amino acid sequences
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Genome ◽  
2022 ◽  
Sakura Hayashi ◽  
Konami Shimizu ◽  
Yusuke Honda ◽  
Yukako Katsura ◽  
Akihiko Koga

An albino infant wallaby was born to a mother with the wild-type body color. PCR and sequencing analyses of <i>TYR</i> (encoding tyrosinase, which is essential for melanin biosynthesis) of this albino wallaby revealed a 7.1-kb-long DNA fragment inserted in the first exon. Because the fragment carried long terminal repeats, we assumed it to be a copy of an endogenous retrovirus, which we named <i>walb</i>. We cloned other <i>walb</i> copies residing in the genomes of this species and another wallaby species. The copies exhibited length variation, and the longest copy (>8.0 kb) contained open reading frames whose deduced amino acid sequences were well aligned with those of <i>gag</i>, <i>pol</i>, and <i>env</i> of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into <i>TYR</i>: endogenization (infection of a germline cell by an exogenous virus), reinfection (infection by a virus produced from a previously endogenized provirus), or retrotransposition (intracellular relocation of a provirus). In any case, the insertion into <i>TYR</i> is considered to have been a recent event on an evolutionary timescale because albino mutant alleles generally do not persist for long because of their deleterious effects in wild circumstances. 

2022 ◽  
Vol 12 ◽  
Yeongjin Yun ◽  
Sangjun Han ◽  
Yoon Sik Park ◽  
Hyunjae Park ◽  
Dogyeong Kim ◽  

Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics, including penicillins, cephalosporins, and carbapenems; however, no effective inhibitors are currently clinically available. MBLs are classified into three subclasses: B1, B2, and B3. Although the amino acid sequences of MBLs are varied, their overall scaffold is well conserved. In this study, we systematically studied the primary sequences and crystal structures of all subclasses of MBLs, especially the core scaffold, the zinc-coordinating residues in the active site, and the substrate-binding pocket. We presented the conserved structural features of MBLs in the same subclass and the characteristics of MBLs of each subclass. The catalytic zinc ions are bound with four loops from the two central β-sheets in the conserved αβ/βα sandwich fold of MBLs. The three external loops cover the zinc site(s) from the outside and simultaneously form a substrate-binding pocket. In the overall structure, B1 and B2 MBLs are more closely related to each other than they are to B3 MBLs. However, B1 and B3 MBLs have two zinc ions in the active site, while B2 MBLs have one. The substrate-binding pocket is different among all three subclasses, which is especially important for substrate specificity and drug resistance. Thus far, various classes of β-lactam antibiotics have been developed to have modified ring structures and substituted R groups. Currently available structures of β-lactam-bound MBLs show that the binding of β-lactams is well conserved according to the overall chemical structure in the substrate-binding pocket. Besides β-lactam substrates, B1 and cross-class MBL inhibitors also have distinguished differences in the chemical structure, which fit well to the substrate-binding pocket of MBLs within their inhibitory spectrum. The systematic structural comparison among B1, B2, and B3 MBLs provides in-depth insight into their substrate specificity, which will be useful for developing a clinical inhibitor targeting MBLs.

2022 ◽  
Vol 18 (1) ◽  
Hasan Ongor ◽  
Necati Timurkaan ◽  
Hasan Abayli ◽  
Burak Karabulut ◽  
Hakan Kalender ◽  

Abstract Background Marek’s disease (MD) is a lymphoproliferative disease caused by Gallid alphaherpesvirus 2 (GaHV-2, MDV-1), which primarily affects chickens. However, the virus is also able to induce tumors and polyneuritis in turkeys, albeit less frequently than in chickens. Results This is the first study in Turkey reporting the molecular characterization of a MDV-1 strain detected in a flock of backyard turkeys exhibiting visceral lymphoma. Here, MEQ, vIL-8, pp38 and 132-bp tandem repeat regions, which are frequently preferred in the pathotyping of MDV-1, were examined. It was determined that the MEQ gene of MDV-1/TR-21/turkey strain obtained in the present study encoded 339 amino acids (1020 nt) and had four proline-rich repeat regions (PPPP). Based on the nucleotide sequence of the MEQ gene of the MDV-1/TR-21/turkey strain, a phylogenetic tree was created using the MEGA-X software with the Maximum Likelihood Method (in 1000 replicates). Our strain was highly identical (> 99.8) to the Italian/Ck/625/16, Polish (Polen5) and some Turkish (Layer-GaHV-2-02-TR-2017, Tr/MDV-1/19) MDV-1 strains. Also, nt and aa sequences of the MEQ gene of our strain were 99.1 and 99.41% identical to another Turkish strain (MDV/Tur/2019) originated from chickens. Sequence analysis of pp38 and vIL-8 genes also supported the above finding. The identity ratios of nucleotide and amino acid sequences of vIL-8 and pp38 genes of MDV-1/TR-21/turkey strain were 99.64–100% and 99.79–100%, respectively, when compared with those of the Polish strain. According to 132-bp tandem repeat PCR results, the MDV-1/TR-21/turkey strain had five copies. Conclusions These results suggested that the MDV-1/TR-21/turkey strain obtained from backyard turkeys can be either very virulent or very virulent plus pathotype, though experimental inoculation is required for precise pathotyping.

