Alternation between taxonomically divergent hosts is not the major determinant of flavivirus evolution

Flaviviruses display diverse epidemiological and ecological features. Tick-borne and mosquito-borne flaviviruses (TBFV and MBFV, respectively) are important human pathogens that alternate replication in invertebrate vectors and vertebrate hosts. The Flavivirus genus also includes insect-specific viruses (ISFVs) and viruses with unknown invertebrate hosts. It is generally accepted that viruses that alternate between taxonomically different hosts evolve slowly and that the evolution of MBFVs and TBFVs is dominated by strong constraints, with limited episodes of positive selection. We exploited the availability of flavivirus genomes to test these hypotheses and to compare their rates and patterns of evolution. We estimated the substitution rates of CFAV and CxFV (two ISFVs) and, by taking into account the time-frame of measurement, compared them with those of other flaviviruses. Results indicated that CFAV and CxFV display relatively different substitution rates. However, these data, together with estimates for single-host members of the Flaviviridae family, indicated that MBFVs do not display relatively slower evolution. Conversely, TBFVs displayed some of lowest substitution rates among flaviviruses. Analysis of selective patterns over longer evolutionary time-frames confirmed that MBFVs evolve under strong purifying selection. Interestingly, TBFVs and ISFVs did not show extremely different levels of constraint, although TBFVs alternate among hosts, whereas ISFVs do not. Additional results showed that episodic positive selection drove the evolution of MBFVs, despite their high constraint. Positive selection was also detected on two branches of the TBFVs phylogeny that define the seabird clade. Thus, positive selection was much more common during the evolution of arthropod-borne flaviviruses than previously thought. Overall, our data indicate that flavivirus evolutionary patterns are complex and most likely determined by multiple factors, not limited to the alternation between taxonomically divergent hosts. The frequency of both positive and purifying selection, especially in MBFVs, suggests that a minority of sites in the viral polyprotein experience weak constraint and can evolve to generate new viral phenotypes and possibly promote adaptation to new hosts.

Characterization of a novel N-acylhomoserine lactonase, AidP, from Antarctic Planococcus sp

BACKGROUND

N-acylhomoserine lactones (AHLs) are well-studied signalling molecules produced by some Gram-negative Proteobacteria for bacterial cell-to-cell communication or quorum sensing. We have previously demonstrated the degradation of AHLs by an Antarctic bacterium, Planococcus versutus L10.15T, at low temperature through the production of an AHL lactonase. In this study, we cloned the AHL lactonase gene and characterized the purified novel enzyme.

RESULTS

Rapid resolution liquid chromatography analysis indicated that purified AidP possesses high AHL-degrading activity on unsubstituted, and 3-oxo substituted homoserine lactones. Liquid chromatography-mass spectrometry analysis confirmed that AidP functions as an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs. Multiple sequence alignment analysis and phylogenetic analysis suggested that the aidP gene encodes a novel AHL lactonase enzyme. The amino acid composition analysis of aidP and the homologous genes suggested that it might be a cold-adapted enzyme, however, the optimum temperature is 28 °C, even though the thermal stability is low (reduced drastically above 32 °C). Branch-site analysis of several aidP genes of Planococcus sp. branch on the phylogenetic trees also showed evidence of episodic positive selection of the gene in cold environments. Furthermore, we demonstrated the effects of covalent and ionic bonding, showing that Zn2+ is important for activity of AidP in vivo. The pectinolytic inhibition assay confirmed that this enzyme attenuated the pathogenicity of the plant pathogen Pectobacterium carotovorum in Chinese cabbage.

CONCLUSION

We demonstrated that AidP is effective in attenuating the pathogenicity of P. carotovorum, a plant pathogen that causes soft-rot disease. This anti-quorum sensing agent is an enzyme with low thermal stability that degrades the bacterial signalling molecules (AHLs) that are produced by many pathogens. Since the enzyme is most active below human body temperature (below 28 °C), and lose its activity drastically above 32 °C, the results of a pectinolytic inhibition assay using Chinese cabbage indicated the potential of this anti-quorum sensing agent to be safely applied in the field trials.

A genome-wide identification and analysis of basic helix-loop-helix transcription factors in cattle

Basic helix-loop-helix (BHLH) transcription factors comprise a large family of regulatory proteins and play critical roles in the developmental processes of higher organisms. Complete lists of BHLH family members have been identified in about 50 organisms, including fruit fly, zebrafish, mouse, giant panda, worm, yeast, rice and apple. Cattle, Bos taurus, is important for agriculture and animal nutrition, and is also a good model organism for health research. In the present study, 116 putative BHLHs were identified in the cattle genome. Phylogenetic analyses revealed that 111 Bos taurus BHLH (BtBHLH: Bos taurus BHLH) members belong to 44 families, with 48, 26, 16, 4, 13 and 4 members in group A, B, C, D, E and F respectively, and the remaining 5 BtBHLHs are orphan members. All of them were named and assigned into the corresponding BHLH families based on acceptable bootstrap values from in-group phylogenetic analyses with orthologous BHLHs from mouse and other mammalian species. A comparison between annotations deposited in the GenBank and KEGG databases with our analyses indicated that the annotations of 2 of the 116 BtBHLH members were inconsistent with our analytical results. Microarray evidence and expressed sequence tags of only 14 BtBHLH genes was now not available. Chromosomal locations of the BtBHLHs showed that the distribution of the BtBHLHs was uneven and some genes, e.g., BtOligo, BtHes and BtMyf6, may arise from gene duplication. The test of positive selection showed episodic positive selection occurs only in 5 families among the studied mammalian BHLHs. These results provide a solid basis for further studies on BHLH protein regulation of key growth and developmental processes.

