Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence

Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants

Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.

Genomic characterization and molecular evolution of human monkeypox viruses

Monkeypox virus is a member of the family Poxviridae, as are variola virus and vaccinia virus. It has a linear double-strand DNA genome approximately 197 kb long, containing ~190 non-overlapping ORFs. Comparison of members of the Central and West African clades shows the presence of unique genes that are associated with different disease presentations, depending on the strain. The last smallpox vaccination efforts ended in the mid-1980s, and there is concern about the recent spread of human monkeypox disease around the world. Almost 87,000 human monkeypox cases have been diagnosed in the world, of which more than 10,900 were in Brazil. The aim of this study was to evaluate the epidemiology and molecular evolution of hMpxV. From computational biology analysis of 640 hMpxV genomes from 1962 to 2022, synteny breaks and gene conservation were observed between Central and West clade genomes, and strains belonged with the 2022 outbreak assigned to the West African clade. Evidence was found for diversifying selective pressure at specific sites within protein coding sequences, acting on immunomodulatory processes. The existence of different sites under diversifying and purifying selection in paralog genes indicates adaptive mechanisms underlying the host-pathogen interaction of monkeypox virus in humans.

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

The COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people since its beginning in 2019. The propagation of new lineages and the discovery of key mechanisms adopted by the virus to overlap the immune system are central topics for the entire public health policies, research and disease management. Since the second semester of 2020, the mutation E484K has been progressively found in the Brazilian territory, composing different lineages over time. It brought multiple concerns related to the risk of reinfection and the effectiveness of new preventive and treatment strategies due to the possibility of escaping from neutralizing antibodies. To better characterize the current scenario we performed genomic and phylogenetic analyses of the E484K mutated genomes sequenced from Brazilian samples in 2020. From October 2020, more than 40% of the sequenced genomes present the E484K mutation, which was identified in three different lineages (P.1, P.2 and B.1.1.33 - posteriorly renamed as N.9) in four Brazilian regions. We also evaluated the presence of E484K associated mutations and identified selective pressures acting on the spike protein, leading us to some insights about adaptive and purifying selection driving the virus evolution.

Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children

Dietary intervention is effective in human health promotion through modulation of gut microbiota. Diet can cause single-nucleotide polymorphisms (SNPs) to occur in the gut microbiota, and some of these variations may lead to functional changes in human health. In this study, we performed a systematic SNP analysis based on metagenomic data collected from children with Prader–Willi syndrome (PWS, n = 17) and simple obese (SO) children (n = 19), who had better healthy conditions after receiving high-fiber diet intervention. We found that the intervention increased the SNP proportions of Faecalibacterium, Bifidobacterium, and Clostridium and decreased those of Bacteroides in all children. Besides, the PWS children had Collinsella increased and Ruminococcus decreased, whereas the SO had Blautia and Escherichia decreased. There were much more BiasSNPs in PWS than in SO (4,465 vs 303), and only 81 of them appeared in both groups, of which 78 were from Faecalibacterium prausnitzii, and 51 were nonsynonymous mutations. These nonsynonymous variations were mainly related to pathways of environmental adaptation and nutrition metabolism, particularly to carbohydrate and nucleotide metabolism. In addition, dominant strains carrying BiasSNPs in all children shifted from F. prausnitzii AF32-8AC and F. prausnitzii 942/30-2 to F. prausnitzii SSTS Bg7063 and F. prausnitzii JG BgPS064 after the dietary intervention. Furthermore, although the abundance of Bifidobacterium increased significantly by the intervention and became dominant strains responsible for nutrition metabolism, they had less BiasSNPs between the pre- and post-intervention group in comparison with Faecalibacterium. The finding of F. prausnitzii as important functional strains influenced by the intervention highlights the superiority of applying SNP analysis in studies of gut microbiota. This study provided evidence and support for the effect of dietary intervention on gut microbial SNPs, and gave some enlightenments for disease treatment.

Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era

Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.

