Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees

Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies

The majority of Legionnaires' disease (LD) cases are caused by Legionella pneumophila, a genetically heterogeneous species composed of at least 17 serogroups. Previously, it was demonstrated that L. pneumophila consists of three subspecies: pneumophila, fraseri and pascullei. During an LD outbreak investigation in 2012, we detected that representatives of both subspecies fraseri and pascullei colonized the same water system and that the outbreak-causing strain was a new member of the least represented subspecies pascullei. We used partial sequence based typing consensus patterns to mine an international database for additional representatives of fraseri and pascullei subspecies. As a result, we identified 46 sequence types (STs) belonging to subspecies fraseri and two STs belonging to subspecies pascullei. Moreover, a recent retrospective whole genome sequencing analysis of isolates from New York State LD clusters revealed the presence of a fourth L. pneumophila subspecies that we have termed raphaeli. This subspecies consists of 15 STs. Comparative analysis was conducted using the genomes of multiple members of all four L. pneumophila subspecies. Whereas each subspecies forms a distinct phylogenetic clade within the L. pneumophila species, they share more average nucleotide identity with each other than with other Legionella species. Unique genes for each subspecies were identified and could be used for rapid subspecies detection. Improved taxonomic classification of L. pneumophila strains may help identify environmental niches and virulence attributes associated with these genetically distinct subspecies.

Molecular detection of hemogregarines and haemosporidians in Brazilian free-living testudines

Morphological and molecular techniques were used to investigate the presence of hemogregarines and haemosporidians in biological samples of free-living Geoffroy's side-necked turtles (Phrynops geoffroanus) and Giant Amazon turtles (Podocnemis expansa) from Brazil. No evolutionary form of haemosporidians or hemogregarines were observed in the blood smears of 83 P. geoffroanus samples, and there were no meronts in the histological sections of 31 necropsied P. geoffroanus samples. All DNA samples extracted from P. geoffroanus tissues and blood aliquots were negative in haemosporidian PCR assays (based on the mitochondrial cytochrome b gene) and hemogregarine PCR assays (based on the 18S rRNA gene). In the analysis of blood smears of all seven Podocnemis expansa evaluated, gametocytes of hemogregarines were observed. The seven P. expansa were negative in the haemosporidian PCR assays. Moreover, hemogregarine DNA was detected in blood samples from all of the sampled P. expansa. The phylogenetic maximum likelihood inference and probabilistic Bayesian inference revealed five closely related genotypes that formed a monophyletic group. There was also a sister group to the lineage that consisted of Haemogregarina spp. of freshwater turtles from Canada, Italy, Mozambique, Kenya, Gabon, Vietnam, and China. The findings suggest that free-living P. expansa were parasitized by a new genotype or even a possible new species of the genus Haemogregarina. Haemosporidians and hemogregarines are not frequently found in P. geoffroanus in the studied region under the local conditions of that period.

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Hemogregarines was detected in blood samples of free-living Brazilian testudines.

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Gametocytes of hemogregarines were observed in Podocnemis expansa blood smears.

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Hemogregarines DNA fragments based on the 18S rRNA gene were detected in P. expansa.

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We propose that P. expansa were parasitized by a new genotype of Haemogregarina.

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Haemosporidians was not observed in either P. expansa or Phrynops geoffroanus samples.

Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria

The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People’s Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles

Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut-and-paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species' lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition.

Role of cis-trans proline isomerization in the function of pathogenic enterobacterial Periplasmic Binding Proteins

Periplasmic Binding Proteins (PBPs) trap nutrients for their internalization into bacteria by ABC transporters. Ligand binding triggers PBP closure by bringing its two domains together like a Venus flytrap. The atomic determinants that control PBP opening and closure for nutrient capture and release are not known, although it is proposed that opening and ligand release occur while in contact with the ABC transporter for concurrent substrate translocation. In this paper we evaluated the effect of the isomerization of a conserved proline, located near the binding site, on the propensity of PBPs to open and close. ArgT/LAO from Salmonella typhimurium and HisJ from Escherichia coli were studied through molecular mechanics at two different temperatures: 300 and 323 K. Eight microseconds were simulated per protein to analyze protein opening and closure in the absence of the ABC transporter. We show that when the studied proline is in trans, closed empty LAO and HisJ can open. In contrast, with the proline in cis, opening transitions were much less frequent and characterized by smaller changes. The proline in trans also renders the open trap prone to close over a ligand. Our data suggest that the isomerization of this conserved proline modulates the PBP mechanism: the proline in trans allows the exploration of conformational space to produce trap opening and closure, while in cis it restricts PBP movement and could limit ligand release until in productive contact with the ABC transporter. This is the first time that a proline isomerization has been related to the control of a large conformational change like the PBP flytrap mechanism.

