Protein Sequence Conservation Research Articles

ERH proteins: connecting RNA processing to tumorigenesis?

With the development of -omics approaches, the scientific community is now submerged by a wealth of information that can be used to analyze various parameters: the degree of protein sequence conservation, protein 3D structures as well as RNA and protein expression levels in various benign and tumor tissues, during organism development or upon exposure to chemicals such as endocrine disrupters. However, if such information can be used to identify genes with potentially important biological function, additional studies are needed to deeply characterize their cellular function in model organisms. Here, we discuss the case of such a gene: ERH, encoding a highly conserved homodimeric protein found in unicellular eukaryotes, plants and metazoan, of yet unknown biological function, which might be linked to mRNA metabolism and that is emerging as important for cell migration and metastasis.

New Perspectives Related to the Bioluminescent System in Dinoflagellates: Pyrocystis lunula, a Case Study.

Pyrocystis lunula is considered a model organism due to its bioluminescence capacity linked to circadian rhythms. The mechanisms underlying the bioluminescent phenomenon have been well characterized in dinoflagellates; however, there are still some aspects that remain an enigma. Such is the case of the presence and diversity of the luciferin-binding protein (LBP), as well as the synthesis process of luciferin. Here we carry out a review of the literature in relation to the molecular players responsible for bioluminescence in dinoflagellates, with particular interest in P. lunula. We also carried out a phylogenetic analysis of the conservation of protein sequence, structure and evolutionary pattern of these key players. The basic structure of the luciferase (LCF) is quite conserved among the sequences reported to date for dinoflagellate species, but not in the case of the LBP, which has proven to be more variable in terms of sequence and structure. In the case of luciferin, its synthesis has been shown to be complex process with more than one metabolic pathway involved. The glutathione S-transferase (GST) and the P630 or blue compound, seem to be involved in this process. In the same way, various hypotheses regarding the role of bioluminescence in dinoflagellates are exposed.

Homeologs of Brassica SOC1, a central regulator of flowering time, are differentially regulated due to partitioning of evolutionarily conserved transcription factor binding sites in promoters

Evolution of Brassica genome post-polyploidization reveals asymmetrical genome fractionation and copy number variation. Herein, we describe the impact of promoter divergence among SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) homeologs on expression and function in Brassica spp. SOC1, a regulated floral pathway integrator, is conserved as 3 redundant homeologs in diploid Brassicas. Even with high sequence identity within coding regions (92.8–100%), the spatio-temporal expression patterns of 9 SOC1 homologs in B. juncea and B. nigra indicates regulatory divergence. While LF and MF2 SOC1 homeologs are upregulated during floral transition, MF1 is barely expressed. Also, MF2 homeolog levels do not decline post-flowering, unlike LF. To investigate the underlying source of divergence, we analyzed the sequence and phylogeny of all reported (22) and isolated (21) upstream regions of Brassica SOC1. Full length upstream regions (4712–19189 bp) reveal 5 ubiquitously conserved ancestral Blocks, harboring binding sites of 18 TFs (TFBSs) characterized in Arabidopsis thaliana. The orthologs of these TFBSs are differentially conserved among Brassica SOC1 homeologs, imparting expression divergence. No crucial TFBSs are exclusively lost from LF_SOC1 promoter, while MF1_SOC1 has lost NF-Y binding site crucial for SOC1 activation by CONSTANS. MF2_SOC1 homeologs have lost important TFBSs (SEP3, AP1 and SMZ), responsible for SOC1 repression post-flowering. BjuAALF_SOC1 promoter (proximal 2 kb) shows ubiquitous reporter expression in B. juncea cv. Varuna transgenics, while BjuAAMF1_SOC1 promoter shows absence of reporter expression, validating the impact of TFBS divergence. Conservation of the original primary protein sequence is discovered in B. rapa homeologs (46) of 18 TFs. Co-regulation pattern of these TFs appeared similar for B. rapa LF and MF2 SOC1 homeologs; MF1 shows significant variation. Strong regulatory association is recorded for AP1, AP2, SEP3, FLC and CONSTANS/NF-Y, highlighting their importance in homeolog-specific SOC1 regulation. Correlation of B. juncea AP1, AP2 and FLC expression with SOC1 homeologs also complies with the TFBS differences. We thus conclude that redundant SOC1 loci contribute differentially to cumulative expression of SOC1 due to divergent selection of ancestral TFBSs.

