Damjan Franjević

Protein phosphorylation in bacterial signal transduction.

BACKGROUND Protein phosphorylation has emerged as one of the major post translational modifications in bacteria, involved in regulating a myriad of physiological processes. In a complex and dynamic system such as the bacterial cell, connectivity of its components accounts for a number of emergent properties. This article is part of a Special Issue entitled: Systems Biology of Microorganisms. SCOPE OF REVIEW This review focuses on the implications of bacterial protein phosphorylation in cell signaling and regulation and highlights the connections and cross talk between various signaling pathways: bacterial two-component systems and serine/threonine kinases, but also the interference between phosphorylation and other post-translational modifications (methylation and acetylation). MAJOR CONCLUSIONS Recent technical developments in high accuracy mass spectrometry have profoundly transformed proteomics, and today exhaustive site-specific phosphoproteomes are available for a number of bacterial species. Nevertheless, prediction of phosphorylation sites remains the main guide for many researchers, so we discuss the characteristics, limits and advantages of available phosphorylation predictors. GENERAL SIGNIFICANCE The advent of quantitative phosphoproteomics has brought the field on the doorstep of systems biology, but a number of challenges remain before the bacterial phosphorylation networks can be efficiently modeled and their physiological role understood. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.

The limits of cryptic diversity in groundwater: phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae)

Recent studies have revealed high local diversity and endemism in groundwaters, and showed that species with large ranges are extremely rare. One of such species is the cave shrimp Troglocaris anophthalmus from the Dinaric Karst on the western Balkan Peninsula, apparently uniform across a range of more than 500 kilometres. As such it contradicts the paradigm that subterranean organisms form localized, long‐term stable populations that cannot disperse over long distances. We tested it for possible cryptic diversity and/or unexpected evolutionary processes, analysing mitochondrial (COI, 16S rRNA) and nuclear (ITS2) genes of 232 specimens from the entire range. The results of an array of phylogeographical procedures congruently suggested that the picture of a widespread, continuously distributed and homogenous T. anophthalmus was wrong. The taxon is composed of four or possibly five monophyletic, geographically defined phylogroups that meet several species delimitation criteria, two of them showing evidence of biological reproductive isolation in sympatry. COI genetic distances between phylogroups turned out to be a poor predictor, as they were much lower than the sometimes suggested crustacean threshold value of 0.16 substitutions per site. Most results confirmed the nondispersal hypothesis of subterranean fauna, but the southern Adriatic phylogroup displayed a paradoxical pattern of recent dispersal across 300 kilometres of hydrographically fragmented karst terrain. We suggest a model of migration under extreme water‐level conditions, when flooded poljes could act as stepping‐stones. In the north of the range (Slovenia), the results confirmed the existence of a zone of unique biogeographical conflict, where surface fauna is concordant with the current watershed, and subterranean fauna is not.

Cross-phosphorylation of bacterial serine/threonine and tyrosine protein kinases on key regulatory residues

Bacteria possess protein serine/threonine and tyrosine kinases which resemble eukaryal kinases in their capacity to phosphorylate multiple substrates. We hypothesized that the analogy might extend further, and bacterial kinases may also undergo mutual phosphorylation and activation, which is currently considered as a hallmark of eukaryal kinase networks. In order to test this hypothesis, we explored the capacity of all members of four different classes of serine/threonine and tyrosine kinases present in the firmicute model organism Bacillus subtilis to phosphorylate each other in vitro and interact with each other in vivo. The interactomics data suggested a high degree of connectivity among all types of kinases, while phosphorylation assays revealed equally wide-spread cross-phosphorylation events. Our findings suggest that the Hanks-type kinases PrkC, PrkD, and YabT exhibit the highest capacity to phosphorylate other B. subtilis kinases, while the BY-kinase PtkA and the two-component-like kinases RsbW and SpoIIAB show the highest propensity to be phosphorylated by other kinases. Analysis of phosphorylated residues on several selected recipient kinases suggests that most cross-phosphorylation events concern key regulatory residues. Therefore, cross-phosphorylation events are very likely to influence the capacity of recipient kinases to phosphorylate substrates downstream in the signal transduction cascade. We therefore conclude that bacterial serine/threonine and tyrosine kinases probably engage in a network-type behavior previously described only in eukaryal cells.

