scholarly journals Elucidation of the complicated scenario of primate APOBEC3 gene evolution

2021 ◽  
Author(s):  
Keiya Uriu ◽  
Yusuke Kosugi ◽  
Narumi Suzuki ◽  
Jumpei Ito ◽  
Kei Sato
Keyword(s):  
Driving Forces ◽  
Gene Evolution ◽  
Sequence Similarity ◽  
Primate Species ◽  
Gene Repertoire ◽  
Host Interactions ◽  
Evolutionary Scenario ◽  
New Information ◽  
Genes Encoding ◽  
Z Domain

APOBEC3 proteins play pivotal roles in defenses against retroviruses, including HIV-1, as well as retrotransposons. Presumably due to the evolutionary arms race between the hosts and retroelements, APOBEC3 genes have rapidly evolved in primate lineages through sequence diversification, gene amplification and loss, and gene fusion. Consequently, modern primates possess a unique set or “repertoire” of APOBEC3 genes. The APOBEC3 gene repertoire of humans has been well investigated. There are three types of catalytic domains (Z domain; A3Z1, A3Z2, and A3Z3), 11 Z domains, and 7 independent genes, including 4 genes encoding double Z domains. However, the APOBEC3 gene repertoires of nonhuman primates remain largely unclear. Here, we characterize APOBEC3 gene repertoires among primates and investigated the evolutionary scenario of primate APOBEC3 genes using phylogenetic and comparative genomics approaches. In the 21 primate species investigated, we identified 145 APOBEC3 genes, including 69 double-domain type APOBEC3 genes. We further estimated the ages of the respective APOBEC3 genes and revealed that APOBEC3B, APOBEC3D, and APOBEC3F are the youngest in humans and were generated in the common ancestor of Catarrhini. Notably, invasion of the LINE1 retrotransposon peaked during the same period as the generation of these youngest APOBEC3 genes, implying that LINE1 invasion was one of the driving forces of the generation of these genes. Moreover, we found evidence suggesting that sequence diversification by gene conversions among APOBEC3 paralogs occurred in multiple primate lineages. Together, our analyses reveal the hidden diversity and the complicated evolutionary scenario of APOBEC3 genes in primates. Importance In terms of virus-host interactions and coevolution, the APOBEC3 gene family is one of the most important subjects in the field of retrovirology. APOBEC3 genes are composed of a repertoire of subclasses based on sequence similarity, and a paper by LaRue et al. provides the standard guideline for the nomenclature and genomic architecture of APOBEC3 genes. However, it has been over 10 years since this publication, and new information, including RefSeq, which we used in this study, is accumulating. Based on accumulating knowledge, APOBEC3 genes, particularly those of primates, should be refined and reannotated. This study updates knowledge of primate APOBEC3 genes and their genomic architectures. We further inferred the evolutionary scenario of primate APOBEC3 genes and the potential driving forces of APOBEC3 gene evolution. This study will be a landmark for the elucidation of the multiple aspects of APOBEC3 family genes in the future.

scholarly journals A Deadly Cargo: Gene Repertoire of Cytotoxic Effector Proteins in the Camelidae

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 304
Author(s):  
Ján Futas ◽  
Jan Oppelt ◽  
Pamela Anna Burger ◽  
Petr Horin
Keyword(s):  
Cytotoxic T Cells ◽  
Effector Proteins ◽  
Target Cells ◽  
Gene Repertoire ◽  
Interspecific Differences ◽  
Genes Encoding ◽  
Bactrian Camels ◽  
Pore Forming Proteins ◽  
Sequence Similarities ◽  
Cytotoxic Effector

Cytotoxic T cells and natural killer cells can kill target cells based on their expression and release of perforin, granulysin, and granzymes. Genes encoding these molecules have been only poorly annotated in camelids. Based on bioinformatic analyses of genomic resources, sequences corresponding to perforin, granulysin, and granzymes were identified in genomes of camelids and related ungulate species, and annotation of the corresponding genes was performed. A phylogenetic tree was constructed to study evolutionary relationships between the species analyzed. Re-sequencing of all genes in a panel of 10 dromedaries and 10 domestic Bactrian camels allowed analyzing their individual genetic polymorphisms. The data showed that all extant Old World camelids possess functional genes for two pore-forming proteins (PRF1, GNLY) and six granzymes (GZMA, GZMB, GZMH, GZMK, GZMM, and GZMO). All these genes were represented as single copies in the genome except the GZMH gene exhibiting interspecific differences in the number of loci. High protein sequence similarities with other camelid and ungulate species were observed for GZMK and GZMM. The protein variability in dromedaries and Bactrian camels was rather low, except for GNLY and chymotrypsin-like granzymes (GZMB, GZMH).

