scholarly journals Anopheles stephensi Dual Oxidase Silencing Activates the Thioester-Containing Protein 1 Pathway to Suppress Plasmodium Development

2019 ◽  
Vol 11 (6) ◽  
pp. 496-505 ◽  
Author(s):  
Parik Kakani ◽  
Mithilesh Kajla ◽  
Tania Pal Choudhury ◽  
Lalita Gupta ◽  
Sanjeev Kumar
Keyword(s):  
Amino Acid ◽  
Calcium Binding ◽  
Anopheles Stephensi ◽  
Developmental Stages ◽  
Transmembrane Protein ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Infected Mosquito ◽  
Parasite Development ◽  
Dual Oxidase

We characterized the dual oxidase (Duox) gene in the major Indian malaria vector Anopheles stephensi, which regulates the generation of reactive oxygen species. The AsDuox gene encodes for a 1,475-amino-acid transmembrane protein that contains an N-terminal noncytoplasmic heme peroxidase domain, a calcium-binding domain, seven transmembrane domains, and a C-terminal cytoplasmic NADPH domain. Phylogenetic analyses revealed that A. stephensi Duox protein is highly conserved and shares 97–100% amino acid identity with other anopheline Duoxes. AsDuox is expressed in all the developmental stages of A. stephensi and the pupal stages revealed relatively higher expressions. The Duox gene is induced in Plasmodium-infected mosquito midguts, and RNA interference-mediated silencing of this gene suppressed parasite development through activation of the thioester-containing protein 1 pathway. We propose that this highly conserved anopheline Duox, being a Plasmodium agonist, is an excellent target to control malaria parasite development inside the insect host.

scholarly journals ampG Gene of Pseudomonas aeruginosa and Its Role in β-Lactamase Expression

2010 ◽  
Vol 54 (11) ◽  
pp. 4772-4779 ◽  
Author(s):  
Ying Zhang ◽  
Qiyu Bao ◽  
Luc A. Gagnon ◽  
Ann Huletsky ◽  
Antonio Oliver ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Transmembrane Protein ◽  
Amino Acid Identity ◽  
Clinical Isolates ◽  
Signal Molecules ◽  
Carbonyl Cyanide ◽  
Increased Sensitivity ◽  
Potential Strategy ◽  
High Level

ABSTRACT In enterobacteria, the ampG gene encodes a transmembrane protein (permease) that transports 1,6-GlcNAc-anhydro-MurNAc and the 1,6-GlcNAc-anhydro-MurNAc peptide from the periplasm to the cytoplasm, which serve as signal molecules for the induction of ampC β-lactamase. The role of AmpG as a transporter is also essential for cell wall recycling. Pseudomonas aeruginosa carries two AmpG homologues, AmpG (PA4393) and AmpGh1 (PA4218), with 45 and 41% amino acid sequence identity, respectively, to Escherichia coli AmpG, while the two homologues share only 19% amino acid identity. In P. aeruginosa strains PAO1 and PAK, inactivation of ampG drastically repressed the intrinsic β-lactam resistance while ampGh1 deletion had little effect on the resistance. Further, deletion of ampG in an ampD-null mutant abolished the high-level β-lactam resistance that is associated with the loss of AmpD activity. The cloned ampG gene is able to complement both the P. aeruginosa and the E. coli ampG mutants, while that of ampGh1 failed to do so, suggesting that PA4393 encodes the only functional AmpG protein in P. aeruginosa. We also demonstrate that the function of AmpG in laboratory strains of P. aeruginosa can effectively be inhibited by carbonyl cyanide m-chlorophenylhydrazone (CCCP), causing an increased sensitivity to β-lactams among laboratory as well as clinical isolates of P. aeruginosa. Our results suggest that inhibition of the AmpG activity is a potential strategy for enhancing the efficacy of β-lactams against P. aeruginosa, which carries inducible chromosomal ampC, especially in AmpC-hyperproducing clinical isolates.

