Papers by Damjan Franjevic
Genome Biology and Evolution, 2014
It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly ... more 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.
European Journal of Entomology, 2014
Predatory carabid beetles are important for regulating prey abundance in terrestrial ecosystems. ... more Predatory carabid beetles are important for regulating prey abundance in terrestrial ecosystems. While surveys of carabid diet have revealed many insights into trophic interactions, the high species diversity and heterogeneous developmental stages of prey identified in the gut have made further advances difficult. in addition, the carabid gut contains partially digested and mainly soft tissue parts of the prey species, difficult to identify by traditional methods. Molecular gut content analysis (MGCA) avoids these disadvantages but to date has been limited primarily to revealing pest species in agricultural fields. Here we used MGCA to screen for the presence of lepidoptera in carabid guts, in woodland ecosystems, in both Croatia and the UK. data on carabids positive for lepidoptera were compared with those from previous work on the same carabid assemblages, screened for earthworms, slugs, woodlice and springtails. in both locations, the prey group most frequently detected was earthworms, followed by slugs and lepidoptera and then finally by woodlice and springtails. The composition of the diet changed with season, carabid sex, and carabid size. in both locations, lepido ptera were the third most frequent prey, with 27% of carabids testing positive in Croatia and 20% in UK, suggesting that carabids could be significant predators of lepidoptera in woodland ecosystems and may potentially play an important role in controlling moth pests.
Phylogenetic position of white-clawed crayfish from the east Adriatic coast
The aim of this work was to determine the effects of 20, 25 and 30 minute UV-irradiation
periods ... more The aim of this work was to determine the effects of 20, 25 and 30 minute UV-irradiation
periods =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.
We studied the highly abundant chromoviral Tekay clade in species from three sister genera – Anem... more We studied the highly abundant chromoviral Tekay clade in species from three sister genera – Anemone, Pulsatilla and Hepatica (Ranunculaceae). With this clade, we performed a concomitant survey of its phylogenetic diversity, chromosomal organisation and transcriptional activity in Anemone s.l. in order to investigate dynamics of the Tekay elements at a finer scale than previously achieved in this or any other flowering clade. The phylogenetic tree built from Tekay sequences conformed to expected evolutionary relationships of the species; exceptions being A. nemorosa and A. sylvestris, which appeared more closely related that expected, and we invoke hybridisation events to explain the observed topology. The separation of elements into six clusters could be explained by episodic bursts of activity since divergence from a common ancestor at different points in their respective evolutionary histories. In Anemone s.l. the Tekay elements do not have a preferential position on chromosomes, i.e. they can have a: (i) centromeric/pericentromeric position; (ii) interstitial position in DAPI-positive AT-rich heterochromatic regions; can be (iii) dispersed throughout chromosomes ; or even (iv) be absent from large heterochromatic blocks. Widespread transcriptional activity of the Tekay elements in Anemone s.l. taxa indicate that some copies of Tekay elements could still be active in this plant group, contributing to gen-ome evolution and speciation within Anemone s.l. Identification of Tekay elements in Anemone s.l. provides valuable information for understanding how different localisa-tion patterns might help to facilitate plant genome organisation in a structural and functional manner.
In this study, the evolutionary history of the white-clawed crayfish (WCC) was evaluated using la... more 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 pale-ogeographic 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.
Background and Purpose: During June 2015 in Zagreb city area (Croatia) samples of tulip tree (Lir... more Background and Purpose: During June 2015 in Zagreb city area (Croatia) samples of tulip tree (Liriodendron tulipifera) leaves were collected with symptoms of attack by some unknown aphid.
Anemone sensu lato (including Pulsatilla and Hepatica), tribe Anemoneae (Ranunculaceae), is arran... more Anemone sensu lato (including Pulsatilla and Hepatica), tribe Anemoneae (Ranunculaceae), is arranged into two subgenera, Anemone and Anemonidium, with basic chromosome numbers x = 8 and x = 7, respectively. We elucidated the level of divergence of 5S rDNA unit arrays between the subgenera, determined intra-individual and interspecific sequence variation and tested 5S rDNA phylogenetic signal in revealing the origin of polyploid species. High intra-individual nucleotide diversity and the presence of 5S rDNA unit array length variants and pseudogenes indicate that weak homogenization forces have shaped 5S rDNA in the investigated species. Our results show that 5S rDNA evolved through two major changes: diversification of 5S rDNA into two lineages, one with long (subgenus Anemone) and one with short 5S rDNA unit arrays (subgenus Anemonidium); and subsequent contraction and expansion of 5S rDNA unit arrays. Phylogenetic analysis based on 5S rDNA supports the hypothesis that A. parviflora could be a parental species and donor of the subgenome D to the allopolyploids A. multifida (BBDD) and A. baldensis (AABBDD). In A. baldensis interlocus exchange possibly occurred, followed by subsequent replacement of the 5S rDNA from subgenome D with those from subgenome B. Here we present evidence that both models, concerted and birth-and-death evolution, were probably involved in the evolution of the 5S rDNA multigene family in subgenera Anemone and Anemonidium.
Despite morphological and molecular data analysed so far, phylogenetic relationships of many line... more Despite morphological and molecular data analysed so far, phylogenetic relationships of many lineages of genus Carabus Linnaeus 1758 (Carabini, Carabinae, Carabidae) present in Europe, have not been yet fully understood and molecular data have not been fully integrated with the morphological classifications. The aim of this research was to: (i) complement the phylogenetic relationships in the systematics of carabids within the genus Carabus with endemic species from Dinaric karst not included so far in molecular systematics research, and to (ii) examine the degree of matching of the molecular data with the existing morphological classifications based on the structure of frontal shields of larvae and the structure of the endophallus in adult specimens.