Genomic and Metabolomic Analyses of Natural Products in Nodularia spumigena Isolated from a Shrimp Culture Pond.

The bloom-forming cyanobacterium Nodularia spumigena CENA596 encodes the biosynthetic gene clusters (BGCs) of the known natural products nodularins, spumigins, anabaenopeptins/namalides, aeruginosins, mycosporin-like amino acids, and scytonemin, along with the terpenoid geosmin. Targeted metabolomics confirmed the production of these metabolic compounds, except for the alkaloid scytonemin. Genome mining of N. spumigena CENA596 and its three closely related Nodularia strains—two planktonic strains from the Baltic Sea and one benthic strain from Japanese marine sediment—revealed that the number of BGCs in planktonic strains was higher than in benthic one. Geosmin—a volatile compound with unpleasant taste and odor—was unique to the Brazilian strain CENA596. Automatic annotation of the genomes using subsystems technology revealed a related number of coding sequences and functional roles. Orthologs from the Nodularia genomes are involved in the primary and secondary metabolisms. Phylogenomic analysis of N. spumigena CENA596 based on 120 conserved protein sequences positioned this strain close to the Baltic Nodularia. Phylogeny of the 16S rRNA genes separated the Brazilian CENA596 strain from those of the Baltic Sea, despite their high sequence identities (99% identity, 100% coverage). The comparative analysis among planktic Nodularia strains showed that their genomes were considerably similar despite their geographically distant origin.

A customized program for the identification of conserved protein sequence motifs.

We searched for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (e.g., pulmonary), irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed an amino acid sequence alignment program and identified the conserved amino acid motif, VAIVLGG, in alphaviruses. The VAIVLGG sequence is located on the structural capsid protein of the chikungunya virus, a mosquito-borne arthrogenic member of the alphaviruses. Capsid protein translocation onto the host cell membrane is a required step for virion budding. Our identified VAIVLGG consensus sequence might potentially be used for developing a pan-vaccine effective against alphaviruses.

Cloning, phylogenetic research, and prokaryotic expression study of the metabolic detoxification gene EoGSTs1 in Empoasca onukii Matsuda.

Due to the misuse of chemical pesticides, small green leafhoppers (Empoasca onukii Matsuda) have developed resistance to pesticides, thereby posing a serious problem to the tea industry. Glutathione S-transferases (GSTs) are an important family of enzymes that are involved in pesticide resistance in Empoasca onukii Matsuda. Empoasca onukii GST sigma 1 (EoGSTs1, GenBank: MK443501) is a member of the GST family. In this study, the full-length cDNA of EoGSTs1 was cloned by reverse transcription polymerase chain reaction (qPCR), and its taxonomic identity was examined. Furthermore, we performed bioinformatics and phylogenetic analyses of the gene and structural and functional domain prediction of the protein. The results demonstrate that EoGSTS1 belongs to the Sigma family of GSTs; the full-length EoGSTs1 cDNA is 841 bp with a 624-bp coding region that encodes a 23.68932-kDa protein containing 207 amino acids. The theoretical isoelectric point (IEP) was calculated to be 6.00. Phylogenetic analysis indicates that EoGSTS1 is closely related to the Sub psaltriayangi subfamily of the Cicadoidea superfamily in order Hemiptera, whereas it is distantly related to Periplaneta americana of order Blattodea. Amino acid sequence alignment of EoGSTS1 and GSTs from four other insects of order Hemiptera revealed protein sequence conservation. Tertiary structure analysis and structural domain functional predictions of the protein revealed that EoGSTS1 contains nine α helices and two β sheets with one conserved GST domain. The results of enzyme activity assay showed that recombinant EoGSTs1 (rEoGSTs1) protein had catalytic activity for substrate 1-chloro-2,4-dinitrobenzene (CDNB) and exhibited the highest activity at pH 7 and 25 °C. The Michaelis constant Km of rEoGSTs1 protein was 0.07782 ± 0.01990 mmol/L, and the maximum reaction rate Vmax was 12.15 ± 1.673 µmol/min⋅mg. Our study clarified the taxonomic identity of small green leafhopper EoGSTs1 and revealed some properties of the gene and its encoded protein sequence. According to the catalytic activity of the rEoGSTs1 enzyme on the model substrate CDNB, we infer that it functions in the degradation of exogenous substances.