An ARV1 homologue from a filarial nematode is functional in yeast

2017 ◽  
Vol 93 (1) ◽  
pp. 12-20
Author(s):  
H.M.L.P.B. Herath ◽  
Y.I.N.S. Gunawardene ◽  
M. Pathiranage ◽  
P.D.S.U. Wickramasinghe ◽  
P.G.T.S. Wickramatunge ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Transmembrane Protein ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Temperature Sensitive ◽  
Permissive Temperature ◽  
Phylogenetic Information ◽  
Setaria Digitata ◽  
Gram Staining ◽  
Polymerase Chain

AbstractThe transmembrane protein, ARV1, plays a key role in intracellular sterol homeostasis by controlling sterol distribution and cellular uptake. To date, only the ARV1s from yeast and humans have been characterized to some extent. In this study, the ARV1 of an animal filarial parasite,Setaria digitata(SdARV1), was characterized; its cDNA was 761 bp and encoded a protein of 217 amino acids, with a predicted molecular weight of 25 kDa, containing a highly conserved ARV1 homology domain and three transmembrane domains in the bioinformatic analyses. Information required to cluster members belonging to a particular taxon has been revealed in phylogenetic analyses of ARV1 sequences derived from different organisms. Reverse transcription-polymerase chain reaction (RT-PCR) analyses indicated thatSdARV1was expressed in different developmental stages – microfilariae and adult male and female worms. Experiments carried out with a single copy of theSdARV1under the control of the PMA-1 promoter in a temperature-sensitiveSaccharomyces cerevisiaemutant strain indicated full complementation of the mutant phenotype, with growth at a non-permissive temperature (37°C). Microscopic observations of cellular morphology with Gram staining revealed alteration of the shape from shrunken to oval, in mutant and complemented strains, respectively. Assessment of free sterol levels extracted from mutant yeast and complemented strains indicated that the level of sterol was significantly higher in the former compared to the latter, which had sterol levels similar to those of the wild type. Thus, the results of the current study suggest that SdARV1 is ubiquitously expressed in different developmental stages ofS. digitata, and that it is a true functional homologue of mammalian and yeast ARV1s, which have crucial phylogenetic information that follows classical evolutionary trends. Finally, this is the first study to report the biological function of nematode ARV1.

scholarly journals Comparative Genomics and Environmental Distribution of Large dsDNA viruses in the family Asfarviridae

2021 ◽  
Author(s):  
Sangita Karki ◽  
Mohammad Moniruzzaman ◽  
Frank O. Aylward
Keyword(s):  
Amino Acid ◽  
African Swine Fever Virus ◽  
Phylogenetic Analyses ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Metagenomic Data ◽  
Genome Comparison ◽  
Marker Genes ◽  
Environmental Distribution ◽  
Acid Identity

AbstractThe Asfarviridae is a family of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) of which African swine fever virus (ASFV) is the most well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and different eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with >95% amino acid identity to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a near-complete genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.

Phylogenetic and topological analyses of the bovine interferon-induced transmembrane protein (IFITM3)

2021 ◽  
Author(s):  
Yong-Chan Kim ◽  
Byung-Hoon Jeong
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Multiple Sequence Alignment ◽  
Transmembrane Domain ◽  
Transmembrane Protein ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Multiple Sequence ◽  
Interspecific Differences ◽  
Distinct Features

AbstractInterferon-induced transmembrane protein 3 (IFITM3) plays a pivotal role in antiviral capacity in several species. However, to date, investigations of the IFITM3 protein in cattle have been rare. According to recent studies, interspecific differences in the IFITM3 protein result in several unique features of the IFITM3 protein relative to primates and birds. Thus, in the present study, we investigated the bovine IFITM3 protein based on nucleotide and amino acid sequences to find its distinct features. We found that the bovine IFITM3 gene showed a significantly different length and homology relative to other species, including primates, rodents and birds. Phylogenetic analyses indicated that the bovine IFITM3 gene and IFITM3 protein showed closer evolutionary distance with primates than with rodents. However, cattle showed an independent clade among primates, rodents and birds. Multiple sequence alignment of the IFITM3 protein indicated that the bovine IFITM3 protein contains 36 bovine-specific amino acids. Notably, the bovine IFITM3 protein was predicted to prefer inside-to-outside topology of intramembrane domain 1 (IMD1) and inside-to-outside topology of transmembrane domain 2 by TMpred and three membrane embedding domains according to the SOSUI system.

scholarly journals Characterization and Complete Nucleotide Sequence of an Unusual Reptilian Retrovirus Recovered from the Order Crocodylia

