Immunoinformatic Analysis to Identify Proteins to Be Used as Potential Targets to Control Bovine Anaplasmosis

Omics sciences and new technologies to sequence full genomes provide valuable data that are revealed only after detailed bioinformatic analysis is performed. In this work, we analyzed the genomes of seven Mexican Anaplasma marginale strains and the data from a transcriptome analysis of the tick Rhipicephalus microplus. The aim of this analysis was to identify protein sequences with predicted features to be used as potential targets to control the bacteria or tick-vector transmission. We chose three amino acid sequences different to all proteins previously reported in A. marginale that have been used as potential vaccine candidates, and also, we report, for the first time, the presence of a peroxinectin protein sequence in the transcriptome of R. microplus, a protein associated with the immune response of ticks. The bioinformatics analyses revealed the presence of B-cell epitopes in all the amino acid sequences chosen, which opens the way for their likely use as single or arranged peptides to develop new strategies for the control and prevention of bovine anaplasmosis transmitted by ticks.

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Analysis of the Amino Acid Sequence Variation of the 67–72p Protein and the Structural Pili Proteins of Corynebacterium diphtheriae for their Suitability as Potential Vaccine Antigens

Polish Journal of Microbiology ◽

10.33073/pjm-2019-025 ◽

2019 ◽

Vol 68 (2) ◽

pp. 233-246

Author(s):

KLAUDIA BRODZIK ◽

KATARZYNA KRYSZTOPA-GRZYBOWSKA ◽

MACIEJ POLAK ◽

JAKUB LACH ◽

DOMINIK STRAPAGIEL ◽

...

Keyword(s):

Amino Acid ◽

Vaccine Development ◽

Corynebacterium Diphtheriae ◽

Amino Acid Sequences ◽

Host Cells ◽

Structural Proteins ◽

Bioinformatics Analyses ◽

Conserved Regions ◽

Vaccine Antigens ◽

Potential Vaccine

The aim of this study was to identify the potential vaccine antigens in Corynebacterium diphtheriae strains by in silico analysis of the amino acid variation in the 67–72p surface protein that is involved in the colonization and induction of epithelial cell apoptosis in the early stages of infection. The analysis of pili structural proteins involved in bacterial adherence to host cells and related to various types of infections was also performed. A polymerase chain reaction (PCR) was carried out to amplify the genes encoding the 67–72p protein and three pili structural proteins (SpaC, SpaI, SapD) and the products obtained were sequenced. The nucleotide sequences of the particular genes were translated into amino acid sequences, which were then matched among all the tested strains using bioinformatics tools. In the last step, the affinity of the tested proteins to major histocompatibility complex (MHC) classes I and II, and linear B-cell epitopes was analyzed. The variations in the nucleotide sequence of the 67–72p protein and pili structural proteins among C. diphtheriae strains isolated from various infections were noted. A transposition of the insertion sequence within the gene encoding the SpaC pili structural proteins was also detected. In addition, the bioinformatics analyses enabled the identification of epitopes for B-cells and T-cells in the conserved regions of the proteins, thus, demonstrating that these proteins could be used as antigens in the potential vaccine development. The results identified the most conserved regions in all tested proteins that are exposed on the surface of C. diphtheriae cells.

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Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil

Ciência Rural ◽

10.1590/0103-8478cr20141810 ◽

2015 ◽

Vol 45 (12) ◽

pp. 2197-2200 ◽

Cited By ~ 2

Author(s):

Thor Vinícius Martins Fajardo ◽

Monique Bezerra Nascimento ◽

Marcelo Eiras ◽

Osmar Nickel ◽

Gilvan Pio-Ribeiro

Keyword(s):

Amino Acid ◽

Molecular Characterization ◽

Molecular Analysis ◽

Nucleotide Sequences ◽

Amino Acid Sequences ◽

Causal Agent ◽

Ringspot Virus ◽

Prunus Necrotic Ringspot Virus ◽

First Time

ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of the MP and CP nucleotide sequences of a Brazilian PNRSV isolate from rose and others from this same host showed highest identities of 96.7% and 98.6%, respectively, and Rose-Br isolate was classified in PV32 group.

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Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases

Biochemical Journal ◽

10.1042/bj20031575 ◽

2004 ◽

Vol 381 (1) ◽

pp. 295-306 ◽

Cited By ~ 80

Author(s):

Senarath B. P. ATHAUDA ◽

Koji MATSUMOTO ◽

Sanath RAJAPAKSHE ◽

Masayuki KURIBAYASHI ◽

Masaki KOJIMA ◽

...