Long inversely oriented subunits form a complex monomer of Tribolium brevicornis satellite DNA.

Highly abundant satellite DNA named TBREV is detected and characterized in the beetle Triboliumbrevicornis (Insecta: Coleoptera). An outstanding peculiarity of the TBREV satellite monomer is its complex structure based on the two ∼470-bp-long subunits, inversely oriented within a 1061-bp-long monomer sequence. The proposed evolutionary history demonstrates a clear trend toward increased complexity and length of the TBREV satellite monomer. This tendency has been observed on three levels: first as direct and inverted duplications of short sequence motifs, then by inverse duplication of the ∼470-bp sequence segment, and, finally, by spread of inversely duplicated elements in a higher-order register and formation of extant monomers. Inversely oriented subunits share a similarity of 82% and have a high capacity to form a thermodynamically stable dyad structure that is, to our knowledge, the longest ever described in any satellite monomer. Analysis of divergences between inversely oriented subunits shows a tendency to a further reduction in similarity between them. Except in its centromeric localization, the TBREV satellite does not show similarity to other known Tribolium satellites, either in nucleotide sequence or in monomer length and complexity. However, TBREV shares common features of other Tribolium satellites that might be under functional constraints: nonconstant rate of evolution along the monomer sequence, short inverted repeats in the vicinity of an A+T tract, nonrandom distribution of A or T ≥3 tracts, and CENP-B box-like motifs. Although long inverted subunits might reinforce structural characteristics of the satellite monomer, their nucleotide sequence does not seem to be under constraints in order to preserve the dyad structure.

Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.

It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly and maintain relaxed substrate specificity to quickly adopt new substrates when evolutionary pressure in that direction arises. Here, we report a phylogenomic and biochemical analysis of BY-kinases, and their relationship to substrates aimed to validate this hypothesis. Our results suggest that BY-kinases are ubiquitously distributed in bacterial phyla and underwent a complex evolutionary history, affected considerably by gene duplications and horizontal gene transfer events. This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes. On the basis of similarity networks, we could classify BY kinases into three main groups with 14 subgroups. Extensive sequence conservation was observed only around the three canonical Walker motifs, whereas unique signatures proposed the functional speciation and diversification within some subgroups. The relationship between BY-kinases and their substrates was analyzed using a ubiquitous substrate (Ugd) and some Firmicute-specific substrates (YvyG and YjoA) from Bacillus subtilis. No evidence of coevolution between kinases and substrates at the sequence level was found. Seven BY-kinases, including well-characterized and previously uncharacterized ones, were used for experimental studies. Most of the tested kinases were able to phosphorylate substrates from B. subtilis (Ugd, YvyG, and YjoA), despite originating from very distant bacteria. Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.

Presence of Ecotoxicologically Relevant Pgp and MRP Transcripts and Proteins in Cyprinid Fish

