amino acid sequence
Recently Published Documents


TOTAL DOCUMENTS

7062
(FIVE YEARS 212)

H-INDEX

174
(FIVE YEARS 6)

2022 ◽  
Author(s):  
Kenneth W Adolph

Multiple metaxin-like proteins are shown to exist in fungi, as also found for the metaxin proteins of vertebrates and invertebrates. In vertebrates, metaxins 1 and 2 are mitochondrial membrane proteins that function in the import of proteins into mitochondria. Fungal metaxin-like proteins were identified by criteria including their homology with human metaxins and the presence of characteristic GST_N_Metaxin, GST_C_Metaxin, and Tom37 protein domains. Fungi in different taxonomic divisions (phyla) were found to possess multiple metaxin-like proteins. These include the Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, Neocallimastigomycota, and Zoopagomycota divisions. Most fungi with multiple metaxin-like proteins contain two proteins, designated MTXa and MTXb. Amino acid sequence alignments show a high degree of homology among MTXa proteins, with over 60% amino acid identities, and also among MTXb proteins of fungi in the same division. But very little homology is observed in aligning MTXa with MTXb proteins of the same or different fungi. Both the MTXa proteins and MTXb proteins have the protein domains that characterize the metaxins and metaxin-like proteins: GST_N_Metaxin, GST_C_Metaxin, and Tom37. The metaxins and metaxin-like proteins of vertebrates, invertebrates, plants, protists, and bacteria all possess these domains. The secondary structures of MTXa and MTXb proteins are both dominated by similar patterns of α-helical segments, but extensive β-strand segments are absent. Nine highly conserved α-helical segments are present, the same as other metaxins and metaxin-like proteins. Phylogenetic analysis reveals that MTXa and MTXb proteins of fungi form two separate and distinct groups. These groups are also separate from the groups of vertebrate metaxins, metaxin-related Sam37 proteins of yeasts, and metaxin-like FAXC proteins.


2021 ◽  
Vol 17 (12) ◽  
pp. e1010203
Author(s):  
Alexandra M. Johansson ◽  
Uma Malhotra ◽  
Yeseul G. Kim ◽  
Rebecca Gomez ◽  
Maxwell P. Krist ◽  
...  

Class II tetramer reagents for eleven common DR alleles and a DP allele prevalent in the world population were used to identify SARS-CoV-2 CD4+ T cell epitopes. A total of 112, 28 and 42 epitopes specific for Spike, Membrane and Nucleocapsid, respectively, with defined HLA-restriction were identified. Direct ex vivo staining of PBMC with tetramer reagents was used to define immunodominant and subdominant T cell epitopes and estimate the frequencies of these T cells in SARS-CoV-2 exposed and naïve individuals. Majority of SARS-CoV-2 epitopes identified have <67% amino acid sequence identity with endemic coronaviruses and are unlikely to elicit high avidity cross-reactive T cell responses. Four SARS-CoV-2 Spike reactive epitopes, including a DPB1*04:01 restricted epitope, with ≥67% amino acid sequence identity to endemic coronavirus were identified. SARS-CoV-2 T cell lines for three of these epitopes elicited cross-reactive T cell responses to endemic cold viruses. An endemic coronavirus Spike T cell line showed cross-reactivity to the fourth SARS-CoV-2 epitope. Three of the Spike cross-reactive epitopes were subdominant epitopes, while the DPB1*04:01 restricted epitope was a dominant epitope. Frequency analyses showed Spike cross-reactive T cells as detected by tetramers were present at relatively low frequency in unexposed people and only contributed a small proportion of the overall Spike-specific CD4+ T cells in COVID-19 convalescent individuals. In total, these results suggested a very limited number of SARS-CoV-2 T cells as detected by tetramers are capable of recognizing ccCoV with relative high avidity and vice versa. The potentially supportive role of these high avidity cross-reactive T cells in protective immunity against SARS-CoV-2 needs further studies.