Keyword(s):

Amino Acid ◽

Computer Modelling ◽

Structural Characteristics ◽

Amino Acid Sequences ◽

Cysteine Residues ◽

Aspartic Proteinases ◽

Protein Databases ◽

Wide Range ◽

First Time

Carnivorous plants are known to secrete acid proteinases to digest prey, mainly insects, for nitrogen uptake. In the present study, we have purified, for the first time, to homogeneity two acid proteinases (nepenthesins I and II) from the pitcher fluid of Nepenthes distillatoria (a pitcher-plant known locally as badura) and investigated their enzymic and structural characteristics. Both enzymes were optimally active at pH approx. 2.6 towards acid-denatured haemoglobin; the specificity of nepenthesin I towards oxidized insulin B chain appears to be similar, but slightly wider than those of other APs (aspartic proteinases). Among the enzymic properties, however, the most notable is their unusual stability: both enzymes were remarkably stable at or below 50 °C, especially nepenthesin I was extremely stable over a wide range of pH from 3 to 10 for over 30 days. This suggests an evolutionary adaptation of the enzymes to their specific habitat. We have also cloned the cDNAs and deduced the complete amino acid sequences of the precursors of nepenthesins I and II (437 and 438 residues respectively) from the pitcher tissue of N. gracilis. Although the corresponding mature enzymes (each 359 residues) are homologous with ordinary pepsin-type APs, both enzymes had a high content of cysteine residues (12 residues/molecule), which are assumed to form six unique disulphide bonds as suggested by computer modelling and are supposed to contribute towards the remarkable stability of nepenthesins. Moreover, the amino acid sequence identity of nepenthesins with ordinary APs, including plant vacuolar APs, is remarkably low (approx. 20%), and phylogenetic comparison shows that nepenthesins are distantly related to them to form a novel subfamily of APs with a high content of cysteine residues and a characteristic insertion, named ‘the nepenthesin-type AP-specific insertion’, that includes a large number of novel, orthologous plant APs emerging in the gene/protein databases.

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Insights into the mysterious genetic variation profile oftprKinTreponema pallidumunder the development of natural human syphilis infection

10.1101/536573 ◽

2019 ◽

Author(s):

Dan Liu ◽

Man-Li Tong ◽

Yong Lin ◽

Li-Li Liu ◽

Li-Rong Lin ◽

...

Keyword(s):

Amino Acid ◽

Immune Evasion ◽

High Frequency ◽

Critical Role ◽

Treponema Pallidum ◽

Secondary Syphilis ◽

Human Infection ◽

Amino Acid Sequences ◽

Potential Vaccine

AbstractAlthough the variations of thetprKgene inTreponema pallidumwere considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics oftprKin the course of natural human infection enabling the pathogen’s survive has thus far remained unclear. Here, we performed NGS to investigatetprKofT. pallidumdirectly from primary and secondary syphilis samples. Compared with diversity intprKof the strains from primary syphilis samples, there were more mixture variants found within seven V regions of thetprKgene among the strains from secondary syphilis samples, and the frequencies of predominant sequences within V regions oftprKwere generally decreased (less than 80%) with the proportion of minor variants in 10-60% increasing. Noteworthy, the variations within V regions oftprKalways obeyed a strict 3 bp changing pattern. AndtprKin the strains from the two-stage samples kept some stable amino acid sequences within V regions. Particularly, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 not only presented a high proportion of inter-population sharing, but also presented a relatively high frequency (above 80%) in the populations. Besides,tprKalways demonstrated remarkable variability in V6 at both the intra- and inter-strain levels regardless of the course. These findings unveiled that the different profile oftprK in T. pallidumdirectly from primary and secondary syphilis samples, indicating that throughout the development of syphilisT. pallidumconstantly varies its domaintprKgene to obtain the best adaptation to the host. While this changing was always subjected a strict gene conversion mechanism to keep an abnormal TprK. The highly stable peptides found in V1 would probably be promising potential vaccine components. And the highly heterogenetic regions (e.g. V6) could provide insight into the mysterious role oftprKin immune evasion.Author summaryAlthough the variations of thetprKgene inTreponema pallidumwere considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics oftprKin the course of natural human infection enabling the pathogen’s survive has thus far remained unclear. Here, we performed next-generation sequencing, a more sensitive and reliable approach, to investigatetprKofTreponema pallidumdirectly from primary and secondary syphilis patients, revealing that the profile oftprKinT. pallidumfrom the two-stage samples was different. Within the strains from secondary syphilis patients, more mixture variants within seven V regions oftprKwere found, the frequencies of their predominant sequences were generally decreased with the proportion of minor variants in 10-60% was increased. And the variations within V regions oftprKalways obeyed a strict 3 bp changing pattern. Noteworthy, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 presented a high proportion of inter-population sharing and presented a relatively high frequency in the populations. And V6 region always demonstrated remarkable variability at intra- and inter-patient levels regardless of the course. These findings provide insights into the mysterious role of TprK in immune evasion and for further exploring the potential vaccine components.

