Nonsynonymous Nucleotide Substitutions Research Articles

English

This study was carried out to analyze the polymorphic region of exon 1 of OsHKT1;5 of 22 high yielding rice varieties that are salt tolerant. The result of the phenotypic screening for salinity stress was done using the standard protocol of the International Rice Research Institute which recorded that all rice varieties developed very well under control condition, 85.38% were quite tolerant to salinity treatment of 4‰, 68.18% were moderately tolerant to salinity treatment of 8‰ and 36.36% were moderately tolerant to salinity treatment of 10‰, similar to Pokalli. The result of sequencing exon 1 region of OsHKT1;5 gene recorded five Single Nucleotide Polymorphisms (SNP) markers. Five nucleotide substitutions in coding sequence of OsHKT1;5 were found at the positions: 382, ​​418, 484, 551 and 994. All five non-synonymous nucleotide substitutions caused changes in amino acids (D51N, P63A, V86I, R107H and H255D).   Key words: High yielding rice, OsHKT1;5, single nucleotide polymorphisms (SNP) makers.

Polymorphism of avirulence genes in potato late blight pathogen Phytophthora infestans as characterized by SSCP analysis

Fighting late blight, economically the most important of potato diseases, is greatly hampered by rapid changes in the populations of the pathogen Phytophthora infestans: new pathotypes turn up owing to pathogen evolution and migration and overcome potato varieties that were previously considered resistant. Early recognition of the changes in P. infestans populations would greatly assist potato protection against late blight. The pathogenicity of P. infestans depends on the (a)virulence genes (Avr genes), among which the best known are the genes encoding RXLR effectors. This is the first report on polymorphism of these genes when characterized by single-strand conformation polymorphism (SSCP) analysis. Highly reproducible SSCP patterns combine electrophoretic zones corresponding to the Avr alleles. Ten Avr genes were studied in two series of P. infestans samples: single cell lines obtained from the isolates collected in the potato genetic collection of the N.I. Vavilov Institute of Plant Genetic Resources (VIR), Pushkin, St. Petersburg, and the reference lines from the Western European and USA collections. The Avr3b, Avr4, and Avr8 genes were monomorphic, while in Avr1, Avr2, Avr3a, Avr9, Avr-blb1, Avr-blb2, and Avr-vnt1, we discerned two to five SSCP patterns, with their frequencies different in two series of P. infestans lines. Sequences of Avr alleles differed in synonymous and non-synonymous single nucleotide substitutions, with 93–100% identity between variants. When Avr polymorphisms were compared with the profiles of virulence factors recognized with the Mastenbroeck-Black differentials, the acceptable agreement between two independent indices was observed only for Avr1, Avr3a and Avr4.

Identification of a novel HLA-C allele, HLA-C*07:778, in an unrelated hematopoietic stem cell donor.

HLA-C*07:778 differs from HLA-C*07:01:01:01 by a single nonsynonymous nucleotide substitution at codon 263 (CAC→CAG).

Comparative Genomic Analysis of a Multidrug-Resistant Listeria monocytogenes ST477 Isolate.

Listeria monocytogenes is an opportunistic human foodborne pathogen that causes severe infections with high hospitalization and fatality rates. Clonal complex 9 (CC9) contains a large number of sequence types (STs) and is one of the predominant clones distributed worldwide. However, genetic characteristics of ST477 isolates, which also belong to CC9, have never been examined, and little is known about the detail genomic traits of this food-associated clone. In this study, we sequenced and constructed the whole-genome sequence of an ST477 isolate from a frozen food sample in China and compared it with 58 previously sequenced genomes of 25 human-associated, 5 animal, and 27 food isolates consisting of 6 CC9 and 52 other clones. Phylogenetic analysis revealed that the ST477 clustered with three Canadian ST9 isolates. All phylogeny revealed that CC9 isolates involved in this study consistently possessed the invasion-related gene vip. Mobile genetic elements (MGEs), resistance genes, and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system were elucidated among CC9 isolates. Our ST477 isolate contained a Tn554-like transposon, carrying five arsenical-resistance genes (arsA-arsD, arsR), which was exclusively identified in the CC9 background. Compared with the ST477 genome, three Canadian ST9 isolates shared nonsynonymous nucleotide substitutions in the condensin complex gene smc and cell surface protein genes ftsA and essC. Our findings preliminarily indicate that the extraordinary success of CC9 clone in colonization of different geographical regions is likely due to conserved features harboring MGEs, functional virulence and resistance genes. ST477 and three ST9 genomes are closely related and the distinct differences between them consist primarily of changes in genes involved in multiplication and invasion, which may contribute to the prevalence of ST9 isolates in food and food processing environment.

