scholarly journals The size, shape and specificity of the sugar-binding site of the jacalin-related lectins is profoundly affected by the proteolytic cleavage of the subunits

2002 ◽  
Vol 367 (3) ◽  
pp. 817-824 ◽  
Author(s):  
Corinne HOULÈS ASTOUL ◽  
Willy J. PEUMANS ◽  
Els J.M. van DAMME ◽  
Annick BARRE ◽  
Yves BOURNE ◽  
...  
Keyword(s):  
Binding Site ◽  
Plant Pathogens ◽  
Higher Plants ◽  
Sequence Similarity ◽  
Binding Specificity ◽  
Proteolytic Cleavage ◽  
Carbohydrate Binding ◽  
High Sequence Similarity ◽  
Intracellular Location ◽  
The Impact

Mannose-specific lectins with high sequence similarity to jacalin and the Maclura pomifera agglutinin have been isolated from species belonging to the families Moraceae, Convolvulaceae, Brassicaceae, Asteraceae, Poaceae and Musaceae. Although these novel mannose-specific lectins are undoubtedly related to the galactose-specific Moraceae lectins there are several important differences. Apart from the obvious differences in specificity, the mannose- and galactose-specific jacalin-related lectins differ in what concerns their biosynthesis and processing, intracellular location and degree of oligomerization of the protomers. Taking into consideration that the mannose-specific lectins are widely distributed in higher plants, whereas their galactose-specific counterparts are confined to a subgroup of the Moraceae sp. one can reasonably assume that the galactose-specific Moraceae lectins are a small-side group of the main family. The major change that took place in the structure of the binding site of the diverging Moraceae lectins concerns a proteolytic cleavage close to the N-terminus of the protomer. To corroborate the impact of this change, the specificity of jacalin was re-investigated using surface plasmon resonance analysis. This approach revealed that in addition to galactose and N-acetylgalactosamine, the carbohydrate-binding specificity of jacalin extends to mannose, glucose, N-acetylmuramic acid and N-acetylneuraminic acid. Owing to this broad carbohydrate-binding specificity, jacalin is capable of recognizing complex glycans from plant pathogens or predators.

scholarly journals Distribution and Phylogenetic Analysis of Family 19 Chitinases in Actinobacteria

2004 ◽  
Vol 70 (2) ◽  
pp. 1135-1144 ◽  
Author(s):  
Tomokazu Kawase ◽  
Akihiro Saito ◽  
Toshiya Sato ◽  
Ryo Kanai ◽  
Takeshi Fujii ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Catalytic Domain ◽  
Higher Plants ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Pcr Amplification ◽  
High Sequence Similarity ◽  
The Family ◽  
Family 19 Chitinase ◽  
Chitinase Genes

ABSTRACT In organisms other than higher plants, family 19 chitinase was first discovered in Streptomyces griseus HUT6037, and later, the general occurrence of this enzyme in Streptomyces species was demonstrated. In the present study, the distribution of family 19 chitinases in the class Actinobacteria and the phylogenetic relationship of Actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. Forty-nine strains were chosen to cover almost all the suborders of the class Actinobacteria, and chitinase production was examined. Of the 49 strains, 22 formed cleared zones on agar plates containing colloidal chitin and thus appeared to produce chitinases. These 22 chitinase-positive strains were subjected to Southern hybridization analysis by using a labeled DNA fragment corresponding to the catalytic domain of ChiC, and the presence of genes similar to chiC of S. griseus HUT6037 in at least 13 strains was suggested by the results. PCR amplification and sequencing of the DNA fragments corresponding to the major part of the catalytic domains of the family 19 chitinase genes confirmed the presence of family 19 chitinase genes in these 13 strains. The strains possessing family 19 chitinase genes belong to 6 of the 10 suborders in the order Actinomycetales, which account for the greatest part of the Actinobacteria. Phylogenetic analysis suggested that there is a close evolutionary relationship between family 19 chitinases found in Actinobacteria and plant class IV chitinases. The general occurrence of family 19 chitinase genes in Streptomycineae and the high sequence similarity among the genes found in Actinobacteria suggest that the family 19 chitinase gene was first acquired by an ancestor of the Streptomycineae and spread among the Actinobacteria through horizontal gene transfer.

