Amino Acid Sequence Variation of Signaling Lymphocyte Activation Molecule and Mortality Caused by Morbillivirus Infection in Cetanceans

ABSTRACT Host immunologic factors, including human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes (CTL), are thought to contribute to the control of HIV type 1 (HIV-1) replication and thus delay disease progression in infected individuals. Host immunologic factors are also likely to influence perinatal transmission of HIV-1 from infected mother to infant. In this study, the potential role of CTL in modulating HIV-1 transmission from mother to infant was examined in 11 HIV-1-infected mothers, 3 of whom transmitted virus to their offspring. Frequencies of HIV-1-specific human leukocyte antigen class I-restricted CTL responses and viral epitope amino acid sequence variation were determined in the mothers and their infected infants. Maternal HIV-1-specific CTL clones were derived from each of the HIV-1-infected pregnant women. Amino acid substitutions within the targeted CTL epitopes were more frequently identified in transmitting mothers than in nontransmitting mothers, and immune escape from CTL recognition was detected in all three transmitting mothers but in only one of eight nontransmitting mothers. The majority of viral sequences obtained from the HIV-1-infected infant blood samples were susceptible to maternal CTL. These findings demonstrate that epitope amino acid sequence variation and escape from CTL recognition occur more frequently in mothers that transmit HIV-1 to their infants than in those who do not. However, the transmitted virus can be a CTL susceptible form, suggesting inadequate in vivo immune control.

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The Wzz (Cld) Protein in Escherichia coli: Amino Acid Sequence Variation Determines O-Antigen Chain Length Specificity

Journal of Bacteriology ◽

10.1128/jb.180.10.2670-2675.1998 ◽

1998 ◽

Vol 180 (10) ◽

pp. 2670-2675 ◽

Cited By ~ 68

Author(s):

Agustin V. Franco ◽

Dan Liu ◽

Peter R. Reeves

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Sequence ◽

Chain Length ◽

Sequence Variation ◽

Length Distribution ◽

Chain Length Distribution ◽

E Coli ◽

O Antigen ◽

Amino Acid Sequence Variation

ABSTRACT The O antigen is a polymer with a repeated unit. The chain length in most Escherichia coli strains has a modal value of 10 to 18 O units, but other strains have higher or lower modal values.wzz (cld/rol) mutants have a random chain length distribution, showing that the modal distribution is determined by the Wzz protein. Cloned wzz genes from E. coli strains with short (7 to 16), intermediate (10 to 18), and long (16 to 25) modal chain lengths were transferred to a model system, and their effects on O111 antigen were studied. The O111 chain length closely resembled that of the parent strains. We present data based on the construction of chimeric wzz genes and site-directed mutagenesis of the wzz gene to show that the modal value of O-antigen chain length of E. coli O1, O2, O7, and O157 strains can be changed by specific amino acid substitutions in wzz. It is concluded that the O-antigen chain length heterogeneity in E. coli strains is the result of amino acid sequence variation of the Wzz protein.

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Genetic polymorphism and amino acid sequence variation in Plasmodium falciparum GLURP R2 repeat region in Assam, India, at an interval of five years

Malaria Journal ◽

10.1186/1475-2875-13-450 ◽

2014 ◽

Vol 13 (1) ◽

pp. 450 ◽

Cited By ~ 9

Author(s):

Dinesh Kumar ◽

Sunil Dhiman ◽

Bipul Rabha ◽

Diganta Goswami ◽

Manab Deka ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Amino Acid ◽

Genetic Polymorphism ◽

Amino Acid Sequence ◽

Sequence Variation ◽

Repeat Region ◽

Amino Acid Sequence Variation

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Nucleotide and amino acid sequence variation in the L1 and E7 open reading frames of human papillomavirus type 6 and type 16

Virology ◽

10.1016/0042-6822(91)90826-w ◽

1991 ◽

Vol 184 (1) ◽

pp. 101-107 ◽

Cited By ~ 33

Author(s):

Joseph P. Icenogle ◽

Pushpa Sathya ◽

Donna L. Miller ◽

Ruth Ann Tucker ◽

William Erawls

Keyword(s):

Human Papillomavirus ◽

Amino Acid ◽

Amino Acid Sequence ◽

Sequence Variation ◽

Open Reading Frames ◽

Amino Acid Sequence Variation ◽

Reading Frames

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Neutral Evolution of the Sex-Determining Gene transformer in Drosophila

Genetics ◽

10.1093/genetics/154.4.1711 ◽

2000 ◽

Vol 154 (4) ◽

pp. 1711-1720 ◽

Cited By ~ 3

Author(s):

Bryant F McAllister ◽

Gilean A T McVean

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Sequence Variation ◽

Nonsynonymous Substitution ◽

Neutral Evolution ◽

Sequence Evolution ◽

Statistical Support ◽

Rapid Pace ◽

Elevated Rate ◽

Evolution Sequence

Abstract The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. These changes in amino acid sequence are the result of either natural selection or neutral evolution. To differentiate between selective and neutral causes of this evolutionary change, analyses of both intraspecific and interspecific patterns of molecular evolution of tra gene sequences are presented. Sequences of 31 tra alleles were obtained from Drosophila americana. Many replacement and silent nucleotide variants are present among the alleles; however, the distribution of this sequence variation is consistent with neutral evolution. Sequence evolution was also examined among six species representative of the genus Drosophila. For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. In exon 3 of D. virilis and D. americana we find evidence for an elevated rate of nonsynonymous substitution, but no statistical support for a greater rate of nonsynonymous relative to synonymous substitutions. Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function.