Mitogenomic data to study the taxonomy of Antarctic springtail species (Hexapoda: Collembola) and their adaptation to extreme environments

Mitochondrial DNA (mtDNA) encodes for proteins mainly involved in the oxidative phosphorylation process, and due to its molecular features, it is one of the most used molecular markers for phylogenetic and taxonomic purposes. Since mitochondria are the primary source of energy for aerobic organisms, it has been suggested that modifications of the mitochondrial genome’s features could be linked with major adaptive processes to particular environmental conditions. In this respect, Antarctic Collembola (springtails) may be considered an interesting model to study whether positive selective pressure has occurred, inducing significant changes in the mtDNA characteristics that have eventually led to cold adaptation. In this study, we describe the molecular features of the mitochondrial genome of Cryptopygus terranovus, a springtail species endemic to Victoria Land. Molecular data are also employed to support the new taxonomic placement of C. terranovus, and to establish if the conspecific lineages of Friesea antarctica, that lives in separated biogeographical regions of the Antarctic Continent, are indeed distinct species. Finally, all the mitochondrial genomes of springtails, so far sequenced, were applied for calculating the ratio (ω) of nonsynonymous versus synonymous nucleotide substitutions. This approach allowed us to investigate if Antarctic collembolans could have experienced Darwinian selective pressures compared to the non-Antarctic springtail species. Indeed, our data does indicate positive selection (ω > 1), suggesting that survival at extreme environmental conditions could be also related to mtDNA modifications.

A Comparison of the Ability of Leu8- and Pro8-Oxytocin to Regulate Intracellular Ca2+ and Ca2+-Activated K+ Channels at Human and Marmoset Oxytocin Receptors.

The neurohypophyseal hormone oxytocin (OT) regulates biologic functions in both peripheral tissues and the central nervous system. In the central nervous system, OT influences social processes, including peer relationships, maternal-infant bonding, and affiliative social relationships. In mammals, the nonapeptide OT structure is highly conserved with leucine in the eighth position (Leu8-OT). In marmosets (Callithrix), a nonsynonymous nucleotide substitution in the OXT gene codes for proline in the eighth residue position (Pro8-OT). OT binds to its cognate G protein-coupled receptor (OTR) and exerts diverse effects, including stimulation (Gs) or inhibition (Gi/o) of adenylyl cyclase, stimulation of potassium channel currents (Gi), and activation of phospholipase C (Gq). Chinese hamster ovary cells expressing marmoset or human oxytocin receptors (mOTRs or hOTRs, respectively) were used to characterize OT signaling. At the mOTR, Pro8-OT was more efficacious than Leu8-OT in measures of Gq activation, with both peptides displaying subnanomolar potencies. At the hOTR, neither the potency nor efficacy of Pro8-OT and Leu8-OT differed with respect to Gq signaling. In both mOTR- and hOTR-expressing cells, Leu8-OT was more potent and modestly more efficacious than Pro8-OT in inducing hyperpolarization. In mOTR cells, Leu8-OT-induced hyperpolarization was modestly inhibited by pretreatment with pertussis toxin (PTX), consistent with a minor role for Gi/o activation; however, the Pro8-OT response in mOTR and hOTR cells was PTX insensitive. These findings are consistent with membrane hyperpolarization being largely mediated by a Gq signaling mechanism leading to Ca2+-dependent activation of K+ channels. Evaluation of the influence of apamin, charybdotoxin, paxilline, and TRAM-34 demonstrated involvement of both intermediate and large conductance Ca2+-activated K+ channels.

Identification of a novel allele, HLA‐DPB1*835:01, in an African American renal transplant candidate

HLA-DPB1*835:01 differs from HLA-DPB1*23:01:01:01 and 72:01:01:01 by four non-synonymous nucleotide substitutions within exon 2.