Evolutionary analysis and protein family classification of chitin deacetylases in Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic fungal pathogen causing cryptococcal meningoencephalitis. Interestingly, the cell wall of C. neoformans contains chitosan, which is critical for its virulence and persistence in the mammalian host. C. neoformans (H99) has three chitin deacetylases (CDAs), which convert chitin to chitosan. Herein, the classification of the chitin-related protein (CRP) family focused on cryptococcal CDAs was analyzed by phylogenetics, evolutionary pressure (d_N/d_S), and 3D modeling. A phylogenetic tree of 110 CRPs revealed that they can be divided into two clades, CRP I and II with bootstrap values (> 99%). CRP I clade comprises five groups (Groups 1-5) with a total of 20 genes, while CRP II clade comprises sixteen groups (Groups 6-21) with a total of 90 genes. CRP I comprises only fungal CDAs, including all three C. neoformans CDAs, whereas CRP II comprises diverse CDAs from fungi, bacteria, and amoeba, along with other carbohydrate esterase 4 family proteins. All CDAs have the signal peptide, except those from group 11. Notably, CDAs with the putative O-gycosylation site possess either the glycosylphosphatidylinositol (GPI)-anchor motif for CRP I or the chitin-binding domain (CBD) for CRP II, respectively. This evolutionary conservation strongly indicates that the O-glycosylation modification and the presence of either the GPI-anchor motif or the chitin-binding domain is important for fungal CDAs to function efficiently at the cell surface. This study reveals that C. neoformans CDAs carrying GPI anchors have evolved divergently from fungal and bacterial CDAs, providing new insights into evolution and classification of CRP family.

Identification of novel antimicrobial peptide from Asian sea bass (Lates calcarifer) by in silico and activity characterization

Background

The global crisis of antibiotic resistance increases the demand for the new promising alternative drugs such as antimicrobial peptides (AMPs). Accordingly, we have described a new, previously unrecognized effective AMP, named dicentracin-like, from Asian sea bass and characterized its antimicrobial activity by comparison with moronecidin.

Methodology/ Results

Gene expression analysis demonstrated the expression of dicentracin-like peptide in tissues of the immune system such as the skin and the head kidney, which is an important endocrine and lymphoid organ. Moronecidin and dicentracin-like exhibited a higher antibacterial activity against gram-positive bacteria relative to gram-negative ones, while both peptides showed a greater binding ability to gram-negative bacteria compared to gram-positive ones. This contradiction between antibacterial activity and binding affinity may be related to the outer membrane from gram-negative bacteria. Compared with moronecidin, dicentracin-like peptide showed more potent binding ability to all gram-positive and gram-negative bacteria. In addition, dicentracin-like peptide exhibited a high antibacterial activity against the investigated microorganisms, except against Staphylococcus aureus. A direct relationship was found between the binding affinity/cationicity and the antibiofilm activity of the peptides wherein, an elevation in pH corresponded to a decrease in their antibiofilm property. Time-kill kinetics analysis against clinical Acinetobacter baumannii isolate indicated that bactericidal effect of dicentracin-like and moronecidin at inhibitory concentration (1XMIC) was observed after 4 and 6 hours, respectively, while bactericidal effect of both AMPs at concentration of 2XMIC was observed after 2 hours. Dicentracin-like peptide showed higher inhibitory activity at subinhibitory concentration (1/2XMIC), relative to moronecidin. Compared with moronecidin, dicentracin-like peptide possessed greater binding affinity to bacteria at high salt concentration, as well as at alkaline pH; In addition, dicentracin-like exhibited a higher antibiofilm activity in comparison to moronecidin even at alkaline pH. Hemolytic analysis against human RBC revealed that hemolytic activity of moronecidin was more potent than that of dicentracin-like, which is consistent with its greater non-polar face hydrophobicity.

Conclusions

In the present study, In Silico comparative sequence analysis and antimicrobial characterization led to identify a new, previously unrecognized antimicrobial function for named dicentracin-like peptide by comparison with moronecidin, representing a possible template for designing new effective AMPs and improving known ones.

