulatory systems. It provokes also the question about their involvement in regulation of gene expression in human.

Evolution and systematics of nematodes based on molecular investigation. The use of molecular phylogenetics to examine the interrelationships between animal parasites, free-living nematodes, and plant parasites versus traditional classification based on morphological-ecological characters was discussed and reviewed. Distinct differences were observed between parasitic nematodes and free-living ones. Within the former group, animal parasites turned out to be distinctly different from plant parasites. Using small subunit of ribosomal RNA gene sequence from a wide range of nematodes, there is a possibility to compare animal-parasitic, plant-parasitic and free-living taxa. Nowadays the parasitic nematodes expressed sequence tag (EST) project is currently generating sequence information to provide a new source of data to examine the evolutionary history of this taxonomic group.

The problem of species recognition in relation to parasite organisms is discussed, based on literature data. Taking into account that over 20 species concepts have hitherto been formulated, the choice of characters, which should define a species differs from author to author. Lately the differences in some gene fragments are regarded as one of most important feature for species differentiation. On this basis some lineages, genotypes or strains have been differentiated within some species, but in most cases the respective authors did not decide to elevate these units to the species level. The present paper focuses on the studies on species representing three genera (Taenia, Echinococcus, Trichinella) as they show, especially the complex studies on the species within the genus Trichinella, how big material is necessary to formulate any proper conclusion and, on the other hand, that the differences in the DNA sequences cannot be the only characters defining species; some other features (morphological, biological, behavioral) should not be considered redundant.

Meanders of systematics of Microsporidia. Taxonomical questions of Microsporidia, its systematic position and evolutionary relationship with other Eukaryota are discussed. Utilizations of modern methods of investigations of microsporidians cause new taxonomical troubles. At the present time it is difficult to create a clear hypothesis concerning the phylogeny and evolution of Microsporidia. Most likely they are representatives of a new kingdom of Eukaryota. Existing problems will not be dissolved until new detailed data concerning the new and common species are obtained.