scholarly journals Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphilaBKME-9

2000 ◽  
Vol 182 (13) ◽  
pp. 3784-3793 ◽  
Author(s):  
Vincent J. J. Martin ◽  
William W. Mohn
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Ring Cleavage ◽  
Catabolic Pathway ◽  
Transcriptional Fusion ◽  
Abietane Diterpenoids ◽  
Genes Encoding ◽  
Dna Fragment ◽  
Reading Frames

ABSTRACT We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. Thedit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the α and β subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8,13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylEtranscriptional fusion strains showed induction of ditA1and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12,14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, thedit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, aditR::Kmr mutation in aditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.

scholarly journals Replication of Staphylococcal Multiresistance Plasmids

2000 ◽  
Vol 182 (8) ◽  
pp. 2170-2178 ◽  
Author(s):  
Neville Firth ◽  
Sumalee Apisiridej ◽  
Tracey Berg ◽  
Brendon A. O'Rourke ◽  
Steve Curnock ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Replication Initiation ◽  
Conjugative Plasmid ◽  
Rolling Circle ◽  
Segregational Stability ◽  
Structural And Functional Properties ◽  
Resistance Plasmids ◽  
Genes Encoding

ABSTRACT Based on structural and functional properties, three groups of large staphylococcal multiresistance plasmids have been recognized, viz., the pSK1 family, pSK41-like conjugative plasmids, and β-lactamase–heavy-metal resistance plasmids. Here we describe an analysis of the replication functions of a representative of each of these plasmid groups. The replication initiation genes from theStaphylococcus aureus plasmids pSK1, pSK41, and pI9789::Tn552 were found to be related to each other and to the Staphylococcus xylosus plasmid pSX267 and are also related to rep genes of several plasmids from other gram-positive genera. Nucleotide sequence similarity between pSK1 and pI9789::Tn552 extended beyond theirrep genes, encompassing upstream divergently transcribed genes, orf245 and orf256, respectively. Our analyses revealed that genes encoding proteins related to the deducedorf245 product are variously represented, in several types of organization, on plasmids possessing six seemingly evolutionarily distinct types of replication initiation genes and including both theta-mode and rolling-circle replicons. Construction of minireplicons and subsequent functional analysis demonstrated that orf245is required for the segregational stability of the pSK1 replicon. In contrast, no gene equivalent to orf245 is evident on the conjugative plasmid pSK41, and a minireplicon encoding only the pSK41 rep gene was found to exhibit a segregational stability approaching that of the parent plasmid. Significantly, the results described establish that many of the large multiresistance plasmids that have been identified in clinical staphylococci, which were formerly presumed to be unrelated, actually utilize an evolutionarily related theta-mode replication system.

scholarly journals Environmental Regulation and Virulence Attributes of the Ysa Type III Secretion System of Yersinia enterocolitica Biovar 1B

2005 ◽  
Vol 73 (9) ◽  
pp. 5961-5977 ◽  
Author(s):  
Krista Venecia ◽  
Glenn M. Young
Keyword(s):  
Yersinia Enterocolitica ◽  
Type Iii Secretion ◽  
Chromosomal Locus ◽  
Host Interactions ◽  
Type Iii ◽  
Genes Encoding ◽  
Transposon Mutants ◽  
Phase Temperature ◽  
Mouse Model Of Infection ◽  
Definitive Role

ABSTRACT Pathogenic biovars of Yersinia enterocolitica maintain the well-studied plasmid-encoded Ysc type III secretion (TTS) system, which has a definitive role in virulence. Y. enterocolitica biovar 1B additionally has a distinct chromosomal locus, the Yersinia secretion apparatus pathogenicity island (YSA PI) that encodes the Ysa TTS system. The signals to which the Ysa TTS system responds and its role in virulence remain obscure. This exploratory study was conducted to define environmental cues that promote the expression of Ysa TTS genes and to define how the Ysa TTS system influences bacterium-host interactions. Using a genetic approach, a collection of Y. enterocolitica Ysa TTS mutants was generated by mutagenesis with a transposon carrying promoterless lacZYA. This approach identified genes both within and outside of the YSA PI that contribute to Ysa TTS. Expression of these genes was regulated in response to growth phase, temperature, NaCl, and pH. Additional genetic analysis demonstrated that two regulatory genes encoding components of the YsrR-YsrS (ysrS) and RcsC-YojN-RcsB (rcsB) phosphorelay systems affect the expression of YSA PI genes and each other. The collection of Ysa TTS-defective transposon mutants, along with other strains carrying defined mutations that block Ysa and Ysc TTS, was examined for changes in virulence properties by using the BALB/c mouse model of infection. This analysis revealed that the Ysa TTS system impacts the ability of Y. enterocolitica to colonize gastrointestinal tissues. These results reveal facets of how Y. enterocolitica controls the function of the Ysa TTS system and uncovers a role for the Ysa TTS during the gastrointestinal phase of infection.