The evolutionary history of LysM-RLKs (LYKs/LYRs) in wild tomatoes

BackgroundThe LysM receptor-like kinases (LysM-RLKs) are important to both plant defense and symbiosis. Previous studies described three clades of LysM-RLKs: LysM-I/LYKs (10+ exons per gene and containing conserved kinase residues), LysM-II/LYRs (1–5 exons per gene, lacking conserved kinase residues), and LysM-III (two exons per gene, with a kinase unlike other LysM-RLK kinases and restricted to legumes). LysM-II gene products are presumably not functional as conventional receptor kinases, but several are known to operate in complexes with other LysM-RLKs. One aim of our study was to take advantage of recently mapped wild tomato transcriptomes to evaluate the evolutionary history of LysM-RLKs within and between species. The second aim was to place these results into a broader phylogenetic context by integrating them into a sequence analysis of LysM-RLKs from other functionally well-characterized model plant species. Furthermore, we sought to assess whether the Group III LysM-RLKs were restricted to the legumes or found more broadly across Angiosperms.ResultsPurifying selection was found to be the prevailing form of natural selection within species at LysM-RLKs. No signatures of balancing selection were found in species-wide samples of two wild tomato species. Most genes showed a greater extent of purifying selection in their intracellular domains, with the exception of SlLYK3 which showed strong purifying selection in both the extracellular and intracellular domains in wild tomato species. The phylogenetic analysis did not reveal a clustering of microbe/functional specificity to groups of closely related proteins. We also discovered new putative LysM-III genes in a range of Rosid species, including Eucalyptus grandis.ConclusionsThe LysM-III genes likely originated before the divergence of E. grandis from other Rosids via a fusion of a Group II LysM triplet and a kinase from another RLK family. SlLYK3 emerges as an especially interesting candidate for further study due to the high protein sequence conservation within species, its position in a clade of LysM-RLKs with distinct LysM domains, and its close evolutionary relationship with LYK3 from Arabidopsis thaliana.

Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations.

Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to preprocess the DNA information. These classifiers were benchmarked against their tree-based alternatives in order to evaluate the performance on a relative scale. We then integrated DNA-based scores generated by CNN with various categories of conservational, evolutionary and functional features into a generalized random forest classifier. The results of this study have demonstrated that CNN can learn high level features from genomic information that are complementary to the ensemble-based predictors often employed for classification of cancer mutations. By combining deep learning-generated score with only two main ensemble-based functional features, we can achieve a superior performance of various machine learning classifiers. Our findings have also suggested that synergy of nucleotide-based deep learning scores and integrated metrics derived from protein sequence conservation scores can allow for robust classification of cancer driver mutations with a limited number of highly informative features. Machine learning predictions are leveraged in molecular simulations, protein stability, and network-based analysis of cancer mutations in the protein kinase genes to obtain insights about molecular signatures of driver mutations and enhance the interpretability of cancer-specific classification models.

Classification of Bisgaard's taxa 14 and 32 and a taxon from kestrels demonstrating satellitic growth and proposal of Spirabiliibacterium gen. nov., including the description of three species: Spirabiliibacterium mucosae sp. nov., Spirabiliibacterium pneumoniae sp. nov. and Spirabiliibacterium falconis sp. nov.

