Special Evolutionary Properties of Genes Encoding a Protein with a Simple Amino Acid Repeat

AbstractTwo homologues of map-1, which encodes a putative avirulence factor, were found in a single egg mass line of the root-knot nematode Meloidogyne javanica that was virulent to the Mi-resistant gene. The main difference between the two encoded proteins of these homologues, MJ-MAP-1 and MJ-MAP-2, was the position of a 13 amino acid repeat region. Genes encoding two related but novel proteins, MJAP-1 and MJAP-2 (290 and 283 amino acids, respectively, including a potential signal secretion peptide), were also isolated from M. javanica. They have high similarity to MAP at the C-terminus. MJAP-1 and MJAP-2 differ from each other in the number and position of a seven-amino-acid repeat and in five other amino acids. The mjap genes are expressed in the subventral pharyngeal glands of second-stage juveniles of M. javanica, and transcription analysis in different developmental stages showed expression in the juvenile stage but not in eggs or adult females. Both mjap-1 and mjap-2 were expressed in both Mi-virulent and avirulent lines of M. javanica.

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A Comparative Proteomic Analysis of the Simple Amino Acid Repeat Distributions in Plasmodia Reveals Lineage Specific Amino Acid Selection

PLoS ONE ◽

10.1371/journal.pone.0006231 ◽

2009 ◽

Vol 4 (7) ◽

pp. e6231 ◽

Cited By ~ 14

Author(s):

Andrew R. Dalby

Keyword(s):

Amino Acid ◽

Proteomic Analysis ◽

Amino Acid Repeat ◽

Specific Amino Acid ◽

Comparative Proteomic Analysis ◽

Simple Amino Acid

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Structural and antigenic polymorphism of the 35- to 48-kilodalton merozoite surface antigen (MSA-2) of the malaria parasite Plasmodium falciparum

Molecular and Cellular Biology ◽

10.1128/mcb.11.2.963-971.1991 ◽

1991 ◽

Vol 11 (2) ◽

pp. 963-971

Author(s):

B Fenton ◽

J T Clark ◽

C M Khan ◽

J V Robinson ◽

D Walliker ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Amino Acid ◽

Surface Antigen ◽

Dna Sequences ◽

Amino Acid Sequences ◽

Merozoite Surface Antigen ◽

Parasite Plasmodium ◽

Genes Encoding ◽

Parasite Plasmodium Falciparum ◽

Group B

Merozoite surface antigen MSA-2 of the human parasite Plasmodium falciparum is being considered for the development of a malaria vaccine. The antigen is polymorphic, and specific monoclonal antibodies differentiate five serological variants of MSA-2 among 25 parasite isolates. The variants are grouped into two major serogroups, A and B. Genes encoding two different variants from serogroup A have been sequenced, and their DNA together with deduced amino acid sequences were compared with sequences encoded by other alleles. The comparison shows that the serological classification reflects differences in DNA sequences and deduced primary structure of MSA-2 variants and serogroups. Thus, the overall homologies of DNA and amino acid sequences are over 95% among variants in the same serogroup. In contrast, similarities between the group A variants and a group B variant are only 70 and 64% for DNA and amino acid sequences, respectively. We propose that the MSA-2 protein is encoded by two highly divergent groups of alleles, with limited additional polymorphism displayed within each group.

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Streptococcus salivarius Isolates of Varying Acid Tolerance Exhibit F1F0-ATPase Conservation

Caries Research ◽

10.1159/000516175 ◽

2021 ◽

pp. 1-4

Author(s):

Lauren L. Allen ◽

Nicholas C.K. Heng ◽

Geoffrey R. Tompkins

Keyword(s):

Molecular Structure ◽

Amino Acid ◽

Acid Tolerance ◽

Mutans Streptococci ◽

Streptococcus Salivarius ◽

Synonymous Substitutions ◽

Carious Lesions ◽

Genes Encoding ◽

Atpase Subunits ◽

Membrane Bound

Genes encoding the subunits of the membrane-bound F1F0-ATPase (responsible for exporting protons from the cytoplasm and contributing to acid tolerance) were sequenced for 24 non-mutans streptococci isolated from carious lesions. Isolates, mostly Streptococcus salivarius, displayed a continuum of acid tolerance thresholds ranging from pH 4.55 to 3.39, but amino acid alignments of F1F0-ATPase subunits revealed few non-synonymous substitutions and these were unrelated to acid tolerance. Thus, the F1F0-ATPase is highly-conserved among S. salivarius isolates despite varying acid tolerance thresholds, supporting the contention that acid tolerance is determined by the level of gene/protein expression rather than variation in molecular structure.

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A50 Whole-genome sequencing of African swine fever isolates from Sardinia

Virus Evolution ◽

10.1093/ve/vez002.049 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

C Torresi ◽

F Granberg ◽

L Bertolotti ◽

A Oggiano ◽

B Colitti ◽

...