2002 ◽  
Vol 76 (9) ◽  
pp. 4651-4654 ◽  
Author(s):  
Joanne Martin ◽  
Peter Kabat ◽  
Elisabeth Herniou ◽  
Michael Tristem
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Conserved Regions

ABSTRACT A novel group of retroviruses found within the order Crocodylia are described. Phylogenetic analyses demonstrate that they are probably the most divergent members of the Retroviridae described to date; even the most conserved regions of Pol show an average of only 23% amino acid identity when compared to other retroviruses.

scholarly journals Triticum mosaic virus: A Distinct Member of the Family Potyviridae with an Unusually Long Leader Sequence

2009 ◽  
Vol 99 (8) ◽  
pp. 943-950 ◽  
Author(s):  
Satyanarayana Tatineni ◽  
Amy D. Ziems ◽  
Stephen N. Wegulo ◽  
Roy French
Keyword(s):  
Amino Acid ◽  
Mosaic Virus ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Recent Common Ancestor ◽  
Acid Identity ◽  
Most Recent Common Ancestor ◽  
Nontranslated Region ◽  
The Family ◽  
Distinct Member

The complete genome sequence of Triticum mosaic virus (TriMV), a member in the family Potyviridae, has been determined to be 10,266 nucleotides (nt) excluding the 3′ polyadenylated tail. The genome encodes a large polyprotein of 3,112 amino acids with the “hall-mark proteins” of potyviruses, including a small overlapping gene, PIPO, in the P3 cistron. The genome of TriMV has an unusually long 5′ nontranslated region of 739 nt with 12 translation initiation codons and three small open reading frames, which resemble those of the internal ribosome entry site containing 5′ leader sequences of the members of Picornaviridae. Pairwise comparison of 10 putative mature proteins of TriMV with those of representative members of genera in the family Potyviridae revealed 33 to 44% amino acid identity within the highly conserved NIb protein sequence and 15 to 29% amino acid identity within the least conserved P1 protein, suggesting that TriMV is a distinct member in the family Potyviridae. In contrast, TriMV displayed 47 to 65% amino acid sequence identity with available sequences of mature proteins of Sugarcane streak mosaic virus (SCSMV), an unassigned member of the Potyviridae. Phylogenetic analyses of the complete polyprotein, NIa-Pro, NIb, and coat protein sequences of representative species of six genera and unassigned members of the family Potyviridae suggested that TriMV and SCSMV are sister taxa and share a most recent common ancestor with tritimoviruses or ipomoviruses. These results suggest that TriMV and SCSMV should be classified in a new genus, and we propose the genus Poacevirus in the family Potyviridae, with TriMV as the type member.

scholarly journals Quaranfil, Johnston Atoll, and Lake Chad Viruses Are Novel Members of the Family Orthomyxoviridae

2009 ◽  
Vol 83 (22) ◽  
pp. 11599-11606 ◽  
Author(s):  
Rachel M. Presti ◽  
Guoyan Zhao ◽  
Wandy L. Beatty ◽  
Kathie A. Mihindukulasuriya ◽  
Amelia P. A. Travassos da Rosa ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Febrile Illness ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Emerging Infections ◽  
Lake Chad ◽  
Acid Identity ◽  
The Family

ABSTRACT Arboviral infections are an important cause of emerging infections due to the movements of humans, animals, and hematophagous arthropods. Quaranfil virus (QRFV) is an unclassified arbovirus originally isolated from children with mild febrile illness in Quaranfil, Egypt, in 1953. It has subsequently been isolated in multiple geographic areas from ticks and birds. We used high-throughput sequencing to classify QRFV as a novel orthomyxovirus. The genome of this virus is comprised of multiple RNA segments; five were completely sequenced. Proteins with limited amino acid similarity to conserved domains in polymerase (PA, PB1, and PB2) and hemagglutinin (HA) genes from known orthomyxoviruses were predicted to be present in four of the segments. The fifth sequenced segment shared no detectable similarity to any protein and is of uncertain function. The end-terminal sequences of QRFV are conserved between segments and are different from those of the known orthomyxovirus genera. QRFV is known to cross-react serologically with two other unclassified viruses, Johnston Atoll virus (JAV) and Lake Chad virus (LKCV). The complete open reading frames of PB1 and HA were sequenced for JAV, while a fragment of PB1 of LKCV was identified by mass sequencing. QRFV and JAV PB1 and HA shared 80% and 70% amino acid identity to each other, respectively; the LKCV PB1 fragment shared 83% amino acid identity with the corresponding region of QRFV PB1. Based on phylogenetic analyses, virion ultrastructural features, and the unique end-terminal sequences identified, we propose that QRFV, JAV, and LKCV comprise a novel genus of the family Orthomyxoviridae.