Avian Pasteurella-like organisms tentatively named taxon 14 of Bisgaard have been obtained from different lesions in birds including ducks, turkeys, pigeons, geese and peafowl. Taxon 32 of Bisgaard was first reported from lesions in pigeon hawks (Accipiter gentiles). The taxon isolated from kestrels (Falco tinnunculus) was V-factor dependent and originally reported as Haemophilus-like. The results of 16S rRNA gene sequence based phylogenetic analysis recently indicated that the taxa 14 and 32 and the kestrel taxon were located in a monophyletic group distantly related to [Pasteurella] testudinis with 92-93 % 16S rRNA gene sequence similarity. Comparison of 41 conserved protein sequences confirmed the monophyletic nature of the three taxa. Partial rpoB gene sequencing of 43 strains of taxon 14, taxon 32 and the kestrel taxon showed a relationship between taxon 14 and 32 of 88.2-90.0 % similarity. Within taxon 14, 93.3-100 % similarity was found, whereas the two strains of taxon 32 showed 99.8 % rpoB similarity. Sequencing of 16S rRNA genes of strains representing the rpoB diversity outlined showed more than 98 % similarity within taxon 14 and 99.4 % within taxon 32, while the kestrel strains showed 100 % 16S rRNA gene sequence similarity. A new genus, Spirabiliibacterium gen. nov., is proposed to include taxon 14, taxon 32 and the kestrel taxon. Phenotypically, members of the genus Spirabiliibacterium can be separated from members of the genera Aggregatibacter, Avibacterium and Volucribacter by maltose, oxidase and methyl red, respectively. Two or more phenotypic characters separate members of the genus Spirabiliibacterium from members of the remaining 27 genera of the family Pasteurellaceae.The G+C content of DNA ranged from 42.9 to 51.2 % (genome sequence) for members of the genus Spirabiliibacterium. The type strain of Spirabiliibacterium mucosae (taxon 14 of Bisgaard) is 20609/3T (=CCUG 16499T=DSM 111429T=HIM 913-3T). The type strain of Spirabiliibacterium pneumoniae is HPA106T (=CCUG 74731T=DSM 111430T). The type strain of Spirabiliibacterium falconis (kestrel taxon) is IPDH 2176T (=NCTC 11878T=CCUG 28587T).

The DDX5/Dbp2 subfamily of DEAD-box RNA helicases.

The mammalian DEAD-box RNA helicase DDX5, its paralog DDX17, and their orthologs in Saccharomyces cerevisiae and Drosophila melanogaster, namely Dbp2 and Rm62, define a subfamily of DEAD-box proteins. Members from this subfamily share highly conserved protein sequences and cellular functions. They are involved in multiple steps of RNA metabolism including mRNA processing, microRNA processing, ribosome biogenesis, RNA decay, and regulation of long noncoding RNA activities. The DDX5/Dbp2 subfamily is also implicated in transcription regulation, cellular signaling pathways, and energy metabolism. One emerging theme underlying the diverse cellular functions is that the DDX5/Dbp2 subfamily of DEAD-box helicases act as chaperones for complexes formed by RNA molecules and proteins (RNP) in vivo. This RNP chaperone activity governs the functions of various RNA species through their lifetime. Importantly, mammalian DDX5 and DDX17 are involved in cancer progression when overexpressed through alteration of transcription and signaling pathways, meaning that they are possible targets for cancer therapy. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Epitope Mapping of Capsid Protein L1 from Human Papillomavirus to Development Cervical Cancer Vaccine through Computational Study

Human papillomavirus (HPV) is a virus that plays an important role in the occurrence of cervical cancer, HPV is a member of the family papovaviridae, genus papillomavirus. The HPV gene is composed of two parts: early and late gene. Early proteins in HPV include E1, E2, E4, E5, E6, and E7 Late gene expressed from the late promoter acting as coders for L1 and L2 protein capsid. The L1 protein has a conserved region composed of cysteine and lysine residues, both of which have involved in the binding process between virions and host receptors. Previous research has shown that vaccines can be developed based on epitopes that have conserved areas. This study is important to identify conserved protein sequences in L1 of HPV capsid, predict epitope mapping of B cells and antigenicity in the conserved region of L1 HPV capsid, as well as the similarity of amino acid residues of epitope composers with surface receptors of human body cells. The conserved areas were identified in L1 HPV as a potential epitope of B cells based on epitope mapping analysis of positions 23-46 and 97-119 with EGRGQPLGGSGHPNDDE DRDKQ and RHNGGPGPSGSSQFNKPYWAQGN peptides and each had a peptide length of 22-mer and 23-mer. The 97-119 epitope has a high antigenicity score and the similarity of the low amino acid residue sequence to the cell surface receptor of the human body. So the 23-mer RHNGGPGPSGSSQFNKPYWAQGN peptide can be used as a reference for the development of cervical cancer prevention vaccine.

Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response.

The omnipresence of allosteric regulation together with the fundamental role of structural dynamics in this phenomenon have initiated a great interest to the detection of regulatory exosites and design of corresponding effectors. However, despite a general consensus on the key role of dynamics most of the earlier efforts on the prediction of allosteric sites are heavily crippled by the static nature of the underlying methods, which are either structure-based approaches seeking for deep surface pockets typical for “traditional” orthosteric drugs or sequence-based techniques exploiting the conservation of protein sequences. Because of the critical role of global protein dynamics in allosteric signaling, we investigate the hypothesis of reversibility in allosteric communication, according to which allosteric sites can be detected via the perturbation of the functional sites. The reversibility is tested here using our structure-based perturbation model of allostery, which allows one to analyze the causality and energetics of allosteric communication. We validate the “reverse perturbation” hypothesis and its predictive power on a set of classical allosteric proteins, then, on the independent extended benchmark set. We also show that, in addition to known allosteric sites, the perturbation of the functional sites unravels rather extended protein regions, which can host latent regulatory exosites. These protein parts that are dynamically coupled with functional sites can also be used for inducing and tuning allosteric communication, and an exhaustive exploration of the per-residue contributions to allosteric effects can eventually lead to the optimal modulation of protein activity. The site-effector interactions necessary for a specific mode and level of allosteric communication can be fine-tuned by adjusting the site’s structure to an available effector molecule and by the design or selection of an appropriate ligand.

Classifying Cardiac Actin Mutations Associated With Hypertrophic Cardiomyopathy.

Mutations in the cardiac actin gene (ACTC1) are associated with the development of hypertrophic cardiomyopathy (HCM). To date, 12 different ACTC1 mutations have been discovered in patients with HCM. Given the high degree of sequence conservation of actin proteins and the range of protein–protein interactions actin participates in, mutations in cardiac actin leading to HCM are particularly interesting. Here, we suggest the classification of ACTC1 mutations based on the location of the resulting amino acid change in actin into three main groups: (1) those affecting only the binding site of the myosin molecular motor, termed M-class mutations, (2) those affecting only the binding site of the tropomyosin (Tm) regulatory protein, designated T-class mutations, and (3) those affecting both the myosin- and Tm-binding sites, called MT-class mutations. To understand the precise pathogenesis of cardiac actin mutations and develop treatments specific to the molecular cause of disease, we need to integrate rapidly growing structural information with studies of regulated actomyosin systems.

Linked homozygous BMPR1B and PDHA2 variants in a consanguineous family with complex digit malformation and male infertility.

In affected members of a consanguineous family, a syndrome, which is concurrence of set of medical signs, is often observed and commonly assumed to have arisen from pleiotropy, i.e., the phenomenon of a single gene variant affecting multiple traits. We detected six sibs afflicted with a unique combination of digit malformation that includes brachydactyly, symphalangism and zygodactyly plus infertility in males owing to azoospermia, sperm immotility or necrospermia, which we hypothesised to have arisen from a defect in a single gene. We mapped the disease locus and by exome sequencing identified in patients homozygous missense variants bone morphogenetic protein receptor type IB (BMPR1B) c.640C>T (p.(Arg214Cys)) and alpha-2 pyruvate dehydrogenase (PDHA2) c.679A>G (p.(Met227Val)). Structural protein modelling, protein sequence conservation and in silico analysis indicate that both variants affect protein function. BMPR1B is known to be responsible for autosomal dominant brachydactyly and autosomal recessive acromesomelic chondrodysplasia. Our findings show that also recessive complex digit malformation can be caused by BMPR1B variant and not all biallelic BMPR1B variants cause acromesomelic dysplasia. PDHA2 is a novel candidate gene for male infertility; the protein product is a mitochondrial enzyme with highest expression in ejaculated sperm. Our findings are a unique example of two linked variants, ~ 711 Kb apart, in different genes that together manifest as a novel syndrome. They demonstrate that exome sequencing and not candidate gene approach should be employed in disease gene hunt, defining new diseases and genetic testing, to rule out the coincidental presence of two variants contributing together to the phenotype, which may be discerned as a novel disease.