Inactivation and Loss of Infectivity of Enterovirus 70 by Solar Irradiation

Enterovirus 70 (EV70) is an emerging viral pathogen that remains viable in final treated effluent. Solar irradiation is, therefore, explored as a low-cost natural disinfection strategy to mitigate potential concerns. EV70 was exposed to simulated sunlight for 24 h at a fluence rate of 28.67 J/cm2/h in three different water matrices, namely, phosphate-buffered saline (PBS), treated wastewater effluent, and chlorinated effluent. In the presence of sunlight, EV70 decreased in infectivity by 1.7 log, 1.0 log, and 1.3 log in PBS, effluent, and chlorinated effluent, respectively. Irradiated EV70 was further introduced to host cell lines and was unable to infect the cell lines. In contrast, EV70 in dark microcosms replicated to titers 13.5, 3.3, and 4.2 times the initial inoculum. The reduction in EV70 infectivity was accompanied by a reduction in viral binding capacity to Vero cells. In addition, genome sequencing analysis revealed five nonsynonymous nucleotide substitutions in irradiated viruses after 10 days of infection in Vero cells, resulting in amino acid substitutions: Lys14Glu in the VP4 protein, Ala201Val in VP2, Gly71Ser in VP3, Glu50Gln in VP1, and Ile47Leu in 3Cpro. Overall, solar irradiation resulted in EV70 inactivation and an inhibition of viral activity in all parameters studied.

Positive Selection Drove the Adaptation of Mitochondrial Genes to the Demands of Flight and High-Altitude Environments in Grasshoppers.

The molecular evolution of mitochondrial genes responds to changes in energy requirements and to high altitude adaptation in animals, but this has not been fully explored in invertebrates. The evolution of atmospheric oxygen content from high to low necessarily affects the energy requirements of insect movement. We examined 13 mitochondrial protein-coding genes (PCGs) of grasshoppers to test whether the adaptive evolution of genes involved in energy metabolism occurs in changes in atmospheric oxygen content and high altitude adaptation. Our molecular evolutionary analysis of the 13 PCGs in 15 species of flying grasshoppers and 13 related flightless grasshoppers indicated that, similar to previous studies, flightless grasshoppers have experienced relaxed selection. We found evidence of significant positive selection in the genes ATP8, COX3, ND2, ND4, ND4L, ND5, and ND6 in flying lineages. This results suggested that episodic positive selection allowed the mitochondrial genes of flying grasshoppers to adapt to increased energy demands during the continuous reduction of atmospheric oxygen content. Our analysis of five grasshopper endemic to the Tibetan Plateau and 13 non-Tibetan grasshoppers indicated that, due to positive selection, more non-synonymous nucleotide substitutions accumulated in Tibetan grasshoppers than in non-Tibetan grasshoppers. We also found evidence for significant positive selection in the genes ATP6, ND2, ND3, ND4, and ND5 in Tibetan lineages. Our results thus strongly suggest that, in grasshoppers, positive selection drives mitochondrial genes to better adapt both to the energy requirements of flight and to the high altitude of the Tibetan Plateau.

Natural allelic variation of GVS1 confers diversity in the regulation of leaf senescence in Arabidopsis.

Leaf senescence affects plant fitness. Plants that evolve in different environments are expected to acquire distinct regulations of leaf senescence. However, the adaptive and evolutionary roles of leaf senescence are largely unknown. We investigated leaf senescence in 259 natural accessions of Arabidopsis by quantitatively assaying dark-induced senescence responses using a high-throughput chlorophyll fluorescence imaging system. A meta-analysis of our data with phenotypic and climatic information demonstrated biological and environmental links with leaf senescence. We further performed genome-wide association mapping to identify the genetic loci underlying the diversity of leaf senescence responses. We uncovered a new locus, Genetic Variants in leaf Senescence (GVS1), with high similarity to reductase, where a single nonsynonymous nucleotide substitution at GVS1 mediates the diversity of the senescence trait. Loss-of-function mutations of GVS1 in Columbia-0 delayed leaf senescence and increased sensitivity to oxidative stress, suggesting that this GVS1 variant promotes optimal responses to developmental and environmental signals. Intriguingly, gvs1 loss-of-function mutants display allele- and accession-dependent phenotypes, revealing the functional diversity of GVS1 alleles not only in leaf senescence, but also oxidative stress. Our discovery of GVS1 as the genetic basis of natural variation in senescence programs reinforces its adaptive potential in modulating life histories across diverse environments.

Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis.

Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of nonsynonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M. tuberculosis. We showed that purifying selection is the dominant force acting on cobalamin-related genes at the levels of individual codons, genes and groups of genes. We conclude that cobalamin-related genes may not be essential but are adaptive for M. tuberculosis in clinical settings. Furthermore, the cobalamin biosynthesis pathway is likely to be functional in this species.