2021 ◽  
Author(s):  
Taiki Saito ◽  
Hirokazu Yagi ◽  
Chu-Wei Kuo ◽  
Kay-Hooi Khoo ◽  
Koichi Kato

Abstract N-glycans are diversified by a panel of glycosyltransferases in the Golgi, which are supposed to modify various glycoproteins in promiscuous manners, resulting in unpredictable glycosylation profiles in general. In contrast, our previous study showed that fucosyltransferase 9 (FUT9) generates Lewis X glycotopes primarily on lysosome-associated membrane protein 1 (LAMP-1) in neural stem cells. Here, we demonstrate that a contiguous 29-amino acid sequence in the N-terminal domain of LAMP-1 is indispensable for FUT9-dependent Lewis X modification. Interestingly, Lewis X modification was induced on erythropoietin as a model glycoprotein both in vivo and in vitro, just by attaching this sequence to its C-terminus. Based on these results, we conclude that the amino acid sequence from LAMP-1 functions as a “Lewis X code”, which is deciphered by FUT9, and can be embedded into other glycoproteins to evoke a Lewis X modification, opening up new possibilities for protein engineering and cell engineering.


Toxins ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 10
Author(s):  
Emmanouil Mavrogeorgis ◽  
Harald Mischak ◽  
Agnieszka Latosinska ◽  
Antonia Vlahou ◽  
Joost P. Schanstra ◽  
...  

Collagen is a major component of the extracellular matrix (ECM) and has an imminent role in fibrosis, in, among others, chronic kidney disease (CKD). Collagen alpha-1(I) (col1a1) is the most abundant collagen type and has previously been underlined for its contribution to the disease phenotype. Here, we examined 5000 urinary peptidomic datasets randomly selected from healthy participants or patients with CKD to identify urinary col1a1 fragments and study their abundance, position in the main protein, as well as their correlation with renal function. We identified 707 col1a1 peptides that differed in their amino acid sequence and/or post-translational modifications (hydroxyprolines). Well-correlated peptides with the same amino acid sequence, but a different number of hydroxyprolines, were combined into a final list of 503 peptides. These 503 col1a1 peptides covered 69% of the full col1a1 sequence. Sixty-three col1a1 peptides were significantly and highly positively associated (rho > +0.3) with the estimated glomerular filtration rate (eGFR), while only six peptides showed a significant and strong, negative association (rho < −0.3). A similar tendency was observed for col1a1 peptides associated with ageing, where the abundance of most col1a1 peptides decreased with increasing age. Collectively the results show a strong association between collagen peptides and loss of kidney function and suggest that fibrosis, potentially also of other organs, may be the main consequence of an attenuation of collagen degradation, and not increased synthesis.


2021 ◽  
Vol 25 (7) ◽  
pp. 787-792
Author(s):  
A. S. Stolbikov ◽  
R. K. Salyaev ◽  
N. I. Rekoslavskaya

This paper describes an attempt to analyze, with the aid of bioinformatics resources (programs and databases), the probable cause of the cross-interaction of antibodies against HPV16 L1 with antigenic protein HPV6 L1, which has been revealed in the investigation of the candidate vaccine obtained on the base of a plant expression system (tomato plants). In our opinion, the most likely reason for the cross-interaction of antibodies with antigens of different pathogenic HPV types is the similarity of their antigenic determinants. In this work, the amino acid sequences of HPV16 L1 and HPV6 L1 used for the development of a binary vaccine against cervical cancer and anogenital papillomatosis have been analyzed. For the analysis of antigenic determinants, the programs BepiPred-2.0: Sequential B-Cell Epitope Predictor, DiscoTope 2.0 Server and SYFPEITHI have been used. As a result of the analysis of probable B-cell linear determinants (epitopes), it has been found that in both types of HPV the proteins have approximately the same location and size of linear antigenic determinants; the difference is observed only in the form of small shifts in the size of several amino acid residues. However, there are some differences in the amino acid composition of epitopes; therefore, the possibility for cross-interaction of the antibodies with the antigens due to the similarity of linear antigenic determinants for B-cells is very small. The analysis of potential threedimensional epitopes for B-cells has shown that due to little difference between them the HPV16 L1 and HPV6 L1 proteins have no prerequisites for cross-interaction of the antibodies with the antigens belonging to the two different pathogenic HPV types. The analysis of probable linear epitopes for T-cells has revealed a common antigenic determinant in the two protein sequences. According to the rank made with the SYFPEITHI program, the amino acid sequence AQL(I)FNKPYWL is the second most likely antigenic determinant for T-cells. Meanwhile, the amino acid sequences of this determinant in HPV16 L1 and HPV6 L1 are virtually identical. There is a difference in only one position, but it is not critical due to the similarity of the physicochemical properties of amino acids, for which there is a replacement in the amino acid sequence of antigenic determinants. Consequently, some moderate cross-interaction of the antibodies to HPV16 L1 with the antigens of HPV6 L1 may be expected.