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Presence of an isoform of H+-pyrophosphatase located in the alveolar sacs of a scuticociliate parasite of turbot: physiological consequences

Parasitology ◽

10.1017/s0031182015001997 ◽

2016 ◽

Vol 143 (5) ◽

pp. 576-587 ◽

Cited By ~ 1

Author(s):

NATALIA MALLO ◽

JESÚS LAMAS ◽

ANA-PAULA DEFELIPE ◽

MARIA-EUGENIA DECASTRO ◽

ROSA-ANA SUEIRO ◽

...

Keyword(s):

Amino Acid ◽

Physiological Role ◽

Amino Acid Sequences ◽

Cell Structures ◽

Gene And Protein Expression ◽

Conserved Gene ◽

Eukaryotic Organisms ◽

Cellular Compartments ◽

First Time

SUMMARYH+-pyrophosphatases (H+-PPases) are integral membrane proteins that couple pyrophosphate energy to an electrochemical gradient across biological membranes and promote the acidification of cellular compartments. Eukaryotic organisms, essentially plants and protozoan parasites, contain various types of H+-PPases associated with vacuoles, plasma membrane and acidic Ca+2storage organelles called acidocalcisomes. We used Lysotracker Red DND-99 staining to identify two acidic cellular compartments in trophozoites of the marine scuticociliate parasitePhilasterides dicentrarchi: the phagocytic vacuoles and the alveolar sacs. The membranes of these compartments also contain H+-PPase, which may promote acidification of these cell structures. We also demonstrated for the first time that theP. dicentrarchiH+-PPase has two isoforms: H+-PPase 1 and 2. Isoform 2, which is probably generated by splicing, is located in the membranes of the alveolar sacs and has an amino acid motif recognized by the H+-PPase-specific antibody PABHK. The amino acid sequences of different isolates of this ciliate are highly conserved. Gene and protein expression in this isoform are significantly regulated by variations in salinity, indicating a possible physiological role of this enzyme and the alveolar sacs in osmoregulation and salt tolerance inP. dicentrarchi.

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Characterization of a 12-Kilodalton Rhodanese Encoded byglpE of Escherichia coli and Its Interaction with Thioredoxin

Journal of Bacteriology ◽

10.1128/jb.182.8.2277-2284.2000 ◽

2000 ◽

Vol 182 (8) ◽

pp. 2277-2284 ◽

Cited By ~ 74

Author(s):

W. Keith Ray ◽

Gang Zeng ◽

M. Benjamin Potters ◽

Aqil M. Mansuri ◽

Timothy J. Larson

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Sequence ◽

Active Site ◽

Amino Acid Sequences ◽

E Coli ◽

Active Site Cysteine ◽

Clusters Of Orthologous Groups ◽

Thioredoxin 1 ◽

First Time

ABSTRACT Rhodaneses catalyze the transfer of the sulfane sulfur from thiosulfate or thiosulfonates to thiophilic acceptors such as cyanide and dithiols. In this work, we define for the first time the gene, and hence the amino acid sequence, of a 12-kDa rhodanese fromEscherichia coli. Well-characterized rhodaneses are comprised of two structurally similar ca. 15-kDa domains. Hence, it is thought that duplication of an ancestral rhodanese gene gave rise to the genes that encode the two-domain rhodaneses. The glpEgene, a member of the sn-glycerol 3-phosphate (glp) regulon of E. coli, encodes the 12-kDa rhodanese. As for other characterized rhodaneses, kinetic analysis revealed that catalysis by purified GlpE occurs by way of an enzyme-sulfur intermediate utilizing a double-displacement mechanism requiring an active-site cysteine. TheKm s for SSO3 2− and CN− were 78 and 17 mM, respectively. The apparent molecular mass of GlpE under nondenaturing conditions was 22.5 kDa, indicating that GlpE functions as a dimer. GlpE exhibited ak cat of 230 s−1. Thioredoxin 1 from E. coli, a small multifunctional dithiol protein, served as a sulfur acceptor substrate for GlpE with an apparentKm of 34 μM when thiosulfate was near itsKm , suggesting that thioredoxin 1 or related dithiol proteins could be physiological substrates for sulfurtransferases. The overall degree of amino acid sequence identity between GlpE and the active-site domain of mammalian rhodaneses is limited (∼17%). This work is significant because it begins to reveal the variation in amino acid sequences present in the sulfurtransferases. GlpE is the first among the 41 proteins in COG0607 (rhodanese-related sulfurtransferases) of the database Clusters of Orthologous Groups of proteins (http://www.ncbi.nlm.nih.gov/COG/ ) for which sulfurtransferase activity has been confirmed.