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets.

Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the “pocketome druggability.” To this end, we first computed the “modelome” (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.

Radically truncated MeCP2 rescues Rett syndrome-like neurological defects.

Heterozygous mutations in the X-linked MECP2 gene cause the profound neurological disorder Rett syndrome (RTT)1. MeCP2 protein is an epigenetic reader whose binding to chromatin primarily depends on 5-methylcytosine (mC)2,3. Functionally, MeCP2 has been implicated in several cellular processes based on its reported interaction with >40 binding partners4, including transcriptional co-repressors (e.g. the NCoR/SMRT complex5), transcriptional activators6, RNA7, chromatin remodellers8,9, microRNA-processing proteins10 and splicing factors11. Accordingly, MeCP2 has been cast as a multi-functional hub that integrates diverse processes that are essential in mature neurons12. At odds with the concept of broad functionality, missense mutations that cause RTT are concentrated in two discrete clusters coinciding with interaction sites for partner macromolecules: the Methyl-CpG Binding Domain (MBD)13 and the NCoR/SMRT Interaction Domain (NID)5. Here, we test the hypothesis that the single dominant function of MeCP2 is to physically connect DNA with the NCoR/SMRT complex, by removing almost all amino acid sequences except the MBD and NID. We find that mice expressing truncated MeCP2 lacking both the N- and C-terminal regions (approximately half of the native protein) are phenotypically near-normal; and those expressing a minimal MeCP2 additionally lacking a central domain survive for over one year with only mild symptoms. This minimal protein is able to prevent or reverse neurological symptoms when introduced into MeCP2-deficient mice by genetic activation or virus-mediated delivery to the brain. Thus, despite evolutionary conservation of the entire MeCP2 protein sequence, the DNA and co-repressor binding domains alone are sufficient to avoid RTT-like defects and may therefore have therapeutic utility.

Transfer of 13 species of the genus Burkholderia to the genus Caballeronia and reclassification of Burkholderia jirisanensis as Paraburkholderia jirisanensis comb. nov.

A recent study of a group of Burkholderia glathei-like bacteria resulted in the description of 13 novel species of the genus Burkholderia. However, our analysis of phylogenetic positions of these species and their molecular signatures (conserved protein sequence indels) showed that they belong to the genus Caballeronia, and we propose to transfer them to this genus. The reclassified species names are proposed as Caballeroniaarationis comb. nov., Caballeroniaarvi comb. nov., Caballeroniacalidae comb. nov., Caballeroniacatudaia comb. nov., Caballeroniaconcitans comb. nov., Caballeroniafortuita comb. nov., Caballeroniaglebae comb. nov., Caballeroniahypogeia comb. nov., Caballeroniapedi comb. nov., Caballeroniaperedens comb. nov., Caballeroniaptereochthonis comb. nov., Caballeroniatemeraria comb. nov. and Caballeronia turbans comb. nov. It is also proposed to reclassify Burkholderia jirisanensis as Paraburkholderiajirisanensis comb. nov. Based on the results of the polyphasic study, B. jirisanensis had been described as a member of the A-group of the genus Burkholderiaand the most closely related to Burkholderia rhizosphaerae, Burkholderia humisilvae and Burkholderia solisilvae currently classified as belonging to the genus Paraburkholderia.

A putative spermidine synthase interacts with flagellar switch protein FliM and regulates motility in Helicobacter pylori.