WGS analysis of ST9-MRSA-XII isolates from live pigs in China provides insights into transmission among porcine, human and bovine hosts.

To elucidate the phylogenetic relationships among ST9-MRSA-XII isolates from different sources and their genetic features in colonization of different hosts. We obtained whole-genome sequences of two ST9-MRSA-XII isolates from nasal swabs associated with live pigs in China, and compared them with 135 previously sequenced genomes of 78 human-associated, 39 bovine and 18 porcine Staphylococcus aureus consisting of 11 MRSA of SCCmecXII, 62 MRSA of other SCCmec types and 62 MSSA. The distribution of diverse mobile genetic elements (MGEs), resistance genes and virulence determinants was investigated in relation to isolate phylogeny. Comparisons of SNPs and small insertion/deletions (indels) were conducted to examine genome-level variation between porcine and bovine ST9-MRSA-XII. Phylogenetic analysis revealed that both of our porcine ST9-MRSA-XII isolates clustered with porcine, bovine and human-associated ST9-MRSA-XII. All of these isolates possessed a novel type V pathogenicity island, νSaα, carrying the von Willebrand-binding protein gene vwb, the immune evasion complex gene scn, the aminoglycoside resistance gene aadE, staphylococcal superantigen-like genes (ssl1-ssl11) and lpl tandem genes. Compared with bovine ST9-MRSA-XII BA01611, our porcine isolates contain non-synonymous nucleotide substitutions in genes encoding adhesins and an indel located in a phosphonate ABC transporter pseudogene. The data suggest transmission of ST9-MRSA-XII among swine, cattle and humans. The extraordinary success of the ST9-MRSA-XII group in colonization of various hosts is likely due to acquisition of many MGEs harbouring functional antimicrobial resistance and virulence genes. Transmission of ST9-MRSA-XII between porcine and bovine hosts was accompanied by changes in binding profile and function in genes involved in metabolism.

Abstract 3587: TCR-transduced T cells targeting a truncal mutation caused by a nsSNV destroy large solid tumors despite intratumoral genetic heterogeneity

Abstract Most if not all cancers have individually specific, so-called unique antigens that we discovered in 1995 to be caused by somatic tumor-specific, non-synonymous single nucleotide substitutions, now usually referred to as nsSNVs, and we showed already then that adoptive transfer of nsSNV-specific T cells has specific anti-cancer effects (Monach P. et al. Immunity 2:45-59, 1995). With the rapid advances in sequencing technologies, these antigens, now generally also called "mutant neoantigens", have been discovered on all primary cancers examined in the past decade, human or experimental, (unless a cancer was the result of artificial genetic engineering). The number of somatic mutations, mostly nsSNVs, differs widely between cancers and tumor types. Importantly however, even patients bearing cancers with a low mutational burden usually have 12 different HLA alleles to possibly present a given mutant peptide as antigen to T cells. Since most mutations in cancers are individually patient-specific, a truly personalized, i.e., patient-specific therapy is required. Encouragement for investing into developing such an approach comes from our recent studies in which we show that a single type of T cell receptor (TCR) targeting a single cancer-specific point mutation, i.e. nsSNV-encoded mutant peptide, can eradicate large solid tumors when the mutation-specific TCR is transduced into peripheral T cells and adoptively transferred (Leisegang, M. et al. Clin. Cancer Res. 22: 2734-43 2016). Here, we examine the relative influence of mutant antigen expression level, intratumoral heterogeneity as well as competence of the transferred mutation-specific T cells on escape of the cancer from therapy using adoptive transfer of T cells specific for a given mutation. The importance and mechanisms of bystander killing in cancer escape will also be discussed and the importance of cross-presentation of the neoantigen by the tumor stroma will be examined. Together, our current studies are consistent with the notion that adoptive transfer of T cells transduced with TCRs recognizing nsSNV-encoded peptides may provide a novel and potentially extremely powerful completely cancer-specific approach in patients with established solid tumors. In addition, the concept should be applicable to most cancer patients, if efforts are made to truly individualize cancer therapy. This requires focus on identifying the set of patient-specific nsSNV and the set of 12 patient-specific MHCI and MHCII that are available to potentially present the mutant peptides of a given patient's cancer as targets for tumor destruction. Supported by NIH grants R01-CA22677 and R01-CA37156, the Cancer Research Foundation, a collaborative research grant by the Berlin Institute of Health and the Einstein-Stiftung Berlin. Citation Format: Matthias Leisegang, Karin Schreiber, Steven P. Wolf, Vasiliki Anastosopolou, Kimberley Borutta, PohYin Yew, Kazuma Kiyotani, Yusuke Nakamura, Hans Schreiber. TCR-transduced T cells targeting a truncal mutation caused by a nsSNV destroy large solid tumors despite intratumoral genetic heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3587.