scholarly journals Two Functional Copies of the DGCR6 Gene Are Present on Human Chromosome 22q11 Due to a Duplication of an Ancestral Locus

2001 ◽  
Vol 11 (2) ◽  
pp. 208-217
Author(s):  
Lisa Edelmann ◽  
Pavel Stankiewicz ◽  
Elizabeth Spiteri ◽  
Raj K. Pandita ◽  
Lisa Shaffer ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Primate Species ◽  
Region Gene ◽  
Chromosome 22Q11 ◽  
Expression Studies ◽  
Low Copy Repeats ◽  
Duplicate Locus ◽  
Human Chromosome 22Q11 ◽  
Velo Cardio Facial Syndrome ◽  
Functional Copy

The DGCR6 (DiGeorge critical region) gene encodes a putative protein with sequence similarity to gonadal(gdl), a Drosophila melanogaster gene of unknown function. We mapped the DGCR6 gene to chromosome 22q11 within a low copy repeat, termed sc11.1a, and identified a second copy of the gene, DGCR6L, within the duplicate locus, termed sc11.1b. Both sc11.1 repeats are deleted in most persons with velo-cardio-facial syndrome/DiGeorge syndrome (VCFS/DGS), and they map immediately adjacent and internal to the low copy repeats, termed LCR22, that mediate the deletions associated with VCFS/DGS. We sequenced genomic clones from both loci and determined that the putative initiator methionine is located further upstream than originally described, but in a position similar to the mouse and chicken orthologs.DGCR6L encodes a highly homologous, functional copy ofDGCR6, with some base changes rendering amino acid differences. Expression studies of the two genes indicate that both genes are widely expressed in fetal and adult tissues. Evolutionary studies using FISH mapping in several different species of ape combined with sequence analysis of DGCR6 in a number of different primate species indicate that the duplication is at least 12 million years old and may date back to before the divergence of Catarrhines from Platyrrhines, 35 mya. These data suggest that there has been selective evolutionary pressure toward the functional maintenance of both paralogs. Interestingly, a full-length HERV-K provirus integrated into the sc11.1a locus after the divergence of chimpanzees and humans.

scholarly journals Genomic comparison of archaeal conjugative plasmids fromSulfolobus

Archaea ◽  
2004 ◽  
Vol 1 (4) ◽  
pp. 231-239 ◽  
Author(s):  
Bo Greve ◽  
Susanne Jensen ◽  
Kim Brügger ◽  
Wolfram Zillig ◽  
Roger A. Garrett
Keyword(s):  
Sequence Similarity ◽  
Comparative Sequence Analysis ◽  
Genomic Comparison ◽  
Variable Regions ◽  
Integrase Gene ◽  
Significant Sequence Similarity ◽  
Genes Encoding ◽  
Putative Origin ◽  
Main Components ◽  
Intercellular Exchange

All of the known self-transmissable plasmids of the Archaea have been found in the genusSulfolobus. To gain more insight into archaeal conjugative processes, four newly isolated self-transmissable plasmids, pKEF9, pHVE14, pARN3 and pARN4, were sequenced and subjected to a comparative sequence analysis with two earlier sequenced plasmids, pNOB8 and pING1. The analyses revealed three conserved and functionally distinct sections in the genomes. Section A is considered to encode the main components of the conjugative apparatus, where two genes show low but significant sequence similarity to sections of genes encoding bacterial conjugative proteins. A putative origin of replication is located in section B, which is highly conserved in sequence and contains several perfect and imperfect direct and inverted repeats. Further downstream, in section C, an operon encoding six to nine smaller proteins is implicated in the initiation and regulation of replication. Each plasmid carries an integrase gene of the type that does not partition on integration, and there is strong evidence for their integration into host chromosomes, where they may facilitate intercellular exchange of chromosomal genes. Two plasmids contain hexameric short regularly spaced repeats (SRSR), which have been implicated in plasmid maintenance, and each plasmid carries multiple recombination motifs, concentrated in the variable regions, which likely provide sites for genomic rearrangements.