Recombination analysis of coxsackievirus B5 genogroup C

Coxsackievirus B5 (CVB5) is a member of the species Enterovirus B of the genus Enterovirus, family Picornaviridae. Based on its VP1 sequence, CVB5 is divided into four genogroups: A, B, C, and D. From 2002 to 2012, CVB5 serotype genogroup C caused an outbreak of aseptic meningitis in China. In order to study the evolution of CVB5 genogroup C, phylogenetic and recombination analysis was performed using the 399 available enterovirus B genome sequences in the GenBank database. The results indicated that 10 strains of CVB5 serotype genogroup C resulted from recombination between members of genogroup B and echovirus serotype E6, and another 5 strains resulted from recombination between members of genogroup C and serotype CVB4. These recombination events were confirmed by phylogenetic analysis.

A Comparative Genomic and Transcriptomic Survey Provides Novel Insights into N-Acetylserotonin Methyltransferase (ASMT) in Fish

Melatonin is a multifunctional bioactive molecule that plays comprehensive physiological roles in all living organisms. N-acetylserotonin methyltransferase (ASMT, also known as hydroxyindole O-methyltransferase or HIOMT) is the final enzyme for biosynthesis of melatonin. Here, we performed a comparative genomic and transcriptomic survey to explore the ASMT family in fish. Two ASMT isotypes (ASMT1 and ASMT2) and a new ASMT-like (ASMTL) are all extracted from teleost genomes on the basis of phylogenetic and synteny analyses. We confirmed that C-terminal of the ASMTL proteins (ASMTL-ASMT) is homology to the full length of ASMT1 and ASMT2. Our results also demonstrate that the two ASMT isotypes and their distribution in teleosts seem to be the result of combinations of whole-genome duplication (WGD) and gene loss. Differences were also observed in tissue distribution and relative transcript abundances of ASMT1, ASMT2 and ASMTL through transcriptomic analysis. Protein sequence alignment and 3D structure prediction of ASMTs and ASMTL suggest differential roles for these ASMT genes. In summary, our current work provides novel insights into the ASMT genes in fish by combination of genomic and transcriptomic data.

Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances

The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.

Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids

Carboxylic acid reductases (CARs) selectively reduce carboxylic acids to aldehydes using ATP and NADPH as cofactors under mild conditions. Although CARs attracts significant interest, only a few enzymes have been characterized to date, whereas the vast majority of CARs have yet to be examined. Herein the authors report that 12 bacterial CARs reduces a broad range of bifunctional carboxylic acids containing oxo-, hydroxy-, amino-, or second carboxyl groups with several enzymes showing activity toward 4-hydroxybutanoic (4-HB) and adipic acids. These CARs exhibits significant reductase activity against substrates whose second functional group is separated from the carboxylate by at least three carbons with both carboxylate groups being reduced in dicarboxylic acids. Purified CARs supplemented with cofactor regenerating systems (for ATP and NADPH), an inorganic pyrophosphatase, and an aldo-keto reductase catalyzes a high conversion (50-76%) of 4-HB to 1,4-butanediol (1,4-BDO) and adipic acid to 1,6-hexanediol (1,6-HDO). Likewise, Escherichia coli strains expressing eight different CARs efficiently reduces 4-HB to 1,4-BDO with 50-95% conversion, whereas adipic acid is reduced to a mixture of 6-hydroxyhexanoic acid (6-HHA) and 1,6-HDO. Thus, our results illustrate the broad biochemical diversity of bacterial CARs and their compatibility with other enzymes for applications in biocatalysis.

Hepatozoon caimani in Caiman crocodilus yacare (Crocodylia, Alligatoridae) from North Pantanal, Brazil

Hepatozoon species are the most common intracellular hemoparasite found in reptiles. Hepatozoon caimani, whose vectors are Culex mosquitoes, has been detected in a high prevalence among caimans in Brazil by blood smears examinations. The present work aimed to detect and characterize the Hepatozoon spp. found in 33 caimans (24 free-ranging and 9 captive; 28 males and 5 females) (Caiman crocodilus yacare) sampled at Poconé, North Pantanal, state of Mato Grosso, Brazil, using blood smears examinations and molecular techniques. Hepatozoon spp.-gametocytes were found in 70.8% (17/24) and 88.8% (8/9) of blood smears from free-ranging and captive caimans, respectively. Hepatozoon spp. 18S rRNA DNA was found in 79.2% (19/24) and 88.8% (8/9) of free-ranging and captive caimans, respectively. Comparative analysis of parasitized and non-parasitized erythrocytes showed that all analyzed features were significantly different (P<0.05) for both linear and area dimensions. Phylogenetic analysis based on 18S rRNA sequences grouped the Hepatozoon spp. sequences detected in the present study together with H. caimani, recently detected in caimans in southern Pantanal.