Keyword(s):

Amino Acid ◽

Sequence Data ◽

Temporal Distribution ◽

African Swine Fever ◽

Amino Acid Identity ◽

Genotype I ◽

Acid Identity ◽

Wide Range ◽

Intergenic Sequences ◽

Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

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Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans

Pathogens ◽

10.3390/pathogens10091178 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1178

Author(s):

Nichari Bamphensin ◽

Peechanika Chopjitt ◽

Rujirat Hatrongjit ◽

Parichart Boueroy ◽

Nahuel Fittipaldi ◽

...

Keyword(s):

Amino Acid ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Streptococcus Suis ◽

Amino Acid Substitutions ◽

Continuous Control ◽

Antimicrobial Resistance Genes ◽

Genes Encoding ◽

Invasive Infections ◽

Almost All

Streptococcus suis is a pathogen that causes invasive infections in humans and pigs. In this study, 448 S. suis isolates recovered from human infections in Thailand were characterized with regard to their antimicrobial susceptibility and antimicrobial resistance genes, including, for non-penicillin-susceptible isolates, sequence analyses of five genes encoding penicillin-binding proteins (pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x). All 448 isolates were susceptible to cefepime and ceftriaxone, whereas 99.6%, 91.7%, and 72.9% of the isolates were susceptible to levofloxacin, penicillin, and chloramphenicol, respectively. Almost all isolates were resistant to tetracycline (98.2%), clindamycin (94%), erythromycin (92.4%), and azithromycin (82.6%). Genes tet(O) and ermB were the predominant resistance genes detected among macrolide- and tetracycline-resistant isolates. A total of 37 out of 448 isolates (8.2%) showed intermediately resistance to penicillin. Most of these isolates (59.5%) belonged to serotype 2-ST233. Comparison of the predicted translated sequences of five PBP proteins of a penicillin-susceptible isolate (strain P1/7) to the respective PBP sequences of ten non-penicillin-susceptible isolates revealed multiple amino acid substitutions. Isolates of CC221/234 showed highly variable amino acid substitutions in all PBP proteins. An ST104 isolate had a higher number of amino acid substitutions in PBP2X. Isolates belonging to CC233/379 had numerous substitutions in PBP2B and PBP2X. ST25 isolates exhibited fewer amino acid substitutions than isolates of other STs in all five PBPs. The antimicrobial resistance of S. suis is increasing worldwide; therefore, restrictions on antimicrobial use, continuous control, and the surveillance of this bacterium throughout the pork supply chain are crucial for ensuring public health and must be a priority concern.

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A Budding Yeast Model for Human Disease Mutations in the EXOSC2 Cap Subunit of the RNA Exosome

10.1101/2020.12.06.413658 ◽

2020 ◽

Author(s):

Maria C. Sterrett ◽

Liz Enyenihi ◽

Sara W. Leung ◽

Laurie Hess ◽

Sarah E. Strassler ◽

...

Keyword(s):

Amino Acid ◽

Budding Yeast ◽

Amino Acid Substitutions ◽

Missense Mutations ◽

Subunit Gene ◽

Rna Targets ◽

Genes Encoding ◽

Rna Exosome ◽

Transcriptomic Changes

AbstractRNA exosomopathies, a growing family of tissue-specific diseases, are linked to missense mutations in genes encoding the structural subunits of the conserved 10-subunit exoribonuclease complex, the RNA exosome. Such mutations in the cap subunit gene EXOSC2 cause the novel syndrome SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies). In contrast, exosomopathy mutations in the cap subunit gene EXOSC3 cause pontocerebellar hypoplasia type 1b (PCH1b). Though having strikingly different disease pathologies, EXOSC2 and EXOSC3 exosomopathy mutations result in amino acid substitutions in similar, conserved domains of the cap subunits, suggesting that these exosomopathy mutations have distinct consequences for RNA exosome function. We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by introducing the EXOSC2 mutations in the orthologous S. cerevisiae gene RRP4. The resulting rrp4 mutant cells have defects in cell growth and RNA exosome function. We detect significant transcriptomic changes in both coding and non-coding RNAs in the rrp4 variant, rrp4-G226D, which models EXOSC2 p.Gly198Asp. Comparing this rrp4-G226D mutant to the previously studied S. cerevisiae model of EXOSC3 PCH1b mutation, rrp40-W195R, reveals that these mutants have disparate effects on certain RNA targets, providing the first evidence for different mechanistic consequences of these exosomopathy mutations. Congruently, we detect specific negative genetic interactions between RNA exosome cofactor mutants and rrp4-G226D but not rrp40-W195R. These data provide insight into how SHRF mutations could alter the function of the RNA exosome and allow the first direct comparison of exosomopathy mutations that cause distinct pathologies.