The Use of Electronic Banking and New Technologies in Cash Management

2011 ◽  
pp. 3914-3920
Author(s):  
Leire San Jose Ruiz de Aguirre
Keyword(s):  
Information And Communication Technologies ◽  
Economies Of Scale ◽  
New Technologies ◽  
Driving Forces ◽  
Communication Technologies ◽  
Cash Management ◽  
Unit Costs ◽  
New Information ◽  
Information And Communication

The use of new information and communication technologies (ICT) as a business tool has increased rapidly for the past 10 years (Bonsón, Coffin, & Watson, 2000; Claessens, Glaessner, & Klingebiel, 2000; Vasarhelyi & Greenstein, 2003). More specifically, financial software, e-banking, and the Internet, as core aspects of the various technologies used, have become driving forces behind the expansion of firms and the development of cash management. New technologies are considered as one of the most attractive ways for businesses to increase revenue and achieve economies of scale that can reduce unit costs (Ballantine & Stray, 1998; Barajas & Villanueva, 2001; Daniel, 1999; Daniel & Storey, 1997; Deyoung, 2001; Downes & Muy, 1998; Faulder, 2001; Jayawardhena & Foley, 2000). There are different studies about the use of ICT in the management of the enterprise that explain the obtaining of enterprise performance. Brynjolfsson and Hitt (2000) and Nájera (2005) have done a review of these works and a classification of these types of researches. Unfortunately, there are not specific works or empirical researches about the use of e-banking in cash management; consequently, this work is focused in this. The rest of the chapter is structured as follows. The theoretical foundation on which the study is based is explained in Section 2. Section 3 presents the data and the analysis procedure used to conduct the empirical study. The main results of the investigation are shown in Section 4, and Section 5 presents conclusions. The chapter ends with a list of bibliographical references.

scholarly journals Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations

2007 ◽  
Vol 6 (7) ◽  
pp. 1200-1209 ◽  
Author(s):  
Howard S. Judelson ◽  
Shuji Tani
Keyword(s):  
Phytophthora Infestans ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Transcriptional Regulator ◽  
Hairpin Rna ◽  
High Sequence Similarity ◽  
Genes Encoding ◽  
Cognate Gene ◽  
Chromatin Packing ◽  
Nif Proteins

ABSTRACT Clustered within the genome of the oomycete phytopathogen Phytophthora infestans are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence. NIFC1, NIFC2, and NIFC3 are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form, NIFS. To test the function of the NIFC family, plasmids expressing full-length hairpin constructs of NIFC1 or NIFC2 were stably transformed into P. infestans. This triggered silencing of the cognate gene in about one-third of transformants, and all three NIFC genes were usually cosilenced. However, NIFS escaped silencing despite its high sequence similarity to the NIFC genes. Silencing of the three NIFC genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the NIFC cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to NIFC1 silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.

scholarly journals Molecular Characterisation of a Novel and Highly Divergent Passerine Adenovirus 1

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1036
Author(s):  
Ajani Athukorala ◽  
Jade K. Forwood ◽  
David N. Phalen ◽  
Subir Sarker
Keyword(s):  
Complete Genome ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Passerine Bird ◽  
The Novel ◽  
Transmembrane Helices ◽  
Novel Genes ◽  
Separate Species ◽  
Natural Host Species ◽  
Genes Encoding

Wild birds harbour a large number of adenoviruses that remain uncharacterised with respect to their genomic organisation, diversity, and evolution within complex ecosystems. Here, we present the first complete genome sequence of an atadenovirus from a passerine bird that is tentatively named Passerine adenovirus 1 (PaAdV-1). The PaAdV-1 genome is 39,664 bp in length, which was the longest atadenovirus to be sequenced, to the best of our knowledge, and contained 42 putative genes. Its genome organisation was characteristic of the members of genus Atadenovirus; however, the novel PaAdV-1 genome was highly divergent and showed the highest sequence similarity with psittacine adenovirus-3 (55.58%). Importantly, PaAdV-1 complete genome was deemed to contain 17 predicted novel genes that were not present in any other adenoviruses sequenced to date, with several of these predicted novel genes encoding proteins that harbour transmembrane helices. Subsequent analysis of the novel PaAdV-1 genome positioned phylogenetically to a distinct sub-clade with all others sequenced atadenoviruses and did not show any obvious close evolutionary relationship. This study concluded that the PaAdV-1 complete genome described here is not closely related to any other adenovirus isolated from avian or other natural host species and that it should be considered a separate species.

scholarly journals Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases

1996 ◽  
Vol 318 (1) ◽  
pp. 133-138 ◽  
Author(s):  
Roberto A GEREMIA ◽  
E Alejandro PETRONI ◽  
Luis IELPI ◽  
Bernard HENRISSAT
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Amino Acid Residues ◽  
Glycosyl Hydrolases ◽  
Hydrophobic Cluster Analysis ◽  
Alignment Algorithms ◽  
Automatic Alignment ◽  
Genes Encoding ◽  
Sequence Similarities

A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309–316].

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