Evolution of the merozoite surface protein 7 (msp7) family in Plasmodium vivax and P. falciparum: A comparative approach

Malaria parasites (genus Plasmodium) are a diverse group found in many species of vertebrate hosts. These parasites invade red blood cells in a complex process comprising several proteins, many encoded by multigene families, one of which is merozoite surface protein 7 (msp7). In the case of Plasmodium vivax, the most geographically widespread human-infecting species, differences in the number of paralogs within multigene families have been previously explained, at least in part, as potential adaptations to the human host. To explore this in msp7, we studied its orthologs in closely related nonhuman primate parasites; investigating both paralog evolutionary history and genetic polymorphism. The emerging patterns were then compared with the human parasite Plasmodium falciparum. We found that the evolution of the msp7 family is consistent with a birth-and-death model, where duplications, pseudogenizations, and gene loss events are common. However, all paralogs in P. vivax and P. falciparum had orthologs in their closely related species in non-human primates indicating that the ancestors of those paralogs precede the events leading to their origins as human parasites. Thus, the number of paralogs cannot be explained as an adaptation to human hosts. Although there is no functional information for msp7 in P. vivax, we found evidence for purifying selection in the genetic polymorphism of some of its paralogs as well as their orthologs in closely related non-human primate parasites. We also found evidence indicating that a few of P. vivax's paralogs may have diverged from their orthologs in non-human primates by episodic positive selection. Hence, they may had been under selection when the lineage leading to P. vivax diverged from the Asian non-human primates and switched into Homininae. All these lines of evidence suggest that msp7 is functionally important in P. vivax.

Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis

Background

The merozoite surface protein 7 (MSP7) is a Plasmodium protein which is involved in parasite invasion; the gene encoding it belongs to a multigene family. It has been proposed that MSP7 paralogues seem to be functionally redundant; however, recent experiments have suggested that they could have different roles.

Results

The msp7 multigene family has been described in newly available Plasmodium genomes; phylogenetic relationships were established in 12 species by using different molecular evolutionary approaches for assessing functional divergence amongst MSP7 members. Gene expansion and contraction rule msp7 family evolution; however, some members could have had concerted evolution. Molecular evolutionary analysis showed that relaxed and/or intensified selection modulated Plasmodium msp7 paralogous evolution. Furthermore, episodic diversifying selection and changes in evolutionary rates suggested that some paralogous proteins have diverged functionally.

Conclusions

Even though msp7 has mainly evolved in line with a birth-and-death evolutionary model, gene conversion has taken place between some paralogous genes allowing them to maintain their functional redundancy. On the other hand, the evolutionary rate of some MSP7 paralogs has become altered, as well as undergoing relaxed or intensified (positive) selection, suggesting functional divergence. This could mean that some MSP7s can form different parasite protein complexes and/or recognise different host receptors during parasite invasion. These results highlight the importance of this gene family in the Plasmodium genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0830-x) contains supplementary material, which is available to authorized users.

Adaptive evolution of virus-sensing toll-like receptor 8 in bats

Recently, bats have gained attention as potential reservoir hosts for emerging zoonotic single-stranded (ssRNA) viruses that may prove fatal for humans and other mammals. It has been hypothesized that some features of their innate immune system may enable bats to trigger an efficient early immune response. Toll-like receptors (TLRs) represent a first line defense within the innate immune system and lie directly at the host–pathogen interface in targeting specific microbe-molecular patterns. However, the direction and strength of selection acting on TLRs are largely unknown for bats. Here, we studied the selection on viral ssRNA sensing TLR8 based on sequence data of 21 bat species. The major part (63 %) of the TLR8 gene evolved under purifying selection, likely due to functional constraints. We also found evidence for persistent positive selection acting on specific amino acid sites (7 %), especially when compared to viral TLR evolution of other mammals. All of these putatively positively selected codons were located in the ligand-binding ectodomain, some coincidenced or were in close proximity to functional sites, as suggested by the crystallographic structure of the human TLR8. This might contribute to the inter-species variation in the ability to recognize molecular patterns of viruses. TLR8 evolution within bats revealed that branches leading to ancestral and recent lineages evolved under episodic positive selection, indicating selective selection pressures in restricted bat lineages. Altogether, we found that the TLR8 displays extensive sequence variation within bats and that unique features separate them from humans and other mammals.

Episodic positive selection during the evolution of naphthalene dioxygenase to nitroarene dioxygenase

Using different maximum-likelihood models of adaptive evolution, signatures of natural selective pressure, operating across the naphthalene family of dioxygenases, were examined. A lineage- and branch-site specific combined analysis revealed that purifying selection pressure dominated the evolutionary history of the enzyme family. Specifically, episodic positive Darwinian selection pressure, affecting only a few sites in a subset of lineages, was found to be responsible for the evolution of nitroarene dioxygenases (NArDO) from naphthalene dioxygenase (NDO). Site-specific analysis confirmed the absence of diversifying selection pressure at any particular site. Different sets of positively selected residues, obtained from branch-site specific analysis, were detected for the evolution of each NArDO. They were mainly located around the active site, the catalytic pocket and their adjacent regions, when mapped onto the 3D structure of the α-subunit of NDO. The present analysis enriches the current understanding of adaptive evolution and also broadens the scope for rational alteration of substrate specificity of enzyme by directed evolution.