Nuttanit Pramounmat ◽  
Katherine Yan ◽  
Jadon Wolf ◽  
Julie Renner

Abstract Platinum-binding peptides have been used for fabrication of complex platinum nanomaterials such as catalysts, metallopharmaceuticals, and electrodes. In this review, we present understanding of the mechanisms behind platinum-binding (Pt-binding) peptides and the applications of the peptides as multifunctional biomaterials. We discuss how the surface recognition, the roles of individual amino acids, and arrangement of amino acid sequences interplay. Our summary on the current state of understanding of Pt-binding peptides highlights opportunities for interdisciplinary research which will expand the applicability of these multifunctional Pt-binding peptides.

2022 ◽  
Nagendran Krishnan ◽  
Shweta Kumari ◽  
Koshlendra Kumar Pandey ◽  
Sudhakar Pandey ◽  
Tusar Kanti Behera ◽  

Abstract The pathogen responsible for yellowing and downward rolling of leaves of squash and watermelon plants from Uttar Pradesh state, India, was identified as probably strains of Cucurbit aphid-borne yellows virus (CABYV) through RT-PCR using universal Polerovirus primers followed by sequencing. The full-length genome sequences of an isolate from squash (POL-SQ - 5650 nt) and one from watermelon (POL-WM - 5647nt) were determined by sequencing the products from RT-PCR with six sets of primers with overlapping products. Sequence comparison and phylogenetic analysis showed that these isolates had closest identity with a recombinant strain obtained between CABYV and Melon aphid-borne yellows virus (MABYV) reported from Taiwan infecting Luffa aegyptiaca (CABYV-R-TW82) rather than other Asian, American, or European isolates. The deduced amino acid sequences of the P0, P1 and P1-P2 proteins showed >10% variation, whereas the P3, P4 and P3-P5 proteins showed <10% variation when compared to the corresponding proteins of other strains of CABYV worldwide. Thus, according to the Polerovirus species demarcation threshold, these new sequences should be regarded as representing strains of a novel previously undescribed Polerovirus species. However, based on their sequence similarity and phylogenetic grouping with the recombinant strain from Taiwan we suggest these sequences represent recombinant strains of CABYV. These are the first full-length genome sequences for CABYV strains from India and this study adds watermelon as host for CABYV in India.

2022 ◽  
Lev I. Levitsky ◽  
Ksenia Kuznetsova ◽  
Anna A. Kliuchnikova ◽  
Irina Y. Ilina ◽  
Anton O. Goncharov ◽  

Mass spectrometry-based proteome analysis usually implies matching mass spectra of proteolytic peptides to amino acid sequences predicted from nucleic acid sequences. At the same time, due to the stochastic nature of the method when it comes to proteome-wide analysis, in which only a fraction of peptides are selected for sequencing, the completeness of protein sequence identification is undermined. Likewise, the reliability of peptide variant identification in proteogenomic studies is suffering. We propose a way to interpret shotgun proteomics results, specifically in data-dependent acquisition mode, as protein sequence coverage by multiple reads, just as it is done in the field of nucleic acid sequencing for the calling of single nucleotide variants. Multiple reads for each position in a sequence could be provided by overlapping distinct peptides, thus, confirming the presence of certain amino acid residues in the overlapping stretch with much lower false discovery rate than conventional 1%. The source of overlapping distinct peptides are, first, miscleaved tryptic peptides in combination with their properly cleaved counterparts, and, second, peptides generated by several proteases with different specificities after the same specimen is subject to parallel digestion and analyzed separately. We illustrate this approach using publicly available multiprotease proteomic datasets and our own data generated for HEK-293 cell line digests obtained using trypsin, LysC and GluC proteases. From 5000 to 8000 protein groups are identified for each digest corresponding to up to 30% of the whole proteome coverage. Most of this coverage was provided by a single read, while up to 7% of the observed protein sequences were covered two-fold and more. The proteogenomic analysis of HEK-293 cell line revealed 36 peptide variants associated with SNP, seven of which were supported by multiple reads. The efficiency of the multiple reads approach depends strongly on the depth of proteome analysis, the digesting features such as the level of miscleavages, and will increase with the number of different proteases used in parallel proteome digestion.