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Amino Acid Substitutions in Mosaic Penicillin-Binding Protein 2 Associated with Reduced Susceptibility to Cefixime in Clinical Isolates of Neisseria gonorrhoeae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00626-06 ◽

2006 ◽

Vol 50 (11) ◽

pp. 3638-3645 ◽

Cited By ~ 68

Author(s):

Sho Takahata ◽

Nami Senju ◽

Yumi Osaki ◽

Takuji Yoshida ◽

Takashi Ida

Keyword(s):

Amino Acid ◽

Neisseria Gonorrhoeae ◽

Molecular Mechanisms ◽

Binding Protein ◽

Complete Sequence ◽

Clinical Isolates ◽

Amino Acid Substitutions ◽

Penicillin Binding Protein ◽

Fourfold Increase ◽

Genes Encoding

ABSTRACT The molecular mechanisms of reduced susceptibility to cefixime in clinical isolates of Neisseria gonorrhoeae, particularly amino acid substitutions in mosaic penicillin-binding protein 2 (PBP2), were examined. The complete sequence of ponA, penA, and por genes, encoding, respectively, PBP1, PBP2, and porin, were determined for 58 strains isolated in 2002 from Japan. Replacement of leucine 421 by proline in PBP1 and the mosaic-like structure of PBP2 were detected in 48 strains (82.8%) and 28 strains (48.3%), respectively. The presence of mosaic PBP2 was the main cause of the elevated cefixime MIC (4- to 64-fold). In order to identify the mutations responsible for the reduced susceptibility to cefixime in isolates with mosaic PBP2, penA genes with various mutations were transferred to a susceptible strain by genetic transformation. The susceptibility of partial recombinants and site-directed mutants revealed that the replacement of glycine 545 by serine (G545S) was the primary mutation, which led to a two- to fourfold increase in resistance to cephems. Replacement of isoleucine 312 by methionine (I312M) and valine 316 by threonine (V316T), in the presence of the G545S mutation, reduced susceptibility to cefixime, ceftibuten, and cefpodoxime by an additional fourfold. Therefore, three mutations (G545S, I312M, and V316T) in mosaic PBP2 were identified as the amino acid substitutions responsible for reduced susceptibility to cefixime in N. gonorrhoeae.

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Molecular Cloning and Characterization of cDNA for a Rice Protein that Contains Seven Repetitive Segments of the Trp-Asp Forty-Amino-Acid Repeat (WD-40 Repeat)

Plant and Cell Physiology ◽

10.1093/oxfordjournals.pcp.a078786 ◽

1995 ◽

Vol 36 (3) ◽

pp. 505-510 ◽

Cited By ~ 25

Author(s):

Yukimoto Iwasaki ◽

Masayasu Komano ◽

Atsushi Ishikawa ◽

Takuji Sasaki ◽

Tadashi Asahi

Keyword(s):

Amino Acid ◽

Molecular Cloning ◽

Amino Acid Repeat ◽

Rice Protein

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Multiple GCD genes required for repression of GCN4, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.3990-3998.1986 ◽

1986 ◽

Vol 6 (11) ◽

pp. 3990-3998

Author(s):

S Harashima ◽

A G Hinnebusch

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acid ◽

Lacz Gene ◽

Gene Products ◽

Wild Type ◽

Double Mutation ◽

Double Stranded Rna ◽

Amino Acid Availability ◽

Genes Encoding ◽

New Alleles

GCN4 encodes a positive regulator of multiple unlinked genes encoding amino acid biosynthetic enzymes in Saccharomyces cerevisiae. Expression of GCN4 is coupled to amino acid availability by a control mechanism involving GCD1 as a negative effector and GCN1, GCN2, and GCN3 as positive effectors of GCN4 expression. We used reversion of a gcn2 gcn3 double mutation to isolate new alleles of GCD1 and mutations in four additional GCD genes which we designate GCD10, GCD11, GCD12, and GCD13. All of the mutations lead to constitutive derepression of HIS4 transcription in the absence of the GCN2+ and GCN3+ alleles. By contrast, the gcd mutations require the wild-type GCN4 allele for their derepressing effect, suggesting that each acts by influencing the level of GCN4 activity in the cell. Consistent with this interpretation, mutations in each GCD gene lead to constitutive derepression of a GCN4::lacZ gene fusion. Thus, at least five gene products are required to maintain the normal repressed level of GCN4 expression in nonstarvation conditions. Interestingly, the gcd mutations are pleiotropic and also affect growth rate in nonstarvation conditions. In addition, certain alleles lead to a loss of M double-stranded RNA required for the killer phenotype. This pleiotropy suggests that the GCD gene products contribute to an essential cellular function, in addition to, or in conjunction with, their role in GCN4 regulation.

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