The flagellar motor is an important virulence factor in infection by many bacterial pathogens. Motor function can be modulated by chemotactic proteins and recently appreciated proteins that are not part of the flagellar or chemotaxis systems. How these latter proteins affect flagellar activity is not fully understood. Here, we identified spermidine synthase SpeE as an interacting partner of switch protein FliM in Helicobacter pylori using pull-down assay and mass spectrometry. To understand how SpeE contributes to flagellar motility, a speE-null mutant was generated and its motility behavior was evaluated. We found that deletion of SpeE did not affect flagellar formation, but induced clockwise rotation bias. We further determined the crystal structure of the FliM-SpeE complex at 2.7 Å resolution. SpeE dimer binds to FliM with micromolar binding affinity, and their interaction is mediated through the β1' and β2' region of FliM middle domain. The FliM-SpeE binding interface partially overlaps with the FliM surface that interacts with FliG and is essential for proper flagellar rotational switching. By a combination of protein sequence conservation analysis and pull-down assays using FliM and SpeE orthologues in E. coli, our data suggest that FliM-SpeE association is unique to Helicobacter species.

Relationships between residue Voronoi volume and sequence conservation in proteins

BackgroundFunctional and biophysical constraints can cause different levels of sequence conservation in proteins. Previously, structural properties, e.g., relative solvent accessibility (RSA) and packing density of the weighted contact number (WCN), have been found to be related to protein sequence conservation (CS). The Voronoi volume has recently been recognized as a new structural property of the local protein structural environment reflecting CS. However, for surface residues, it is sensitive to water molecules surrounding the protein structure. Herein, we present a simple structural determinant termed the relative space of Voronoi volume (RSV); it uses the Voronoi volume and the van der Waals volume of particular residues to quantify the local structural environment. MethodsRSV (range, 0–1) is defined as (Voronoi volume−van der Waals volume)/Voronoi volume of the target residue. The concept of RSV describes the extent of available space for every protein residue. ResultsRSV and Voronoi profiles with and without water molecules (RSVw, RSV, VOw, and VO) were compared for 554 non-homologous proteins. RSV (without water) showed better Pearson's correlations with CS than did RSVw, VO, or VOw values. The mean correlation coefficient between RSV and CS was 0.51, which is comparable to the correlation between RSA and CS (0.49) and that between WCN and CS (0.56). ConclusionsRSV is a robust structural descriptor with and without water molecules and can quantitatively reflect evolutionary information in a single protein structure. Therefore, it may represent a practical structural determinant to study protein sequence, structure, and function relationships.

The human cytomegalovirus nuclear egress complex unites multiple functions: Recruitment of effectors, nuclear envelope rearrangement, and docking to nuclear capsids.

Nuclear replication represents a common hallmark of herpesviruses achieved by a number of sequentially unrolled regulatory processes. A rate-limiting step is provided by nucleo-cytoplasmic capsid export, for which a defined multiregulatory protein complex, namely, the nuclear egress complex (NEC), is assembled comprising both viral and cellular components. The NEC regulates at least 3 aspects of herpesviral nuclear replication: (1) multimeric recruitment of NEC-associated effector proteins, (2) reorganization of the nuclear lamina and membranes, and (3) the docking to nuclear capsids. Here, we review published data and own experimental work that characterizes the NEC of HCMV and other herpesviruses. A systematic review of information on nuclear egress of HCMV compared to selected alpha-, beta-, and gamma-herpesviruses: proteomics-based approaches, high-resolution imaging techniques, and functional investigations. A large number of reports on herpesviral NECs have been published during the last two decades, focusing on protein-protein interactions, nuclear localization, regulatory phosphorylation, and functional validation. The emerging picture provides an illustrated example of well-balanced and sophisticated protein networking in virus-host interaction. Current evidence refined the view about herpesviral NECs. Datasets published for HCMV, murine CMV, herpes simplex virus, and Epstein-Barr virus illustrate the marked functional consistency in the way herpesviruses achieve nuclear egress. However, this compares with only limited sequence conservation of core NEC proteins and a structural conservation restricted to individual domains. The translational use of this information might help to define a novel antiviral strategy on the basis of NEC-directed small molecules.