Presence of Ecotoxicologically Relevant Pgp and MRP Transcripts and Proteins in Cyprinid Fish One of the most intriguing defence strategies which aquatic organisms developed through evolution is multixenobiotic resistance (MXR). The key mediators of MXR activity are ATP-binding cassette (ABC) transport proteins. They provide resistance of aquatic organisms by binding xenobiotics and extruding them from cells in an energy-dependent manner. Since Cyprinid fish species are common target in freshwater biomonitoring programs, we have studied the presence of two main MDR/MXR efflux transporters P-glycoprotein (Pgp, Abcb1) and MRP-like protein(s) (Abcc) in the liver of five Cyprinid species: common carp, European chub, sneep, barbel, and silver prussian carp. Their presence was evaluated on the mRNA and protein level. Various pairs of primers were designed to clone homologous fragments of MXR-related genes. At the protein level, we used Western blotting with specific monoclonal antibodies against human Pgp (Abcb1, Ab C219), MRP1 (Abcc1; Ab MRPm6) or MRP2 (Abcc2; Ab M2I-4). Transcripts of both key types of MXR transporters were identified in all species examined and here we provide the phylogenetic analysis of new partial sequences. Immunochemical determinations with mammalian antibodies failed to identify the presence of MRP(s), but Pgp expression was found in all five Cyprinid species. These results support that MXR is a defence system mediated by both Pgp and MRP types of ABC transport proteins. Određivanje prisutnosti ekotoksikološki važnih Pgp i MRP-proteina u šarankama na genskoj i proteinskoj razini Mehanizam multiksenobiotičke otpornosti (MXR) stanični je obrambeni sustav odgovoran za svojstvo istovremene otpornosti na različite ksenobiotike, koje se očituje smanjenjem akumulacije, odnosno povećanjem izbacivanja potencijalno toksičnih tvari iz stanica vodenih organizama. MXR-mehanizam pokazuje odlike analogne fenomenu istovremene otpornosti na različite lijekove (engl. multidrug resistance, MDR) prvi put dokazanom u tumorskim stanicama. Posredovan je istim ABC transportnim proteinima kao i MDR. Istraživanja vezana uz MXR vodenih životinja uglavnom su imala težište na određivanju prisutnosti i funkcije P-glikoproteina (Pgp). Budući da se ribe iz reda šaranki često rabe u biomonitoringu slatkovodnih voda, cilj ovog istraživanja bilo je određivanje prisutnosti dvaju glavnih MDR/MXR-tipova proteina - Pgp i MRP-tip proteina - u jetri iz pet vrsta šaranki; šarana (Cyprinus carpio), klena (Sqalius cephalus), mrene (Barbus barbus), babuške (Carassius auratus gibelio) i podusta (Chondrostoma nasus). Njihova prisutnost utvrđena je na razini mRNA te na proteinskoj razini. Različiti parovi početnica dizajnirani su kako bi se identificirali homologni fragmenti gena sličnih MXR-u. Detekcija na razini proteina napravljena je putem Western blot analize s pomoću specifičnih monoklonskih protutijela proizvedenih da prepoznaju konzervirane epitope; Pgp (C219), MRP1 (MRPm6) ili MRP2 (M2I-4) u sisavaca. Transkripti obaju ključnih MXR-transportera identificirani su u svim jedinkama, a napravljena je i filogenetska analiza dobivenih sekvenci. Imunokemijskom detekcijom s protutijelima sisavaca nismo uspjeli detektirati prisutnost MRP-proteina, dok je Pgp-ekspresija potvrđena u svih pet vrsta šaranki. Nove spoznaje da je za MXR-mehanizam zaslužno više transportnih proteina zasigurno će pridonijeti potpunijoj karakterizaciji MXR-a kao integralnog dijela detoksikacijskog, odnosno temeljnog obrambenog sustava vodenih organizama te njegovoj znanstvenoj afirmaciji kao vjerodostojnog pokazatelja kvalitete okoliša.

Insights into the molecular phylogeny and historical biogeography of the white-clawed crayfish (Decapoda, Astacidae).

In this study, the evolutionary history of the white-clawed crayfish (WCC) was evaluated using large-scale datasets comprising >1350 specimens from the entire distribution range. Using species delimitation methods on mitochondrial DNA (mtDNA) sequences, we propose four primary species hypotheses for WCC. Sequences for several nuclear regions were screened but none showed significant variation within WCC. This result favours a single secondary species hypothesis and indicates the existence of a mito-nuclear discordance in WCC. Therefore, mtDNA groups were considered only as genetic units that carry information about ancient divergences within WCC and not as taxonomic units. The reconstruction of ancestral ranges and divergence time estimates were used to link the current genetic structure with paleogeographic processes. These results showed that the emergence of mtDNA groups in WCC could be related to the Messinian Salinity Crisis, the climate cooling during the Pliocene and Pleistocene, and (paleo)shifting of the Adriatic Sea coastline in the Padanovenezian Plain. The most recent common ancestor of the mtDNA groups most likely originated from Dalmatia (eastern Adriatic coast) as indicated by the reconstruction of ancestral ranges. This ecoregion, along with the Gulf of Venice Drainages, harbours a high genetic diversity and should be emphasised as an area of the highest conservation priority.

