Genetics of Marine Organisms Associated with Human Health

Marine habitats harbour a large variety of organisms that belong to diverse taxa ; from bacteria and unicellular eukaryotes to fungi, animals, and plants. Although we have only started to understand the diversity and structure of marine communities, it is clear that numerous marine species have or might have an impact on human health. Some are a source of natural products with potential or actual medical applications, others are toxic and harmful to humans, and some are used in biomedical research to help understand the molecular basis of human diseases. New molecular genetics and genomic methods provide powerful and ever more indispensable tools for studying marine organisms and all aspects of their influence on human health. Herein, we present work using the latest research, which mostly uses genomics, to tackle the questions related with the topic of the issue

Dvije nukleozid-difosfat kinaze (NDPK/Nm23) iz morske spužve Suberites domuncula

Suberites domuncula is a member of the most ancient and simplest extant phylum of multicellular animals – sponges (Porifera). A database of S. domuncula expressed sequence tags (ESTs) was recently constructed by random cDNA sequencing. Two NDPK/Nm23 proteins from the sponge Suberites domuncula are reported here. Sponge proteins were named Nm23-SD1 and Nm23-SD6, because they display the highest sequence similarity with human Nm23-H1 and -H6 proteins. Overall sequence conservation of Nm23-SD1 with human Nm23-H1 is very high – 79 % (71 % identical amino acids). Nm23-SD6 possesses an insertion at the C-terminus and displays 55 % overall homology (40 % identical amino acids) with human Nm23 H6. Secondary structure predictions for both sponge and human Nm23 protein pairs are almost identical. S. domuncula Nm23 proteins display high similarity to homologues from mammals/humans, higher than to e.g. NDPK/Nm23 proteins from Drosophila or other invertebrates. Sponge Nm23 proteins are more similar to mammalian/human Nm23 proteins than most known Nm23 proteins of invertebrates.Suberites domuncula je pripadnik najstarije i najjednostavnije postojeće skupine (koljena) višestaničnih životinja – spužvi (Porifera). Nasumičnim sekvenciranjem cDNA S. domuncula nedavno je konstruirana baza EST-ova (expressed sequence tags). U ovom radu opisana su dva NDPK/Nm23 proteina iz spužve Suberites domuncula. Spužvini proteini nazvani su Nm23-SD1 i Nm23-SD6 jer su po aminokiselinskim sljedovima najslič niji ljudskim Nm23-H1 i -H6 proteinima. Ukupna sačuvanost sekvence izme|u Nm23-SD1 i Nm23-H1 vrlo je visoka i iznosi 79 % (71 % je identična). Nm23-SD6 ima inserciju na C-kraju i pokazuje ukupnu homologiju od 55 % (40 % identičnosti) s ljudskim Nm23-H6. Predikcija sekundarne strukture pokazuje da su oba proteinska para gotovo jednaka. Nm23 proteini iz spužve S. domuncula pokazuju visoku sličnost s homolozima iz sisavaca/čovjeka, višu nego s npr. NDPK/Nm23 proteinima iz vinske mušice ili drugih beskralješnjaka. Osim toga, sličniji su proteinima iz sisavaca/čovjeka od većine poznatih Nm23 proteina iz beskralješnjak

Integrin-Mediated Adhesion in the Unicellular Holozoan Capsaspora owczarzaki.

In animals, cell-matrix adhesions are essential for cell migration, tissue organization, and differentiation, which have central roles in embryonic development [1-6]. Integrins are the major cell surface adhesion receptors mediating cell-matrix adhesion in animals. They are heterodimeric transmembrane proteins that bind extracellular matrix (ECM) molecules on one side and connect to the actin cytoskeleton on the other [7]. Given the importance of integrin-mediated cell-matrix adhesion in development of multicellular animals, it is of interest to discover when and how this machinery arose during evolution. Comparative genomic analyses have shown that core components of the integrin adhesome pre-date the emergence of animals [8-11]; however, whether it mediates cell adhesion in non-metazoan taxa remains unknown. Here, we investigate cell-substrate adhesion in Capsaspora owczarzaki, the closest unicellular relative of animals with the most complete integrin adhesome [11, 12]. Previous work described that the life cycle of C. owczarzaki (hereafter, Capsaspora) includes three distinct life stages: adherent; cystic; and aggregative [13]. Using an adhesion assay, we show that, during the adherent life stage, C. owczarzaki adheres to surfaces using actin-dependent filopodia. We show that integrin β2 and its associated protein vinculin localize as distinct patches in the filopodia. We also demonstrate that substrate adhesion and integrin localization are enhanced by mammalian fibronectin. Finally, using a specific antibody for integrin β2, we inhibited cell adhesion to a fibronectin-coated surface. Our results suggest that adhesion to the substrate in C. owczarzaki is mediated by integrins. We thus propose that integrin-mediated adhesion pre-dates the emergence of animals

Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans

<p>Abstract</p> <p>Background</p> <p>Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge <it>Suberites domuncula</it>, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme.</p> <p>Results</p> <p>We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues.</p> <p>Conclusions</p> <p>This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues and the origin of tumors and metastasis.</p

Low Genetic Diversity of the Turopolje Pig Breed

We have performed a genetic diversity study of the Turopolje pig breed. Microsatellite genotyping on ten loci recommended by International Society for Animal Genetics (ISAG) and Food and Agriculture Organization (FAO) as well as mitochondrial D-loop sequencing were chosen as methods. Allele numbers, effective allele numbers (Ne), polymorphism information content (PIC), observed and expected heterozygosities were calculated. Mitochondrial sequences were compared to the sequences in the National Center for Biotechnology Information (NCBI) database. We have found relatively low genetic diversity at ten microsatellite loci and no differences in the partial D-loop sequence. Reasons for and consequences of low genetic diversity are discussed