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Production of Enterocins L50A, L50B, and IT, a New Enterocin, by Enterococcus faecium IT62, a Strain Isolated from Italian Ryegrass in Japan

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01409-07 ◽

2008 ◽

Vol 52 (6) ◽

pp. 1917-1923 ◽

Cited By ~ 19

Author(s):

Esther Izquierdo ◽

Audrey Bednarczyk ◽

Christine Schaeffer ◽

Yimin Cai ◽

Eric Marchioni ◽

...

Keyword(s):

Amino Acid ◽

Enterococcus Faecium ◽

Amino Acid Sequences ◽

Italian Ryegrass ◽

Gram Positive ◽

Gram Negative ◽

Gram Positive Bacteria ◽

Wide Range ◽

Molecular Masses ◽

First Time

ABSTRACT Enterococcus faecium IT62, isolated from ryegrass in Japan, was shown to produce three different bacteriocins, two of which had molecular masses and amino acid sequences that corresponded to those of enterocin L50A and enterocin L50B. These peptides existed, however, as chemically modified forms that were either N formylated or N formylated and oxidized at Met24. The third bacteriocin, named enterocin IT, had a molecular mass of 6,390 Da, was made up of 54 amino acids, and did not correspond to any known bacteriocin. However, enterocin IT was identical to the C-terminal part of the 16-amino-acid-longer bacteriocin 32 (T. Inoue, H. Tomita, and Y. Ike, Antimicrob. Agents Chemother., 50:1202-1212, 2006). For the first time, the antimicrobial activity spectra for enterocins L50A and L50B were determined separately and included a wide range of gram-positive bacteria but also a few gram-negative strains that were weakly sensitive. Slight differences in the activities of enterocins L50A and L50B were observed, as gram-positive bacteria showed an overall higher level of sensitivity to L50A than to L50B, as opposed to gram-negative ones. Conversely, enterocin IT showed a very narrow antimicrobial spectrum that was limited to E. faecium strains, one strain of Bacillus subtilis, and one strain of Lactococcus lactis. This study showed that E. faecium IT62, a grass-borne strain, produces bacteriocins with very different activity features and structures that may be found in strains associated with food or those of clinical origin, which demonstrates that a particular enterocin structure may be widespread and not related to the producer's origin.

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Molecular cloning, characterization and antigenicity ofBabesiasp. BQ1 (Lintan) (Babesiacf.motasi) apical membrane antigen-1 (AMA-1)

Parasitology ◽

10.1017/s0031182016002304 ◽

2016 ◽

Vol 144 (5) ◽

pp. 641-649 ◽

Cited By ~ 1

Author(s):

QINGLI NIU ◽

ZHIJIE LIU ◽

JIFEI YANG ◽

GUIQUAN GUAN ◽

YUPING PAN ◽

...

Keyword(s):