scholarly journals Biological Control Potential of Streptomyces sp. AR10 Producing Albocycline Isolated from Soil around Ant Nest

2018 ◽  
Vol 10 (3) ◽  
pp. 54
Author(s):  
Tatsuya Ohike ◽  
Tetsuya Matsukawa ◽  
Masahiro Okanami ◽  
Shin’ichiro Kajiyama ◽  
Takashi Ano
Keyword(s):  
Biological Control ◽  
Plant Pathogens ◽  
Sequence Similarity ◽  
Antifungal Compound ◽  
Dual Culture ◽  
High Sequence Similarity ◽  
Genus Streptomyces ◽  
Fungal Plant Pathogens ◽  
Biological Control Potential ◽  
Dual Culture Assay

Fifty actinomycetes were isolated from fifteen soil samples and were screened for their antagonism against fungal plant pathogens by dual culture assay, and one of the strain named AR10 was shown to be most effective in suppression of growth of plant pathogen. An antifungal compound of AR10 was extracted, and purified by TLC and HPLC. As a result of NMR and LC-MS analysis, the antifungal compound was identified as albocycline. AR10 suppressed Rhizoctonia damping-off of cucumber in infection control assay. The 16S rDNA sequence of AR10 shows high sequence similarity to those of genus Streptomyces, and the closest similarity was found in the sequence of S. lanatus NBRC 12787T with 98.7% similarity. However, the production of albocycline in Streptomyces closely related to AR10 in the phylogenetic tree has not been reported. Our finding suggests that AR10 can be a candidate for biological control agents.

scholarly journals Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

2021 ◽  
Author(s):  
Robin-Lee Troskie ◽  
Yohaann Jafrani ◽  
Tim R Mercer ◽  
Adam D Ewing ◽  
Geoffrey J Faulkner ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Cdna Sequencing ◽  
High Sequence Similarity ◽  
Protein Coding ◽  
Dynamic Component ◽  
Gene Copies ◽  
Sequencing Platforms ◽  
The Impact

Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. When transcribed, pseudogenes may encode proteins or enact RNA-intrinsic regulatory mechanisms. However, the extent, characteristics and functional relevance of the human pseudogene transcriptome are unclear. Short-read sequencing platforms have limited power to resolve and accurately quantify pseudogene transcripts owing to the high sequence similarity of pseudogenes and their parent genes. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes. Pseudogene transcripts are expressed in tissue-specific patterns, exhibit complex splicing patterns and contribute to the coding sequences of known genes. We survey pseudogene transcripts encoding intact open reading frames (ORFs), representing potential unannotated protein-coding genes, and demonstrate their efficient translation in cultured cells. To assess the impact of noncoding pseudogenes on the cellular transcriptome, we delete the nucleus- enriched pseudogene PDCL3P4 transcript from HAP1 cells and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the transcriptional landscape underpinning human biology and disease.

Biodiversity of foliar fungal endophytes in white spruce (Picea glauca) from southern Québec

2006 ◽  
Vol 84 (5) ◽  
pp. 777-790 ◽  
Author(s):  
F.O.P. Stefani ◽  
J.A. Bérubé
Keyword(s):  
Picea Glauca ◽  
Sequence Similarity ◽  
Fungal Endophytes ◽  
Biological Significance ◽  
Its Region ◽  
White Spruce ◽  
Nuclear Ribosomal Dna ◽  
High Sequence Similarity ◽  
Forestry Practices ◽  
The Impact