Toxins ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 862
Author(s):  
Stefania Maiello ◽  
Rosario Iglesias ◽  
Letizia Polito ◽  
Lucía Citores ◽  
Massimo Bortolotti ◽  
...  

Kirkiin is a new type 2 ribosome-inactivating protein (RIP) purified from the caudex of Adenia kirkii with a cytotoxicity compared to that of stenodactylin. The high toxicity of RIPs from Adenia genus plants makes them interesting tools for biotechnology and therapeutic applications, particularly in cancer therapy. The complete amino acid sequence and 3D structure prediction of kirkiin are here reported. Gene sequence analysis revealed that kirkiin is encoded by a 1572 bp open reading frame, corresponding to 524 amino acid residues, without introns. The amino acid sequence analysis showed a high degree of identity with other Adenia RIPs. The 3D structure of kirkiin preserves the overall folding of type 2 RIPs. The key amino acids of the active site, described for ricin and other RIPs, are also conserved in the kirkiin A chain. Sugar affinity studies and docking experiments revealed that both the 1α and 2γ sites of the kirkiin B chain exhibit binding activity toward lactose and D-galactose, being lower than ricin. The replacement of His246 in the kirkiin 2γ site instead of Tyr248 in ricin causes a different structure arrangement that could explain the lower sugar affinity of kirkiin with respect to ricin.


2021 ◽  
Vol 8 ◽  
Author(s):  
Alexander A. Tokmakov ◽  
Atsushi Kurotani ◽  
Ken-Ichi Sato

The protein isoelectric point (pI) can be calculated from an amino acid sequence using computational analysis in a good agreement with experimental data. Availability of whole-genome sequences empowers comparative studies of proteome-wide pI distributions. It was found that the whole-proteome distributions of protein pI values are multimodal in different species. It was further hypothesized that the observed multimodality is associated with subcellular localization-specific differences in local pI distributions. Here, we overview the multimodality of proteome-wide pI distributions in different organisms focusing on the relationships between protein pI and subcellular localization. We also discuss the probable factors responsible for variation of the intracellular localization-specific pI profiles.


Plant Disease ◽  
2021 ◽  
Author(s):  
Ashwini Kumar ◽  
Bichhinna Maitri Rout ◽  
Shakshi Choudhary ◽  
Amish K. Sureja ◽  
V. K. Baranwal ◽  
...  