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Strain-specific and common epitopes of gonococcal pili.

Journal of Experimental Medicine ◽

10.1084/jem.160.1.208 ◽

1984 ◽

Vol 160 (1) ◽

pp. 208-221 ◽

Cited By ~ 50

Author(s):

J B Rothbard ◽

R Fernandez ◽

G K Schoolnik

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Synthetic Peptides ◽

Cyanogen Bromide ◽

Sequence Variation ◽

Antigenic Structure ◽

Carboxyl Terminus ◽

Specific Epitope ◽

Absorption Studies ◽

Strain Ms11

The antigenic structure of gonococcal pilin, strain MS11 (Tr), was investigated by assaying the binding of antisera engendered by intact pili from strains MS11 and R10 and their two major cyanogen bromide-generated fragments, CNBr-2 (residues 9-92) and CNBr-2 (residues 93-159), to synthetic peptides corresponding to the amino acid sequence of MS11 pilin. Four peptides were synthesized corresponding to regions of sequence variation between MS11 and R10 gonococcal pilin. Antisera against the homologous pilus filament and against its CNBr-3 fragment bind peptides equivalent to residues 121-134 and 135-151, which comprise the 30 amino acid disulfide loop near the carboxyl terminus of the protein. Heterologous pili antisera did not bind these peptides. Absorption studies proved that each peptide contained an independent, strain-specific epitope. Synthetic peptides corresponding to regions of identical sequence between MS11 and R10 pilin were used in similar binding experiments to localize a weakly immunogenic, common determinant between residues 48 and 60. less than 15% of the antibodies raised against intact pili were directed at this site. Antisera raised against MS11 or R10 CNBr-2 bind a separate peptide, residues 69-80. This region is immunogenic only as a fragment, not in the intact pilus filament.

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Characterization of a transcriptionally active Tc1-like transposon in the microsporidian Nosema bombycis

Acta Parasitologica ◽

10.2478/s11686-010-0010-x ◽

2010 ◽

Vol 55 (1) ◽

Cited By ~ 3

Author(s):

Jinshan Xu ◽

Jie Luo ◽

Bettina Debrunner-Vossbrinck ◽

Xiaoyan Zhang ◽

Hangdeng Liu ◽

...

Keyword(s):

Amino Acid ◽

Transposable Element ◽

Transcriptional Activity ◽

Sequence Variation ◽

Biological Control Agents ◽

Functional Motif ◽

Nosema Bombycis ◽

Amino Acid Sequence Variation ◽

Unique Clade

AbstractThe Tc1 transposable element has been found in a wide variety of organisms including vertebrates, insects and fungi but has not been previously reported in Microsporidia. In this study we characterize an intact DNA transposon (NbTc1) from the microsporidian Nosema bombycis. This transposable element encodes a 337 amino acid transposase sequence, which contains the D,D34E functional motif required for transposition. A Southern blot of N. bombycis DNA separated by pulsedesis shows that copies of the NbTc1 transposon are present on 10 of the 14 chromosomes of N. bombycis. Amino acid sequence variation among copies of the NbTc1 is low, suggesting a conserved function for this transposon within N. bombycis. Phylogenetic analysis indicates that NbTc1 is a new member of the Tc1 family lineage, quite distinct from all previously described Tc1 elements, including those from fungi, indicating that NbTc1 forms a unique clade of the Tc1 superfamily. However, the Tc1 transposon is too divergent to resolve the major phylogenetic relationships among these superfamilies. Reverse transcriptase PCR and Solexa sequencing suggest that NbTc1 possesses transcriptional activity. Considering the interest in Microsporidia as biological control agents, the NbTc1 transposon may be a useful vector for the efficient transfection of these important parasites into host species.

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Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection

Scientific Reports ◽

10.1038/s41598-021-82925-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Michael J. Ormsby ◽

Robert L. Davies

Keyword(s):

Rainbow Trout ◽

Amino Acid ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Atlantic Salmon ◽

Sequence Variation ◽

Housekeeping Genes ◽

Housekeeping Gene ◽

Yersinia Ruckeri ◽

Amino Acid Sequence Variation

AbstractYersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.

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A β-Hairpin Epitope as Novel Structural Requirement for Protein Arginine Rhamnosylation

10.26434/chemrxiv.13046393 ◽

2020 ◽

Author(s):

Nathaniel Martin ◽

Marthe Walvoort ◽

Liubov Yakovlieva ◽

Thomas Wood ◽

Johan Kemmink ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Cyclic Peptides ◽

Protein Glycosylation ◽

Recognition Sequence ◽

Structural Requirement ◽

Amino Acid Sequence Variation ◽

Substrate Peptide ◽

Domains Of Life

Protein N-glycosylation is ubiquitously present in all domains of life, and confers a plethora of functions to the protein including increased solubility, protection from degradation, interaction with receptors, and activation for function. For canonical asparagine glycosylation, the recognition sequence that directs glycosylation at specific asparagine residues is well-established. It generally holds for protein glycosylation that the primary amino acid sequence is most important for substrate recognition. Here we reveal that a recently discovered bacterial enzyme called EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P in vitro, the enzyme readily glycosylates the same sequence when presented in a cyclized β-hairpin mimic containing an l-Pro-d-Pro motif. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to inform future identifications of rhamnosylation sites in other protein substrates.

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