Resistance of Two Planarian Species to UV-irradiation

The aim of this work was to determine the effects of 20, 25 and 30 minute UV-irradiation periods lambda = 253.5 nm to two planarian species Dugesia tigrina (Gir.) and Polycelis felina (Daly.). In vivo, UV light effects have been reported to affect intracellular receptors and disrupt simple behaviour. The effects of UV-rays on mortality and behavior as well as morphological, cytological and histological changes in the two planarian species were assessed, and the course and the dynamics of regenerative processes were compared between them. Experimental populations of Dugesia tigrina and Polycelis felina species were maintained in laboratory conditions at room temperature. Mortality, behavioral and morphological changes were monitored daily by means of a light stereomicroscope. For cytological and histopathological analysis, planarians were fixed in Bouine fixative on the first, second, third, fifth and seventh day after exposure to UV-irradiation, respectively. They were embedded in paraffin, cut on a microtome, stained with toluidin blue and embedded in Canada-balsam. UV-rays caused mortality, behavioral, morphological, cytological and histological changes in each planarian species. In regeneration of damaged body parts reticular cells and neoblasts played the main role. Neoblasts as totipotent cells extremely increased in number in the area of damaged tissue, immediately after UV-exposure. Dugesia tigrina was more sensitive to UV-rays than Polycelis felina due to possession of less pigmented cells. The course of regeneration in both species was similar. Most individuals of both species regenerated in 5 to 12 days after UV-irradiation.

Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis

3-Hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from K. pneumoniae. Genetic engineering, driven by in silico optimization, and optimization of cultivation conditions resulted in a 3-HP titer of 10 g/L, in a standard batch cultivation. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis. With this relatively high titer in batch, and the robustness of B. subtilis in high density fermentation conditions, we expect that our production strains may constitute a solid basis for commercial production of 3-HP.

Bryozoans are returning home: recolonization of freshwater ecosystems inferred from phylogenetic relationships

Bryozoans are aquatic invertebrates that inhabit all types of aquatic ecosystems. They are small animals that form large colonies by asexual budding. Colonies can reach the size of several tens of centimeters, while individual units within a colony are the size of a few millimeters. Each individual within a colony works as a separate zooid and is genetically identical to each other individual within the same colony. Most freshwater species of bryozoans belong to the Phylactolaemata class, while several species that tolerate brackish water belong to the Gymnolaemata class. Tissue samples for this study were collected in the rivers of Adriatic and Danube basin and in the wetland areas in the continental part of Croatia (Europe). Freshwater and brackish taxons of bryozoans were genetically analyzed for the purpose of creating phylogenetic relationships between freshwater and brackish taxons of the Phylactolaemata and Gymnolaemata classes and determining the role of brackish species in colonizing freshwater and marine ecosystems. Phylogenetic relationships inferred on the genes for 18S rRNA, 28S rRNA, COI, and ITS2 region confirmed Phylactolaemata bryozoans as radix bryozoan group. Phylogenetic analysis proved Phylactolaemata bryozoans close relations with taxons from Phoronida phylum as well as the separation of the Lophopodidae family from other families within the Plumatellida genus. Comparative analysis of existing knowledge about the phylogeny of bryozoans and the expansion of known evolutionary hypotheses is proposed with the model of settlement of marine and freshwater ecosystems by the bryozoans group during their evolutionary past. In this case study, brackish bryozoan taxons represent a link for this ecological phylogenetic hypothesis. Comparison of brackish bryozoan species Lophopus crystallinus and Conopeum seurati confirmed a dual colonization of freshwater ecosystems throughout evolution of this group of animals.