2022 ◽  
Ming Zhang ◽  
Jun Liu ◽  
Zhenzhen Yin ◽  
Li Zhang

Bacillus cereus is a food contaminant with widely varying enterotoxic potential of its virulence proteins. In this article, phylogenetic analysis of the whole-genome amino acid sequences of 41 strains, evolutionary distance calculation of the amino acid sequences of the virulence genes, and functional and structural prediction of the virulence proteins were performed to reveal the taxonomically diverse distribution of virulence factors. The genome evolution of the strains showed a clustering trend based on the coding virulence genes. The strains of B. cereus have evolved into non-toxic risk and toxic risk clusters with medium-high- and medium-low-risk clusters. The distances of evolutionary transfer relative to housekeeping genes of incomplete virulence genes were greater than those of complete virulence genes, and the distance values of HblACD were higher than those of nheABC and CytK among the complete virulence genes. Cytoplasmic localization was impossible for all the virulence proteins, and NheB, NheC, Hbl-B, and Hbl-L 1 were extracellular according to predictive analysis. Nhe and Hbl proteins except CytK had similar spatial structures. The predicted structures of Nhe and Hbl mainly showed ‘head’ and ‘tail’ domains. The ‘head’ of NheA and Hbl-B, including two α-helices separated by β-tongue strands, might play a special role in Nhe trimers and Hbl trimers, respectively. The ‘cap’ of CytK, which includes two ‘latches’ with many β-sheets, formed a β-barrel structure with pores, and a ‘rim’ balanced the structure. The evolution of B. cereus strains showed a clustering tendency based on the coding virulence genes, and the complete virulence-gene operon combination had higher relative genetic stability. The beta-tongue or latch associated with β-sheet folding might play an important role in the binding of virulence structures and pore-forming toxins in B. cereus .

2022 ◽  
Vol 23 (2) ◽  
pp. 618
Kirill V. Khabudaev ◽  
Darya P. Petrova ◽  
Yekaterina D. Bedoshvili ◽  
Yelena V. Likhoshway ◽  
Mikhail A. Grachev

Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms.

2022 ◽  
Fateh Singh ◽  
Katherukamem Rajukumar ◽  
Dhanapal Senthilkumar ◽  
Govindarajulu Venkatesh ◽  
Deepali Srivast ◽  

Abstract During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n=264) and clotted blood (n=779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infective cell supernatant revealed the presence of two types of virions. Next generation sequencing (de novo) enabled complete genome assembly of Mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and all 10 gene segments of Mammalian orthoreovirus (MRV; 22219 bp and 20512 bp). Genetic analysis of the MRuV5 revealed grouping of the Indian MRuV5 with those isolated from various mammalian species in South Korea and China, sharing more than 99% nucleotide identity. Deduced amino acid sequences of the HN, NP and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S) and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. The Indian MRV isolates were identified as MRV type-3 based on genetic analysis of S1 gene, showing the highest nucleotide identity (97.73%) with the MRV3 strain ZJ2013 isolated from pigs in China. Deduced amino acid sequences of MRV3 S1 gene revealed amino acid residues 198-204NLAIRLP, 249I, 340D, 419E known for sialic acid binding and neurotropism. We report the co-isolation and whole-genomic characterization of MRuV5 and MRV3 recorded incidentally for the first time from domestic pigs in India. It attracts attention to perform detailed surveillance studies and continuous monitoring of evolution and spread of emerging viruses, which may have pathogenic potential in animal and human hosts.

PeerJ ◽  
2022 ◽  
Vol 10 ◽  
pp. e12654
Qiangqiang Ding ◽  
Hongyuan Zhao ◽  
Peilei Zhu ◽  
Xiangting Jiang ◽  
Fan Nie ◽  

The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.

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