Fungal lifestyle reflected in serine protease repertoire

Fungi are able to switch between different lifestyles in order to adapt to environmental changes. Their ecological strategy is connected to their secretome as fungi obtain nutrients by secreting hydrolytic enzymes to their surrounding and acquiring the digested molecules. We focus on fungal serine proteases (SPs), the phylogenetic distribution of which is barely described so far. In order to collect a complete set of fungal proteases, we searched over 600 fungal proteomes. Obtained results suggest that serine proteases are more ubiquitous than expected. From 54 SP families described in MEROPS Peptidase Database, 21 are present in fungi. Interestingly, 14 of them are also present in Metazoa and Viridiplantae - this suggests that, except one (S64), all fungal SP families evolved before plants and fungi diverged. Most representatives of sequenced eukaryotic lineages encode a set of 13-16 SP families. The number of SPs from each family varies among the analysed taxa. The most abundant are S8 proteases. In order to verify hypotheses linking lifestyle and expansions of particular SP, we performed statistical analyses and revealed previously undescribed associations. Here, we present a comprehensive evolutionary history of fungal SP families in the context of fungal ecology and fungal tree of life.

Nuclear matrix metalloproteinases: functions resemble the evolution from the intracellular to the extracellular compartment

Matrix metalloproteinase (MMP) is defined as an endopeptidase in the extracellular matrix (ECM), which plays essential roles in physiological processes such as organogenesis, wound healing, angiogenesis, apoptosis and motility. MMPs are produced and assembled in the cytoplasm as proenzymes with a cytoplasmic domain and require extracellular activation. MMPs can degrade receptors, extracellular matrix proteins, PARPs and release apoptotic substances. MMPs have been found in the cytosol, organelles and extracellular compartments and recently many types of MMPs have been found in the nucleus. However, the mechanisms and roles of MMPs inside the cell nucleus are still poorly understood. Here we summarized the nuclear localization mechanisms of MMPs and their functions in the nucleus such as apoptosis, tissue remodeling upon injury and cancer progression. Most importantly, we found that nuclear MMPs have evolved to translocate to membrane and target ECM possibly through evolution of nuclear localization signal (NLS), natural selection and anti-apoptotic survival. Thus, the knowledge about the evolution and regulation of nuclear MMPs appears to be essential in understanding a variety of cellular processes along with the development of MMP-targeted therapeutic drugs against the progression of certain diseases.

Acidic C-terminal domains autoregulate the RNA chaperone Hfq

The RNA chaperone Hfq is an Sm protein that facilitates base pairing between bacterial small RNAs (sRNAs) and mRNAs involved in stress response and pathogenesis. Hfq possesses an intrinsically disordered C-terminal domain (CTD) that may tune the function of the Sm domain in different organisms. In Escherichia coli, the Hfq CTD increases kinetic competition between sRNAs and recycles Hfq from the sRNA-mRNA duplex. Here, de novo Rosetta modeling and competitive binding experiments show that the acidic tip of the E. coli Hfq CTD transiently binds the basic Sm core residues necessary for RNA annealing. The CTD tip competes against non-specific RNA binding, facilitates dsRNA release, and prevents indiscriminate DNA aggregation, suggesting that this acidic peptide mimics nucleic acid to auto-regulate RNA binding to the Sm ring. The mechanism of CTD auto-inhibition predicts the chaperone function of Hfq in bacterial genera and illuminates how Sm proteins may evolve new functions.

Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences

The alignment of three or more protein or nucleotide sequences is known as Multiple Sequence Alignment problem. The complexity of this problem increases exponentially with the number of sequences; therefore, many of the current approaches published in the literature suffer a computational overhead when thousands of sequences are required to be aligned. We introduce a new approach for dealing with ultra-large sets of sequences. A two-level clustering method is considered. The first level clusters the input sequences by using their biological composition, that is, the number of positive, negative, polar, special, and hydrophobic amino acids. In the second level, each cluster is divided into different clusters according to their similarity. Then, each cluster is aligned by using any method/aligner. After aligning the centroid sequences of each second-level cluster, we extrapolate the new gaps to each cluster of sequences to obtain the final alignment. We present a study on biological data with up to ∼100,000 sequences, showing that the proposed approach is able to obtain accurate alignments in a reduced amount of time; for example, in >10,000 sequences datasets, it is able to reduce up to ∼45 times the required runtime of the well-known Kalign.