Genetička raznolikost pasmine Turopoljska svinja

We have performed a genetic diversity study of the Turopolje pig breed. Microsatellite genotyping on ten loci recommended by International Society for Animal Genetics (ISAG) and Food and Agriculture Organization (FAO) as well as mitochondrial D-loop sequencing were chosen as methods. Allele numbers, effective allele numbers (Ne), polymorphism information content (PIC), observed and expected heterozygosities were calculated. Mitochondrial sequences were compared to the sequences in the National Center for Biotechnology Information (NCBI) database. We have found relatively low genetic diversity at ten microsatellite loci and no differences in the partial D-loop sequence. Reasons for and consequences of low genetic diversity are discussed.U ovom je radu provedeno istraživanje genetičke raznolikosti Turopoljske svinje. Genotipizacija je provedena analizom mikrosatelita i sekvencioniranjem mitohondrijske D-petlje. Odabrano je deset mikrosatelitskih lokusa prema preporuci International Society for Animal Genetics (ISAG) i The Food and Agriculture Organization (FAO). Izračunat je broj alela, efektivni broj alela (Ne), informacijski sadržaj polimorfizma, te očekivana i opažena heterozigotnost. Mitohondrijske sekvencije uspoređene su sa sekvencijama pohranjenim u bazi National Center for Biotechnology Information (NCBI). Na osnovi analize deset mikrosatelitskih lokusa ustanovljena je razmjerno niska razina genetičke raznolikosti. Također je utvrđeno da sve jedinke u uzorku imaju identičnu sekvenciju mitohondrijske D-petlje. U radu su komentirani mogući uzroci i posljedice niske razine genetičke raznolikosti ove pasmine

Predatory capabilities of the Filasterean Capsaspora Owczarzaki reveals its potential for a free-living lifestyle

Trabajo presentado en el Moscow Forum PROTIST 2016, celebrado en Moscú del 6 al 10 de junio de 2016.Capsaspora owczarzaki is one of only two known members of Filasterea – a group of protists closely related to animals. Due to its phylogenetic position, complex life cycle, and wide gene repertoire, it has become an important non-model organism in evolutionary studies, especially on the origin of animals. C. owczarzaki was isolated from several strains of freshwater snail Biomphalaria glabrata. However, it remains unclear whether it is an obligate symbiont or it can have a free-living lifestyle. In order to answer this question, we tested the interaction of C. owczarzaki with bacteria (Enterobacter aerogenes), with other unicellular eukaryotes (Dyctiostelium discoideum and Acanthamoeba castellani), and with B. glabrata embryonic (BGE) cells. The interactions were observed and documented by microscopy. In addition, we followed the growth of C. owczarzaki in the presence of these organisms. We found that C. owczarzaki is able to grow on a diet consisting only of bacteria. Furthermore, it efficiently kills and consumes Dictyostelium discoideum and BGE cells, and ingests material from live Acathamoeba castellanii. We performed RNAseq of C. owczarzaki fed by the organisms mentioned before and found distinct expression profiles for each food type. Our results strongly suggest that C. owczarzaki is not an obligate snail symbiont, but rather an opportunistic predatory organism able to feed on a variety of food types. This research increases the knowledge on the diversity of lifestyles among unicellular holozoans, and has implications on our understanding of the origin of animals.N

Jako eksprimirani geni morske spužve Suberites domuncula daju prednost citozinu i gvaninu na trećoj poziciji kodona

Sponges are the simplest extant phylum of Metazoa; they are closest to the common ancestor of all multicellular animals. A total of 223 coding sequences from Suberites domuncula (Demospongiae) represent the dataset for the codon usage analysis. A total of 46038 codons had an average guanine and cytosine (G+C) content of 45.8 % and an average content of guanine and cytosine at the synonymous third position of codons (GC3S) of 43.4 %. In this sample of genes considerable variations in synonymous codon usage were found. The G+C content of the coding sequences varied from 34 to 56.1 % and GC3S from 19 to 58.7 %. Correspondence analysis revealed that highly expressed genes preferentially use a limited subset of codons (preferred codons). A total of 15 preferred codons were found and they all, with one exception, end with C or G. The preferential use of C- or G-ending codons in highly expressed genes was possibly developed in a common ancestor of sponges and other Metazoa and it has remained conserved throughout the sponge evolution.Spužve su najprimitivniji živi pripadnici Metazoa i ujedno najbliže zajedničkom pretku svih višestaničnih životinja. Bazu podataka za analizu upotrebe kodona iz morske spužve Suberites domuncula (Demospongia) predstavljaju ukupno 223 kodirajuće sekvencije. Prosječni je udjel gvanina i citozina u 46 038 kodona bio 45,8 %, a njihov prosječni udjel na trećoj poziciji kodona 43,4 %. U ovom su uzorku uočene bitne razlike u upotrebi kodona koji kodiraju istu aminokiselinu. Udjel gvanina i citozina u kodirajućim sljedovima nukleotida varira od 34 do 56,1 %, a udjel gvanina i citozina na trećoj poziciji kodona od 19 do 58,7 %. Statistička metoda \u27Correspondence analysis\u27 pokazala je da jako eksprimirani geni više koriste preferirane kodone. Utvrđeno je ukupno 15 preferiranih kodona, a svi osim jednog završavaju sa citozinom ili gvaninom. Davanje prednosti citozinu ili gvaninu na trećoj poziciji kodona jako eksprimiranih gena vjerojatno se pojavilo već kod zajedničkog pretka spužva i drugih Metazoa te sačuvalo tijekom evolucije spužva