Abstract 4213: Molecular biomarker study of programmed death receptor ligand 1 (PD-L1) in Korean patients with lung adenocarcinoma

Abstract Purpose We explored the association between different molecular biomarkers and PD-L1 mRNA and protein expression in Asian patients with lung adenocarcinoma. Experimental design PD-L1 protein expression level was evaluated using a prototype immunohistochemistry (IHC) assay with the 22C3 antibody in tumor samples from 157 patients with lung adenocarcinoma from Samsung Medical Center. Other biomarkers, including PD-L1, PD-L2 and IFN-γ mRNA expression detected using the Affymetrix array, EGFR and KRAS mutation detected using the Sequenom platform, ALK fusion detected using the NanoString system and tumor mutation burden (TMB) calculated as total number of non-synonymous single nucleotide substitution from Illumina HiSeq 2000 sequencing platform were provided as part of the Asian Cancer Research Group collaboration. Spearman correlation test, t test, Fisher exact test, and multivariate regression models were utilized to test the association between different biomarkers and PD-L1 mRNA/protein expression. PD-L1 IHC tumor proportion score was analyzed as a continuous or categorical variable, where PD-L1 strong and weak positivity were defined to be traceable to the 1% and 50% cutoffs used in the clinical trial version of the assay. Results The median age was 61 years (range, 20-84), 50% were female, 40% were smokers, and 77% had stage I/II disease. There was strong correlation between PD-L1 mRNA and protein expression (N = 79, Spearman R = 0.762, P < 0.0001). Absence of EGFR mutation was associated with higher PD-L1 expression (for mRNA, N = 166, t test P = 0.023; for protein, N = 83, Fisher test P = 0.051), and presence of ALK fusion was associated with higher PD-L1 expression (for mRNA, N = 229, t test P = 0.001; for protein, N = 144, Fisher test P = 0.002). Similar associations between EGFR mutation, ALK fusion, and PD-L1 mRNA and protein expression were observed after adjusting for age, sex, smoking status, and disease stage. No association was found between PD-L1 expression and KRAS mutation (for mRNA, N = 140, t test P = 0.305; for protein, N = 78, Fisher test P = 0.243). mRNA expression of PD-L2, the other PD-1 ligand, was highly correlated with PD-L1 expression (for mRNA, N = 253, Spearman R = 0.650, P < 0.0001; for protein, N = 79, Spearman R = 0.444, P < 0.0001). As evidence for IFN-γ-inducible biology, IFN-γ mRNA expression was significantly correlated with PD-L1 expression (for mRNA, N = 253, Spearman R = 0.57, P < 0.0001; for protein, N = 79, Spearman R = 0.44, P < 0.0001). TMB was not significantly correlated with PD-L1 expression (for mRNA, N = 31, Spearman R = 0.092, P = 0.62; for protein, N = 8, Spearman R = 0.19, P = 0.65), which suggested independent predictive ability for anti-PD-1 therapy. Conclusion Our study provides evidence that DNA and RNA features, including PD-L1 mRNA, lack of EGFR mutation, and ALK fusion are associated with PD-L1 protein expression for Asian lung adenocarcinoma patients. Citation Format: Xiaoqiao Liu, Jinseon Lee, Soo Jung Lee, Jong Ho Cho, Jong-Mu Sun, Lu Zhang, Yunfei Pei, Lan Chen, Marisa Dolled-Filhart, Kenneth Emancipator, Jared Lunceford, Ronghua Chen, Wei Zhou, Jhingook Kim. Molecular biomarker study of programmed death receptor ligand 1 (PD-L1) in Korean patients with lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4213.

Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae).

Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.