Contrasting patterns of nucleotide polymorphism suggest different selective regimes within different parts of the PgiC1 gene in Festuca ovina L

Background

Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5’ and 3’ portions of the gene.

Methods

In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene.

Results

Our study confirms that the two portions of the PgiC1 gene show substantially different levels of DNA polymorphism and also suggests that the peptide encoded by the 3’ portion of PgiC1 is functionally and structurally more important than that encoded by the 5’ portion. Although there was some evidence of purifying selection (d_N/d_S test) on the 5’ portion of the gene, the signature of purifying selection was considerably stronger on the 3’ portion of the gene (d_N/d_S and McDonald–Kreitman tests). Several tests support the action of balancing selection within the 5’ portion of the gene. Wall’s B and Q tests were significant only for the 5’ portion of the gene. There were also marked peaks of nucleotide diversity, Tajima’s D and the d_N/d_S ratio at or around a PgiC1 codon site (within the 5’ portion of the gene) that a previous study had suggested was subject to positive diversifying selection.

Conclusions

Our results suggest that the two portions of the gene have been subject to different selective regimes. Purifying selection appears to have been the main force contributing to the relatively low level of polymorphism within the 3’ portion of the sequence. In contrast, it is possible that balancing selection has contributed to the maintenance of the polymorphism within the 5’ portion of the gene.

Electronic supplementary material

The online version of this article (doi:10.1186/s41065-017-0032-6) contains supplementary material, which is available to authorized users.

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain

H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily conserved nucleosome-binding globular domain, GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species studied so far, linker histones are highly heterogenous, with numerous nonallelic variants cooccurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established. This contrasts markedly with the rather limited knowledge concerning the phylogeny and structural and functional roles of an unusually diverse group of GH1-containing proteins in plants. The dearth of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead to misunderstandings regarding their identity and possible relationships, thereby hampering plant chromatin research. Based on published data and our in silico and high-throughput analyses, we propose a systematization and coherent nomenclature of GH1-containing proteins of Arabidopsis (Arabidopsis thaliana [L.] Heynh) that will be useful for both the identification and structural and functional characterization of homologous proteins from other plant species.

Analysis of origin and protein-protein interaction maps suggests distinct oncogenic role of nuclear EGFR during cancer evolution

Receptor tyrosine kinase EGFR usually is localized on plasma membrane to induce progression of many cancers including cancers in children (Bodey et al. In Vivo. 2005, 19:931-41), but it contains a nuclear localization signal (NLS) that mediates EGFR nuclear translocation (Lin et al. Nat Cell Biol. 2001, 3:802-8). Here we report that NLS of EGFR has its old evolutionary origin. Protein-protein interaction maps suggests that nEGFR pathways are different from membrane EGFR and EGF is not found in nEGFR network while androgen receptor (AR) is found, which suggests the evolution of prostate cancer, a well-known AR driven cancer, through changes in androgen- or EGF-dependence. Database analysis suggests that nEGFR correlates with the tumor grades especially in prostate cancer patients. Structural predication analysis suggests that NLS can compromise the differential protein binding to EGFR through stretch linkers with evolutionary mutation from N to V. In experiment, elevation of nEGFR but not membrane EGFR was found in castration resistant prostate cancer cells. Finally, systems analysis of NLS and transmembrane domain (TM) suggests that NLS has old origin while NLS neighboring domain of TM has been undergone accelerated evolution. Thus nEGFR has an old origin resembling the cancer evolution but TM may interfere with NLS driven signaling for natural selection of survival to evade NLS induced aggressive cancers. Our data suggest NLS is a dynamic inducer of EGFR oncogenesis during evolution for advanced cancers. Our model provides novel insights into the evolutionary role of NLS of oncogenic kinases in cancers.

QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families

The ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins.

Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers

Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now, cloning and Sanger sequencing of about 100 sequences was usually used to identify the enriched candidates. However, High-Throughput Sequencing (HTS) is now extensively used to replace such low throughput sequencing approaches. Providing a deeper analysis of the library, HTS is expected to accelerate the identification of aptamers as well as to identify aptamers with higher affinity. It is also expected that it can provide important information on the binding site of the aptamers. Nevertheless, HTS requires handling a large amount of data that is only possible through the development of new in silico methods. Here, this review presents these different strategies that have been recently developed to improve the identification and characterization of aptamers using HTS.