Molecular evolution and functional divergence of alcohol dehydrogenases in animals, fungi and plants

Alcohol dehydrogenases belong to the large superfamily of medium-chain dehydrogenases/reductases, which occur throughout the biological world and are involved with many important metabolic routes. We considered the phylogeny of 190 ADH sequences of animals, fungi, and plants. Non-class III Caenorhabditis elegans ADHs were seen closely related to tetrameric fungal ADHs. ADH3 forms a sister group to amphibian, reptilian, avian and mammalian non-class III ADHs. In fishes, two main forms are identified: ADH1 and ADH3, whereas in amphibians there is a new ADH form (ADH8). ADH2 is found in Mammalia and Aves, and they formed a monophyletic group. Additionally, mammalian ADH4 seems to result from an ADH1 duplication, while in Fungi, ADH formed clusters based on types and genera. The plant ADH isoforms constitute a basal clade in relation to ADHs from animals. We identified amino acid residues responsible for functional divergence between ADH types in fungi, mammals, and fishes. In mammals, these differences occur mainly between ADH1/ADH4 and ADH3/ADH5, whereas functional divergence occurred in fungi between ADH1/ADH5, ADH5/ADH4, and ADH5/ADH3. In fishes, the forms also seem to be functionally divergent. The ADH family expansion exemplifies a neofunctionalization process where reiterative duplication events are related to new activities.

Identification and functional characterization of an uncharacterized antimicrobial peptide from a ciliate Paramecium caudatum

The global ever-growing concerns about multi-drug resistant (MDR) microbes leads to urgent demands for exploration of new antibiotics including antimicrobial peptides (AMPs). Here we demonstrated that a cDNA from Ciliata Paramecium caudatum, designated Pcamp1, coded for a protein with features characteristic of AMPs, which is not homologous to any AMPs currently known. Both the C-terminal 91 amino acid residues of PcAMP1, cPcAMP1, expressed in Escherichia coli and the C-terminal 26 amino acid residues (predicted mature AMP), cPcAMP1/26, synthesized, underwent a coil-to-helix transition in the presence of TFE, SDS or DPC. Functional assays revealed that cPcAMP1 and cPcAMP1/26 were both able to kill Aeromonas hydrophila and Staphylococcus aureus. ELISA showed that cPcAMP1 and cPcAMP1/26 were able to bind to microbe-associated molecular pattern molecules LPS and LTA, which was further corroborated by the observations that cPcAMP1 could deposit onto the bacterial membranes. Importantly, both cPcAMP1 and cPcAMP1/26 were able to induce bacterial membrane permeabilization and depolarization, and to increase intracellular ROS levels. Additionally, cPcAMP1 and cPcAMP1/26 were not cytotoxic to mammalian cells. Taken together, our results show that PcAMP1 is a potential AMP with a membrane selectivity towards bacterial cells, which renders it a promising template for the design of novel peptide antibiotics against MDR microbes. It also shows that use of signal conserved sequence of AMPs can be an effective tool to identify potential AMPs across different animal classes.

Identification of a novel antimicrobial peptide from amphioxus Branchiostoma japonicum by in silico and functional analyses

The emergence of multi-drug resistant (MDR) microbes leads to urgent demands for novel antibiotics exploration. We demonstrated a cDNA from amphioxus Branchiostoma japonicum, designated Bjamp1, encoded a protein with features typical of antimicrobial peptides (AMPs), which is not homologous to any AMPs currently discovered. It was found that Bjamp1 was expressed in distinct tissues, and its expression was remarkably up-regulated following challenge with LPS and LTA. Moreover, the synthesized putative mature AMP, mBjAMP1, underwent a coil-to-helix transition in the presence of TFE or SDS, agreeing well with the expectation that BjAMP1 was a potential AMP. Functional assays showed that mBjAMP1 inhibited the growth of all the bacteria tested, and induced membrane/cytoplasmic damage. ELISA indicated that mBjAMP1 was a pattern recognition molecule capable of identifying LPS and LTA. Importantly, mBjAMP1 disrupted the bacterial membranes by a membranolytic mechanism. Additionally, mBjAMP1 was non-cytotoxic to mammalian cells. Collectively, these data indicate that mBjAMP1 is a new AMP with a high bacterial membrane selectivity, rendering it a promising template for the design of novel peptide antibiotics against MDR microbes. It also shows for the first time that use of signal conserved sequence of AMPs is effective identifying potential AMPs across different animal classes.

Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana

Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the ‘edges’ of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters.

Molecular adaptation of telomere associated genes in mammals

BACKGROUND

Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these traits, there are exceptions that warrant further investigation. Species such as naked mole rat, human and certain bat species all exhibit extreme longevity with respect to body size. It has long been established that telomeres and telomere maintenance have a clear role in ageing but it has not yet been established whether there is evidence for adaptation in telomere maintenance proteins that could account for increased longevity in these species.

RESULTS

Here we carry out a molecular investigation of selective pressure variation, specifically focusing on telomere associated genes across placental mammals. In general we observe a large number of instances of positive selection acting on telomere genes. Although these signatures of selection overall are not significantly correlated with either longevity or body size we do identify positive selection in the microbat species Myotis lucifugus in functionally important regions of the telomere maintenance genes DKC1 and TERT, and in naked mole rat in the DNA repair gene BRCA1.

CONCLUSION

These results demonstrate the multifarious selective pressures acting across the mammal phylogeny driving lineage-specific adaptations of telomere associated genes. Our results show that regardless of the longevity of a species, these proteins have evolved under positive selection thereby removing increased longevity as the single selective force driving this rapid rate of evolution. However, evidence of molecular adaptations specific to naked mole rat and Myotis lucifugus highlight functionally significant regions in genes that may alter the way in which telomeres are regulated and maintained in these longer-lived species.

Adaptive selection on bracovirus genomes drives the specialization of Cotesia parasitoid wasps

The geographic mosaic of coevolution predicts parasite virulence should be locally adapted to the host community. Cotesia parasitoid wasps adapt to local lepidopteran species possibly through their symbiotic bracovirus. The virus, essential for the parasitism success, is at the heart of the complex coevolutionary relationship linking the wasps and their hosts. The large segmented genome contained in the virus particles encodes virulence genes involved in host immune and developmental suppression. Coevolutionary arms race should result in the positive selection of particular beneficial alleles. To understand the global role of bracoviruses in the local adaptation or specialization of parasitoid wasps to their hosts, we studied the molecular evolution of four bracoviruses associated with wasps of the genus Cotesia, including C congregata, C vestalis and new data and annotation on two ecologically differentiated populations of C sesamie, Kitale and Mombasa. Paired orthologs analyses revealed more genes under positive selection when comparing the two C sesamiae bracoviruses belonging to the same species, and more genes under strong evolutionary constraint between species. Furthermore branch-site evolutionary models showed that 17 genes, out of the 54 currently available shared by the four bracoviruses, harboured sites under positive selection including: the histone H4-like, a C-type lectin, two ep1-like, ep2, a viral ankyrin, CrV1, a ben-domain, a Serine-rich, and eight unknown genes. Lastly the phylogenetic analyses of the histone, ep2 and CrV1 genes in different African C sesamiae populations showed that each gene described differently the individual relationships. In particular we found recombination had happened between the ep2 and CrV1 genes, which are localized 37.5 kb apart on the wasp chromosomes. Involved in multidirectional coevolutionary interactions, C sesamiae wasps rely on different bracovirus mediated molecular pathways to overcome local host resistance.

Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase

Myeloperoxidase (MPO) is a member of the mammalian heme peroxidase (MHP) multigene family. Whereas all MHPs oxidize specific halides to generate the corresponding hypohalous acid, MPO is unique in its capacity to oxidize chloride at physiologic pH to produce hypochlorous acid (HOCl), a potent microbicide that contributes to neutrophil-mediated host defense against infection. We have previously resolved the evolutionary relationships in this functionally diverse multigene family and predicted in silico that positive Darwinian selection played a major role in the observed functional diversities (Loughran NB, O'Connor B, O'Fagain C, O'Connell MJ. 2008. The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions. BMC Evol Biol. 8:101). In this work, we have replaced positively selected residues asparagine 496 (N496), tyrosine 500 (Y500), and leucine 504 (L504) with the amino acids present in the ancestral MHP and have examined the effects on the structure, biosynthesis, and activity of MPO. Analysis in silico predicted that N496F, Y500F, or L504T would perturb hydrogen bonding in the heme pocket of MPO and thus disrupt the structural integrity of the enzyme. Biosynthesis of the mutants stably expressed in human embryonic kidney 293 cells yielded apoproMPO, the heme-free, enzymatically inactive precursor of MPO, that failed to undergo normal maturation or proteolytic processing. As a consequence of the maturational arrest at the apoproMPO stage of development, cells expressing MPO with mutations N496F, Y500F, L504T, individually or in combination, lacked normal peroxidase or chlorinating activity. Taken together, our data provide further support for the in silico predictions of positive selection and highlight the correlation between positive selection and functional divergence. Our data demonstrate that directly probing the functional importance of positive selection can provide important insights into understanding protein evolution.

Identification of antimicrobial peptides from teleosts and anurans in expressed sequence tag databases using conserved signal sequences

The problem of multidrug resistance requires the efficient and accurate identification of new classes of antimicrobial agents. Endogenous antimicrobial peptides produced by most organisms are a promising source of such molecules. We have exploited the high conservation of signal sequences in teleost and anuran antimicrobial peptides to search cDNA (expressed sequence tag) databases for likely candidates. Subject sequences were then analysed for the presence of potential antimicrobial peptides based on physicochemical properties (amphipathic helical structure, cationicity) and use of the D-descriptor model to predict the therapeutic index (relation between the minimum inhibitory concentration and the concentration giving 50% haemolysis). This analysis also suggested mutations to probe the role of the primary structure in determining potency and selectivity. Selected sequences were chemically synthesized and the antimicrobial activity of the peptides was confirmed. In particular, a short (21-residue) sequence, likely of sticklefish origin, showed potent activity and it was possible to tune the spectrum of action and/or selectivity by combining three directed mutations. Membrane permeabilization studies on both bacterial and host cells indicate that the mode of action was prevalently membranolytic. This method opens up the possibility for more effective searching of the vast and continuously growing expressed sequence tag databases for novel antimicrobial peptides, which are likely abundant, and the efficient identification of the most promising candidates among them.

Testing the ortholog conjecture with comparative functional genomic data from mammals

A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the “ortholog conjecture”). Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act.

The use of model organisms in biological research rests upon the assumption that gene and protein functions discovered in one organism are likely to be the same or similar in another organism. Hence, the assumption that experiments in mouse will tell us about the function of genes in humans. A guiding principle in the assignment of function from one organism to another is that single-copy genes (“orthologs”) are statistically more likely to provide functional information than are multi-copy genes, whether in the same organism or different organisms. Here we have tested this idea by examining genes with known functions in human and mouse. Surprisingly, we find that multi-copy genes are equally or more likely to provide accurate functional information than are single-copy genes. Our results suggest that the organism itself plays at least as large a role in determining the function of genes as does the particular sequence of the gene alone. This insight will benefit the assignment of function to genes whose roles are not yet known by widening the pool of appropriate genes from which function can be inferred.

How confident can we be that orthologs are similar, but paralogs differ?

Homologous genes are classified into orthologs and paralogs, depending on whether they arose by speciation or duplication. It is widely assumed that orthologs share similar functions, whereas paralogs are expected to diverge more from each other. But does this assumption hold up on further examination? We present evidence that orthologs and paralogs are not so different in either their evolutionary rates or their mechanisms of divergence. We emphasize the importance of appropriately designed studies to test models of gene evolution between orthologs and between paralogs. Thus, functional change between orthologs might be as common as between paralogs, and future studies should be designed to test the impact of duplication against this alternative model.