Microbial Symbionts of Insects: Genetic Organization, Adaptive Role, and Evolution

The microorganisms forming symbioses with insects play an important role in nutrition, development and evolution of their hosts. They make it possible for their hosts to use poorly digestible nutrients, to resist the biotic and abiotic stresses, and to regulate the metamorphosis. The microsymbionts of insects may be facultative (genetically specialized for symbiosis but retaining the capacity for autonomous existence; they are usually located extracellularly, in the gut, hemolymph, or salivary glands of the host) or obligatory (incapable of autonomous existence due to the loss of large parts of their genomes; they are usually located inside specialized host cells). The intracellular symbionts (endocytobionts) are capable of vertical transmission during the host reproduction, which determines the loss of many housekeeping genes, including the genes for replication, transcription and translation. In some obligatory symbionts, amplification of genes performing the functions useful for the hosts, such as the synthesis of essential amino acids, was found. These symbionts exhibit increased rates of accumulation of mutations, including non-synonymous nucleotide substitutions, reflecting suppression of the purifying selection and activation of genetic drift stimulating the genome reduction. Transfer of some genes from endocytobionts to the nuclear chromosomes of insects enables them to implement the novel metabolic functions, including assimilation of rare nutrients. The obligatory intracellular insect symbionts may be used as models to reconstruct the early stages of evolution of cellular organelles, which involve reduction of essential genes and the loss of genetic individuality of the symbionts, i.e., the ability for self-maintenance and expression of their residual genomes. Genetic analysis of insect microsymbionts extends the opportunities for their practical application associated with biological control of harmful insects (herbivorous, bloodsucking) and stimulation of the beneficial ones (honey collectors, pollinators, antagonists of pests).

Parasite infection of specific host genotypes relates to changes in prevalence in two natural populations of bumblebees

The antagonistic relationship between parasites and their hosts is strongly influenced by genotype-by-genotype interactions. Defense against parasitism is commonly studied in the context of immune system-based mechanisms and, thus, the focus in the search for candidate genes in host-parasite interactions is often on immune genes. In this study, we investigated the association between prevalence of parasite infection and host mitochondrial DNA (mtDNA) haplotypes in two natural populations of bumblebees (Bombus terrestris). The two most common haplotypes of the host populations, termed A and B, differ by a single nonsynonymous nucleotide substitution within the coding region of cytochrome oxidase I, an important player in metabolic pathways. We screened infection by Nosema bombi, a common endoparasite of bumblebees, and the corresponding host mtDNA-haplotype frequencies in over 1400 bumblebees between 2000 and 2010. The island population of Gotland showed lower mtDNA diversity compared to the mainland population in Switzerland. Over time, we observed large fluctuations in infection prevalence, as well as variation in host haplotype frequencies in both populations. Our long-term observation revealed that N. bombi infection of specific host genotypes is transient: We found that with increasing infection prevalence, proportionally more individuals with haplotype B, but fewer individuals with haplotype A were infected. This suggests that the presence of N. bombi in specific host genotypes relates to infection prevalence. This may be a result of parasite competition, or differential resilience of host types to ward off infections. The findings highlight the important role of host mtDNA haplotypes in the interaction with parasites.

HLA-B*40:302, a novel allele identified by sequence-based typing in a Korean individual.

B*40:302 differs from B*40:02:01:01 by a single nonsynonymous nucleotide substitution at codon 81 (CCG→CTG).

Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

BackgroundThe Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.MethodsWe used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19).Principal findings/ConclusionsWe found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data.

Mutations in Cancer Cause Gain of Cysteine, Histidine, and Tryptophan at the Expense of a Net Loss of Arginine on the Proteome Level.

Accumulation of somatic mutations is critical for the transition of a normal cell to become cancerous. Mutations cause amino acid substitutions that change properties of proteins. However, it has not been studied as to what extent the composition and accordingly chemical properties of the cell proteome is altered as a result of the increased mutation load in cancer. Here, we analyzed data on amino acid substitutions caused by mutations in about 2000 protein coding genes from the Cancer Cell Line Encyclopedia that contains information on nucleotide and amino acid alterations in 782 cancer cell lines, and validated the analysis with information on amino acid substitutions for the same set of proteins in the Catalogue of Somatic Mutations in Cancer (COSMIC; v78) in circa 18,000 tumor samples. We found that nonsynonymous single nucleotide substitutions in the analyzed proteome subset ultimately result in a net gain of cysteine, histidine, and tryptophan at the expense of a net loss of arginine. The extraordinary loss of arginine may be attributed to some extent to composition of its codons as well as to the importance of arginine in the functioning of prominent tumor suppressor proteins like p53.