The objective of this study was to investigate the foliar endophyte biodiversity of white spruce ( Picea glauca (Moench) Voss to establish a baseline for future comparative studies examining the impact of forestry practices. It identifies for the first time endophytic fungi living inside the needles of white spruce from 280 needles collected in seven natural stands in southern Québec. The endophyte colonization rate on surface sterilized needles was 53.2%. We performed a PCR-RFLP and sequence analysis on the ITS region of the nuclear ribosomal DNA to achieve molecular identification. Isolate ITS sequences were compared with data from GenBank presenting the best similarity and were analyzed by a maximum of parsimony and Bayesian inference. Relationships between morphological groups, digestion groups, and sequence groups were investigated. In all, 23 morphotypes were found to belong to 14 sequence groups and we demonstrated that morphological groups are poor indicators for estimating species diversity. This study is the first to establish species richness values for foliar endophytes. Among the 141 isolates in this study, 75.15% have a high sequence similarity with Lophodermium piceae , 10.95% with an unknown species of Mycosphaerella , and 5.5% with two species of the genus Hypoxylon . Distribution, incidence and biological significance of all the endophytes found in this study are discussed.

scholarly journals Overview of the Structure–Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi

2019 ◽  
Vol 20 (2) ◽  
pp. 254 ◽  
Author(s):  
Annick Barre ◽  
Yves Bourne ◽  
Els Van Damme ◽  
Pierre Rougé
Keyword(s):  
Structure Function ◽  
Binding Site ◽  
High Specificity ◽  
Binding Specificity ◽  
Binding Pocket ◽  
Carbohydrate Binding ◽  
Specific Recognition ◽  
Mannose Binding ◽  
High Mannose ◽  
Function Relationship

To date, a number of mannose-binding lectins have been isolated and characterized from plants and fungi. These proteins are composed of different structural scaffold structures which harbor a single or multiple carbohydrate-binding sites involved in the specific recognition of mannose-containing glycans. Generally, the mannose-binding site consists of a small, central, carbohydrate-binding pocket responsible for the “broad sugar-binding specificity” toward a single mannose molecule, surrounded by a more extended binding area responsible for the specific recognition of larger mannose-containing N-glycan chains. Accordingly, the mannose-binding specificity of the so-called mannose-binding lectins towards complex mannose-containing N-glycans depends largely on the topography of their mannose-binding site(s). This structure–function relationship introduces a high degree of specificity in the apparently homogeneous group of mannose-binding lectins, with respect to the specific recognition of high-mannose and complex N-glycans. Because of the high specificity towards mannose these lectins are valuable tools for deciphering and characterizing the complex mannose-containing glycans that decorate both normal and transformed cells, e.g., the altered high-mannose N-glycans that often occur at the surface of various cancer cells.

scholarly journals Ca2+ ions promote fusion of Middle East Respiratory Syndrome coronavirus with host cells and increase infectivity

2019 ◽  
Author(s):  
Marco R. Straus ◽  
Tiffany Tang ◽  
Alex L. Lai ◽  
Annkatrin Flegel ◽  
Miya Bidon ◽  
...  
Keyword(s):  
Middle East ◽  
Viral Entry ◽  
Sequence Similarity ◽  
Isothermal Calorimetry ◽  
Mutant Cell ◽  
Proteolytic Cleavage ◽  
Middle East Respiratory Syndrome ◽  
Host Cells ◽  
Cell Surface Expression ◽  
High Sequence Similarity

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) is a major emerging zoonotic infectious disease. Since its first outbreak in 2012, the virus has repeatedly transmitted from camels to humans with 2,468 confirmed cases, causing 851 deaths. To date, there are no efficacious drugs and vaccines against MERS-CoV, increasing its potential to cause a public health emergency. A critical step in the life cycle of MERS-CoV is the fusion with the host cell with its spike (S) protein as main determinant of viral entry. Proteolytic cleavage of S exposes its fusion peptide (FP), which initiates membrane fusion. Previous studies on the related severe acute respiratory syndrome coronavirus (SARS-CoV) FP have shown that calcium (Ca2+) plays an important role for fusogenic activity via a Ca2+ binding pocket with conserved glutamic acid (E) and aspartic acid (D) residues. SARS-CoV and MERS-CoV FP share a high sequence homology and here, we investigated whether Ca2+ is required for MERS-CoV fusion by substituting E and D residues in the MERS-CoV FP with neutrally charged alanines. Upon verifying mutant cell surface expression and proteolytic cleavage, we tested the mutants ability to mediate infection of pseudo-particles (PPs) on host cells without and with Ca2+. Our results demonstrate that intracellular Ca2+ enhances MERS-CoV WT PPs infection by approximately two-fold and that E891 is a crucial residue for Ca2+ interaction. Electron spin resonance revealed that this enhancement could be attributed to Ca2+ increasing MERS-CoV FP fusion-relevant membrane ordering. Intriguingly, isothermal calorimetry titration showed that MERS-CoV FP binds one Ca2+, as opposed to SARS-CoV FP which binds two. Our data suggests that there are significant differences in FP-Ca2+ interactions of MERS-CoV and SARS-CoV FP despite their high sequence similarity and that the number of Ca2+ ions interacting with the FP has implications on the fusion dynamics of the virus.