Amino Acid ◽

Apical Membrane ◽

Amino Acid Sequences ◽

Amino Acid Residues ◽

Gene Characterization ◽

Reading Frame ◽

Apical Membrane Antigen 1 ◽

Apical Membrane Antigen ◽

Potential Vaccine

SUMMARYApical membrane antigen-1 (AMA-1) has been described as a potential vaccine candidate in apicomplexan parasites. Here we characterize theama-1gene. The full-lengthama-1gene ofBabesiasp. BQ1 (Lintan) (BLTAMA-1) is 1785 bp, which contains an open reading frame (ORF) encoding a 65-kDa protein of 594 amino acid residues; by definition, the 5′ UTR precedes the first methionine of the ORF. Phylogenetic analysis based on AMA-1 amino acid sequences clearly separated Piroplasmida from other Apicomplexa parasites. TheBabesiasp. BQ1 (Lintan) AMA-1 sequence is most closely associated with that ofB. ovataandB. bigemina, with high bootstrap value. A recombinant protein encoding a conserved region and containing ectodomains I and II of BLTAMA-1 was constructed. BLTrAMA-1-DI/DII proteins were tested for reactivity with sera from sheep infected byBabesiasp. BQ1 (Lintan). In Western-blot analysis, nativeBabesiasp. BQ1 (Lintan) AMA-1 proteins were recognized by antibodies raised in rabbits against BLTrAMA-1in vitro. The results of this study are discussed in terms of gene characterization, taxonomy and antigenicity.

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The Surface Glycoproteins of H5 Influenza Viruses Isolated from Humans, Chickens, and Wild Aquatic Birds Have Distinguishable Properties

Journal of Virology ◽

10.1128/jvi.73.2.1146-1155.1999 ◽

1999 ◽

Vol 73 (2) ◽

pp. 1146-1155 ◽

Cited By ~ 409

Author(s):

Mikhail Matrosovich ◽

Nannan Zhou ◽

Yoshihiro Kawaoka ◽

Robert Webster

Keyword(s):

Hong Kong ◽

Amino Acid ◽

Amino Acid Sequences ◽

Influenza Viruses ◽

Amino Acid Deletion ◽

Aquatic Birds ◽

Avian Influenza Viruses ◽

Binding Properties ◽

Characteristic Features ◽

First Time

ABSTRACT In 1997, 18 confirmed cases of human influenza arising from multiple independent transmissions of H5N1 viruses from infected chickens were reported from Hong Kong. To identify possible phenotypic changes in the hemagglutinin (HA) and neuraminidase (NA) of the H5 viruses during interspecies transfer, we compared the receptor-binding properties and NA activities of the human and chicken H5N1 isolates from Hong Kong and of H5N3 and H5N1 viruses from wild aquatic birds. All H5N1 viruses, including the human isolate bound to Sia2-3Gal-containing receptors but not to Sia2-6Gal-containing receptors. This finding formally demonstrates for the first time that receptor specificity of avian influenza viruses may not restrict initial avian-to-human transmission. The H5N1 chicken viruses differed from H5 viruses of wild aquatic birds by a 19-amino-acid deletion in the stalk of the NA and the presence of a carbohydrate at the globular head of the HA. We found that a deletion in the NA decreased its ability to release the virus from cells, whereas carbohydrate at the HA head decreased the affinity of the virus for cell receptors. Comparison of amino acid sequences from GenBank of the HAs and NAs from different avian species revealed that additional glycosylation of the HA and a shortened NA stalk are characteristic features of the H5 and H7 chicken viruses. This finding indicates that changes in both HA and NA may be required for the adaptation of influenza viruses from wild aquatic birds to domestic chickens and raises the possibility that chickens may be a possible intermediate host in zoonotic transmission.

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Size and structure of the sequence space of repeat proteins

10.1101/635581 ◽

2019 ◽

Author(s):

Jacopo Marchi ◽

Ezequiel A. Galpern ◽

Rocio Espada ◽

Diego U. Ferreiro ◽

Aleksandra M. Walczak ◽

...

Keyword(s):

Amino Acid ◽

Protein Design ◽

Amino Acid Sequences ◽

Sequence Alignments ◽

Multiple Sequence ◽

Multiple Sequence Alignments ◽

Repeat Proteins ◽

The Impact ◽

New Strategies ◽

Amino Acid Conservation

AbstractThe coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family —the total number of sequences in that family— can be estimated using models of maximum entropy trained on multiple sequence alignments of naturally occuring amino acid sequences. We analyzed and calculated the size of three abundant repeat proteins families, whose members are large proteins made of many repetitions of conserved portions of ∼30 amino acids. While amino acid conservation at each position of the alignment explains most of the reduction of diversity relative to completely random sequences, we found that correlations between amino acid usage at different positions significantly impact that diversity. We quantified the impact of different types of correlations, functional and evolutionary, on sequence diversity. Analysis of the detailed structure of the coding space of the families revealed a rugged landscape, with many local energy minima of varying sizes with a hierarchical structure, reminiscent of fustrated energy landscapes of spin glass in physics. This clustered structure indicates a multiplicity of subtypes within each family, and suggests new strategies for protein design.

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