Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. Due to their positive charge, hydrophobicity and amphipathicity, they preferentially disrupt negatively charged bacterial membranes. AMPs are considered an important alternative to traditional antibiotics, especially at the time when multidrug-resistant bacteria being on the rise. Therefore, to reduce the costs of experimental research, robust computational tools for AMP prediction and identification of the best AMP candidates are essential. AmpGram is our novel tool for AMP prediction; it outperforms top-ranking AMP classifiers, including AMPScanner, CAMPR3R and iAMPpred. It is the first AMP prediction tool created for longer AMPs and for high-throughput proteomic screening. AmpGram prediction reliability was confirmed on the example of lactoferrin and thrombin. The former is a well known antimicrobial protein and the latter a cryptic one. Both proteins produce (after protease treatment) functional AMPs that have been experimentally validated at molecular level. The lactoferrin and thrombin AMPs were located in the antimicrobial regions clearly detected by AmpGram. Moreover, AmpGram also provides a list of shot 10 amino acid fragments in the antimicrobial regions, along with their probability predictions; these can be used for further studies and the rational design of new AMPs. AmpGram is available as a web-server, and an easy-to-use R package for proteomic analysis at CRAN repository.

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One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed.

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont’s genome, and have identified more than 30 genes that have been transferred to the host cell’s nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that five proteins carry potential signal peptides, implying they are targeted via the host endomembrane system. One sequence encodes a mitochondrial-like transit peptide, which suggests an import pathway involving a channel protein residing in the outer membrane of the endosymbiont. No N-terminal targeting signals were identified in the four other genes, but their encoded proteins could utilize non-classical targeting signals contained internally or in C-terminal regions. Several amino acids more often found in the Paulinella EGT-derived proteins than in their ancestral set (proteins still encoded in the endosymbiont genome) could constitute such signals. Characteristic features of the EGT-derived proteins are low molecular weight and nearly neutral charge, which both could be adaptations to enhance passage through the peptidoglycan wall present in the intermembrane space of the endosymbiont’s envelope. Our results suggest that Paulinella endosymbionts/plastids have evolved several different import routes, as has been shown in classical primary plastids.

Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species. These processes were additionally complicated by introgressions of mitochondrial DNA, which made the evolutionary history of this group quite complex and difficult to infer. To tackle the problem, we performed multi-method phylogenetic analyses based on mitochondrial cytochrome b that is considered a good molecular marker available for many representatives of Sorex. The results were compared with phylogenies based on chromosomal rearrangement data and put into temporal and spatial context using molecular dating and historical biogeography methods. We complemented the study with the estimation of diversification rates within the S. araneus group as well as comparing the results with paleontological records and climatic oscillations within the last 4 million years. Based on the gathered data, we proposed a hypothetical scenario for the evolution and geographic dispersion of species belonging to the S. araneus group. The shrews began to diversify about 2.7 million years ago in Eurasia and then migrated at least twice to North America. The evolution of shrews was driven by Pleistocene glacial and interglacial cycles, which increased their speciation rate and the emergence of new lineages. The migrations of populations were accompanied by introgressions of mitochondrial DNA into native shrews and occurred at least twice.