scholarly journals External Loops at the C Terminus of Erwinia chrysanthemi Pectate Lyase C Are Required for Species-Specific Secretion through the Out Type II Pathway

1998 ◽  
Vol 180 (6) ◽  
pp. 1431-1437 ◽  
Author(s):  
Magdalen Lindeberg ◽  
Carol M. Boyd ◽  
Noel T. Keen ◽  
Alan Collmer
Keyword(s):  
Plant Pathogens ◽  
Sequence Similarity ◽  
Pectate Lyase ◽  
Extracellular Proteins ◽  
Erwinia Chrysanthemi ◽  
Terminal Branch ◽  
Type Ii ◽  
High Sequence Similarity ◽  
Hybrid Proteins ◽  
Species Specific

ABSTRACT The type II secretion system (main terminal branch of the general secretion pathway) is used by diverse gram-negative bacteria to secrete extracellular proteins. Proteins secreted by this pathway are synthesized with an N-terminal signal peptide which is removed upon translocation across the inner membrane, but the signals which target the mature proteins for secretion across the outer membrane are unknown. The plant pathogens Erwinia chrysanthemi andErwinia carotovora secrete several isozymes of pectate lyase (Pel) by the out-encoded type II pathway. However, these two bacteria cannot secrete Pels encoded by heterologously expressed pel genes from the other species, suggesting the existence of species-specific secretion signals within these proteins. The functional cluster of E. chrysanthemi out genes carried on cosmid pCPP2006 enables Escherichia coli to secreteE. chrysanthemi, but not E. carotovora, Pels. We exploited the high sequence similarity between E. chrysanthemi PelC and E. carotovora Pel1 to construct 15 hybrid proteins in which different regions of PelC were replaced with homologous sequences from Pel1. The differential secretion of these hybrid proteins by E. coli(pCPP2006) revealed M118 to D175 and V215 to C329 as regions required for species-specific secretion of PelC. We propose that the primary targeting signal is contained within the external loops formed by G274 to C329 but is dependent on residues in M118 to D170 and V215 to G274 for proper positioning.

scholarly journals Targeting the Achilles Heel of FtsZ: The Interdomain Cleft

2021 ◽  
Vol 12 ◽  
Author(s):  
Pinkilata Pradhan ◽  
William Margolin ◽  
Tushar Kant Beuria
Keyword(s):  
Cell Division ◽  
Binding Site ◽  
Mammalian Cells ◽  
Antibacterial Agents ◽  
Sequence Similarity ◽  
Bacterial Colonization ◽  
Drug Binding ◽  
Globular Domain ◽  
High Sequence Similarity ◽  
Gtp Binding

Widespread antimicrobial resistance among bacterial pathogens is a serious threat to public health. Thus, identification of new targets and development of new antibacterial agents are urgently needed. Although cell division is a major driver of bacterial colonization and pathogenesis, its targeting with antibacterial compounds is still in its infancy. FtsZ, a bacterial cytoskeletal homolog of eukaryotic tubulin, plays a highly conserved and foundational role in cell division and has been the primary focus of research on small molecule cell division inhibitors. FtsZ contains two drug-binding pockets: the GTP binding site situated at the interface between polymeric subunits, and the inter-domain cleft (IDC), located between the N-terminal and C-terminal segments of the core globular domain of FtsZ. The majority of anti-FtsZ molecules bind to the IDC. Compounds that bind instead to the GTP binding site are much less useful as potential antimicrobial therapeutics because they are often cytotoxic to mammalian cells, due to the high sequence similarity between the GTP binding sites of FtsZ and tubulin. Fortunately, the IDC has much less sequence and structural similarity with tubulin, making it a better potential target for drugs that are less toxic to humans. Over the last decade, a large number of natural and synthetic IDC inhibitors have been identified. Here we outline the molecular structure of IDC in detail and discuss how it has become a crucial target for broad spectrum and species-specific antibacterial agents. We also outline the drugs that bind to the IDC and their modes of action.

