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

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

A global synthesis reveals biodiversity-mediated benefits for crop production

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society. [Abstract copyright: Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

Highly Expressed Genes in Marine Sponge Suberites domuncula Prefer C- and G-Ending Codons

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

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