scholarly journals Molecular cloning and centrosomal localization of human caltractin

1993 ◽  
Vol 90 (23) ◽  
pp. 11039-11043 ◽  
Author(s):  
V D Lee ◽  
B Huang
Keyword(s):  
Amino Acid ◽  
Calcium Binding ◽  
Animal Cell ◽  
Amino Acid Identity ◽  
Microtubule Organizing Center ◽  
Unicellular Green Alga ◽  
Organizing Center ◽  
High Level ◽  
And Function ◽  
High Degree

Caltractin, a 20-kDa calcium-binding protein, was previously purified and cloned at the DNA level from the unicellular green alga Chlamydomonas. It is a structural component of the basal body complex, the major microtubule-organizing center in Chlamydomonas and the functional homolog of the centrosome in the animal cell. Here we report the characterization of a cDNA encoding a human caltractin that shares a high degree of amino acid identity (70%) with its algal counterpart. Caltractin was identified in both HeLa and BHK cells as a 21-kDa polypeptide specifically localized to the centrosome of interphase and mitotic cells. The high level of conservation in the amino acid sequence of caltractin from algae to humans and its association with the major microtubule-organizing center in the cell suggest that caltractin plays a fundamental role in microtubule-organizing center structure and function.

scholarly journals Molecular identification and characterization of two proposed new enterovirus serotypes, EV74 and EV75

2004 ◽  
Vol 85 (11) ◽  
pp. 3205-3212 ◽  
Author(s):  
M. Steven Oberste ◽  
Suzanne M. Michele ◽  
Kaija Maher ◽  
David Schnurr ◽  
Daniel Cisterna ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Human Enterovirus ◽  
Sequence Difference ◽  
Amino Acid Sequence Difference ◽  
Complete Capsid ◽  
Capsid Protein Vp1 ◽  
Enterovirus Serotypes

Sequencing of the gene that encodes the capsid protein VP1 has been used as a surrogate for antigenic typing in order to distinguish enterovirus serotypes; three new serotypes were identified recently by this method. In this study, 14 enterovirus isolates from six countries were characterized as members of two new types within the species Human enterovirus B, based on sequencing of the complete capsid-encoding (P1) region. Isolates within each of these two types differed significantly from one another and from all other known enterovirus serotypes on the basis of sequences that encode either VP1 alone or the entire P1 region. Members of each type were ⩾77·2 % identical to one another (89·5 % amino acid identity) in VP1, but members of the two different types differed from one another and from other enteroviruses by ⩾31 % in nucleotide sequence (25 % amino acid sequence difference), indicating that the two groups represent separate new candidate enterovirus types. The complete P1 sequences differed from those of all other enterovirus serotypes by ⩾31 % (26 % amino acid sequence difference), but were highly conserved within a serotype (<8 % amino acid sequence difference). Phylogenetic analyses demonstrated that isolates of the same serotype were monophyletic in both VP1 and the capsid as a whole, as shown previously for other enterovirus serotypes. This paper proposes that these 14 isolates should be classified as members of two new human enterovirus types, enteroviruses 74 and 75 (EV74 and EV75).

scholarly journals Genome Survey Sequencing of the Wine Spoilage Yeast Dekkera (Brettanomyces) bruxellensis

2007 ◽  
Vol 6 (4) ◽  
pp. 721-733 ◽  
Author(s):  
Megan Woolfit ◽  
Elżbieta Rozpędowska ◽  
Jure Piškur ◽  
Kenneth H. Wolfe
Keyword(s):  
Amino Acid ◽  
Burkholderia Cepacia ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Volatile Phenols ◽  
Brettanomyces Bruxellensis ◽  
Genome Survey ◽  
Spoilage Yeast ◽  
Wine Spoilage ◽  
Genome Survey Sequencing

ABSTRACT The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4× coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.

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