Pumpkin (Cucurbita moschata), a member of the family Cucurbitaceae, is widely cultivated throughout the world including India. During August 2020 to January 2021, stunted pumpkin plants (cv. Pusa Vishwas), showing chlorotic patches, mosaic, and vein banding on leaves (e-Xtra Fig.1), were observed in the experimental fields of the Indian Agricultural Research Institute (IARI), New Delhi, India. Leaf-dip electron microscopy (EM) of the symptomatic plants (12 out of 37 samples) revealed the association of long flexuous virus particles measuring 650-950nm×10-12nm, suggestive of the presence of either crinivirus or potyvirus or both. Subsequently, a reverse transcription-polymerase chain reaction (RT-PCR) was performed on RNA extracted from the samples that had long flexuous virus particles using generic primers for criniviruses i.e. CriniPol-F: GCY CCS AGR GTK AAT GA and CriniPol-R: ACC TTG RGA YTT RTC AAA targeting partial RNA-dependent RNA polymerase coding region (Martin et al. 2003) and specific primers for papaya ringspot virus (PRSV) targeting a part of 3’ NIb and full coat protein (CP) gene (Basavaraj et al., 2019) separately. All tested samples were positive for both crinivirus and PRSV as expected size amplicons were obtained, accounting for about 32% prevalence. As PRSV is a well-studied virus infecting cucurbits, further work was not carried on this virus and only the RT-PCR amplicon indicative of crinivirus (~515 bp) was cloned into the pGEM-T easy cloning vector (Promega, Madison, WI) and sequenced for further confirmation of the virus presence. The obtained sequence (GenBank accession No MZ318672) shared up to 90% nucleotide and 100% amino acid sequence identity with the corresponding genomic region of a cucurbit chlorotic yellows virus (CCYV) isolate from Greece (LT841297). To confirm the identity of the crinivirus species present in the same pumpkin sample, the CP gene (753bp) was amplified and sequenced using CCYV CP gene-specific primers CP-F (5’-ATG GAG AAG ACY GAC AAT AAA CAA AAT GAT GA-3’) and CP-R (5’-TTA TTT ACT ACA ACC TCC CGG TGC CAA C-3’) (modified from Kheireddine et al. 2020). Sequence analysis using the BioEdit tool (version 2.0) revealed that the crinivirus present in pumpkin (KC577202) shared 95 to 100% nucleotide (and 98 to 100% amino acid) sequence identity with the corresponding gene sequences of CCYV isolates originating from cucurbitaceous hosts from diverse locations. The presence of CCYV was further validated by a whitefly transmission-based bioassay followed by RT-PCR confirmation. The bioassay was performed by the whitefly species Bemisia tabaci (biotype Asia II7) using the acquisition access period and inoculation access period of 24 hours each. Six whitefly individuals per plant were used for inoculating ten pumpkin plants (cv. Pusa Vishwas) at the first true leaf stage grown in pots containing soilrite as the medium in insect-proof cages. All ten plants inoculated using whiteflies exhibited chlorosis and stunting symptoms 12-15 days post-inoculation (e-Xtra Fig.2) and were found positive for CCYV in RT-PCR assay performed using CCYV CP gene-specific primers. Though CCYV had been reported worldwide (Tzanetakis et al. 2013), its occurrence had not been reported from India. Results of the present study confirm the infection of pumpkin plants by CCYV and constitute the first report of its presence in India. Further, there is a need to investigate the extent of its spread and impact of this virus on the production of cucurbitaceous crops in the country.


Antibiotics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1415
Author(s):  
María M. Tavío ◽  
Ana S. Ramírez ◽  
Carlos Poveda ◽  
Rubén S. Rosales ◽  
Cristina F. Malla ◽  
...  

Acholeplasma (A.) laidlawii is an opportunistic pathogen with the ability to disseminate resistance determinants to antibiotics; however, its resistance to macrolides has been less studied. The aim of the present study was to characterize the mechanisms responsible for the resistance to macrolides, tiamulin and lincomycin found in a strain of A. laidlawii isolated from a pig with pneumonia. MICs of erythromycin, 15- and 16-membered macrolides, tiamulin and lincomycin were determined by microdilution method with and without reserpine, an inhibitor of ABC efflux pumps and regions of the genome were sequenced. Reserpine only decreased lincomycin MIC but it did not change the MICs of macrolides and tiamulin. The analysis of the DNA sequence of 23S rRNA showed nucleotide substitutions at eight different positions, although none of them were at positions previously related to macrolide resistance. Five mutations were found in the L22 protein, one of them at the stop codon. In addition, two mutations were found in the amino acid sequence of L4. The combination of multiple mutations in the ribosomal proteins L22 and L4 together with substitutions in 23S rRNA DNA sequence was associated with the resistance to macrolides, the pleuromutilin and lincomycin in the studied A. laidlawii strain.


2021 ◽  
Author(s):  
Osamu Okamoto ◽  
Shinji Hirano ◽  
Hirotsugu Miyoshi ◽  
Natsumi Ichinohe

Abstract We detected three chicken astrovirus strains from 4-day-old broiler chickens with a high mortality rate and visceral gout, and one strain from 150-day-old hens without clinical symptoms in Saga prefecture, Japan. Phylogenetic analysis based on the ORF1 amino acid sequence revealed that the strains from the visceral gout case were classified into subgroup Bi, and the strain from chickens without clinical symptoms was classified into subgroup Aiii. Our data indicate that diseases caused by chicken astrovirus can occur in Japan, and that chicken astrovirus infection should be included in the differential diagnosis of chickens with visceral gout.


Sign in / Sign up

Export Citation Format

Share Document