This study examines phylogeography and phylogeny of the threatened stone crayfish, Austropotamobi... more This study examines phylogeography and phylogeny of the threatened stone crayfish, Austropotamobius torrentium, in order to elucidate the role of the Dinaric Karst geology in shaping the evolutionary history and genetic diversity of aquatic fauna in the western Balkans. Mitochondrial 16S rRNA and COI genes were partially sequenced from 188 and 159 crayfish, respectively, sampled from 70 localities. Phylogenetic relationships were reconstructed using four methods of phylogenetic inference. Divergence times between phylogroups were estimated in a Bayesian framework, and their demographic history was examined using neutrality tests and mismatch distribution analysis. 2. Seven geographically localised phylogroups separated by pronounced genetic gaps were found. Five of them have a distribution range within the northern-central Dinaric (NCD) region, while the remaining two include populations from the southern Balkans (SB) and central and southeastern Europe (CSE). The oldest divergence event separated two NCD lineages from the rest of populations in the Late Miocene or Early Pliocene. Divergences amongst the five NCD phylogroups and SB + CSE occurred in the Pliocene. The most recent split separated SB and CSE phylogroups during the Late Pliocene. For both genes, uncorrected pairwise divergences between most of the phylogroups (4.1–8.7% for COI and 1.6–4.8% for 16S rRNA) were of the same range as, or higher than, some of the interspecific distances previously reported for the genus Austropot-amobius. 3. Geographically isolated and deeply divergent cryptic monophyletic phylogroups within A. torrentium in the NCD region arose in the course of intensification of Neotectonic movements during the Pliocene and the beginning of the Pleistocene and the development of karstification that has heavily fragmented the palaeohydrography of the area. The results confirm a gradual north– south expansion of stone crayfish during the pre-Pleistocene that preceded the rapid northward post-glacial re ⁄ colonisation of central Europe (CSE phylogroup) through the Danube drainage. 4. Austropotamobius torrentium comprises morphologically cryptic but molecularly distinct taxa. Considering the relatively small geographical areas they inhabit, the NCD phylogroups of stone crayfish should be given the highest conservation priority.
This work examines the bioaccumulated organochlorine compounds in Muraena helena to draw attentio... more This work examines the bioaccumulated organochlorine compounds in Muraena helena to draw attention to this species as a potential bioindicator organism. The morays were caught in the East Adriatic Sea, Elaphite Islands, near Dubrovnik, Croatia (lat: 42°45′38.8″; long: 17°45′53.6″) at the same location in summer (August, 2009) and winter (January, 2010), at depths from 5 to 10 m. Nine fish were caught by longline hooks per each field trip (total in summer and winter, N = 18). No single fish was free of organochlorines (OC), but not all pesticides were present in every fish. The concentration level was: Endrin > ppDDE > Heptachlor epoxide > Heptachlor > Aldrine > Lindane > bHCH > dHCH > Endrin aldehyde). Endrin was the only pesticide approaching the maximum concentrations proposed by the European Union and Croatia (summer max. concentration = 14.75 lg kg À1 ; winter max. concentration = 8.35 lg kg À1). All other pesticides ranged from 0.1 to 0.7 lg kg À1. Heptachlor was absent in winter and d-HCH and Endrin aldehyde in summer, while Lindane and pp-DDE had higher (P ≤ 0.05) concentrations in summer. Other residues had similar seasonal concentration levels. The p-DDT was similar as in other biota from the Adriatic or Mediterranean. HCH concentrations corresponded to those found in organisms from the Italian area of the Adriatic. The endocrine and reproductive disrupting potential of the detected OCs are bases for future studies. Results show that morays are a good bioindicator model, with slight interspecies and seasonal variability in OC bioaccumulation as a consequence of diverse food consumption.
Molecular phylogenetics and evolution, Jan 25, 2015
Symbiotic associations are of broad significance in evolution and biodiversity. Green Hydra is a ... more Symbiotic associations are of broad significance in evolution and biodiversity. Green Hydra is a classic example of endosymbiosis. In its gastrodermal myoepithelial cells it harbors endosymbiotic unicellular green algae, most commonly from the genus Chlorella. We reconstructed the phylogeny of cultured algal endosymbionts isolated and maintained in laboratory conditions for years from green Hydra strains collected from four different geographical sites within Croatia and one from Germany and one from Israel. Nuclear (18S rDNA, ITS region) and chloroplast markers (16S, rbcL) for maximum likelihood phylogenetic analyses were used. We focused on investigating the positions of these algal endosymbiotic strains within the chlorophyte lineage. Molecular analyses established that different genera and species of unicellular green algae are present as endosymbionts in green Hydra, showing that endosymbiotic algae growing within green Hydra sampled from four Croatian localities are not monoph...
Molecular Ecology, 2009
Recent studies have revealed high local diversity and endemism in groundwaters, and showed that s... more 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.
Biochimica et Biophysica Acta (BBA) - General Subjects, 2011
Background: Protein phosphorylation has emerged as one of the major post translational modificati... more 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.
Folia Biologica
The results of preliminary karyological investigations of two geographically distant and morpholo... more The results of preliminary karyological investigations of two geographically distant and morphologically slightly different Polycelis felina (Daly.) populations from central Croatia are reported. The results have shown that individuals of both populations are diploids, with the same chromosome number in their neoblasts (2n=18). Their karyotypes were composed of nine chromosome pairs, three of them are metacentric and the other six are submetacentric. Statistical evaluation of data indicated that both populations of Polycelis felina (Daly.), despite minor differences observed between them, belong to the same karyological biotype.
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Papers by Damjan Franjevic
periods =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.