Characterization of a type D1A EUL-related lectin from rice expressed in Pichia pastoris

2014 ◽  
Vol 395 (4) ◽  
pp. 413-424 ◽  
Author(s):  
Bassam Al Atalah ◽  
Dieter Vanderschaeghe ◽  
Yehudi Bloch ◽  
Paul Proost ◽  
Kirsten Plas ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Recombinant Proteins ◽  
Sequence Similarity ◽  
Full Length ◽  
Carbohydrate Binding ◽  
Terminal Sequence ◽  
The Family ◽  
Carbohydrate Binding Site

Abstract OrysaEULD1A is one of the five EUL genes in rice (Oryza sativa) encoding a putative carbohydrate-binding protein belonging to the family of Euonymus related lectins (EUL). The OrysaEULD1A sequence comprises two highly similar EUL domains (91% sequence similarity and 72% sequence identity) separated by a 23 amino acid linker sequence and preceded by a 19 amino acid N-terminal sequence. In the present study, the full-length protein OrysaEULD1A as well as its individual domains OrysaEULD1A domain 1 and 2 were expressed in Pichiapastoris. After purification of the recombinant proteins, their carbohydrate-binding specificity was analyzed and compared. Interestingly, all recombinant lectins showed clear specificity towards galactosylated structures. Furthermore, all recombinant proteins agglutinated red blood cells, indicating that the full-length protein OrysaEULD1A and its domains are true lectins. These results taken together with data previously reported for single-domain EUL proteins indicate that although the amino acids – responsible for the formation of the carbohydrate-binding site – are identical for all EUL proteins in rice, these lectins show different carbohydrate specificities. This promiscuity of the carbohydrate-binding site can be attributed to gene divergence.

scholarly journals Glutathione-S-transferase from the arsenic hyperaccumulator fernPteris vittatacan confer increased arsenate resistance inEscherichia coli

2018 ◽  
Author(s):  
Aftab A. Khan ◽  
Danielle R. Ellis ◽  
Xinyuan Huang ◽  
Gareth J. Norton ◽  
Andrew A. Meharg ◽  
...  
Keyword(s):  
Higher Plants ◽  
Culture Media ◽  
Sequence Similarity ◽  
Pteris Vittata ◽  
Department Of Energy ◽  
High Sequence Similarity ◽  
Design Data ◽  
E Coli ◽  
Arsenate Resistance ◽  
Arsenic Hyperaccumulation

AbstractAlthough arsenic is generally a toxic compound, there are a number of ferns in the genusPteristhat can tolerate large concentrations of this metalloid. In order to probe the mechanisms of arsenic hyperaccumulation, we expressed aPteris vittatacDNA library in anEscherichia coli ΔarsC(arsenate reductase) mutant. We obtained three independent clones that conferred increased arsenate resistance on this host. DNA sequence analysis indicated that these clones specify proteins that have a high sequence similarity to the phi class of glutathione-S-transferases (GSTs) of higher plants. Detoxification of arsenate by theP. vittataGSTs inE. coliwas abrogated by agshAmutation, which blocks the synthesis of glutathione, and by agormutation, which inactivates glutathione reductase. Direct measurements of the speciation of arsenic in culture media of theE. colistrains expressing theP. vittataGSTs indicated that these proteins facilitate the reduction of arsenate. Our observations suggest that the detoxification of arsenate by theP. vittataGSTs involves reduction of As(V) to As(III) by glutathione or a related sulfhydro compound.FundingThe authors acknowledge support from the Indiana 21st Century Research and technology Fund (912010479) to DES and LNC, from the U.S. Department of Energy (grant no. DE-FG02-03ER63622) to DES, and from BBSRC-DFID (grant no. BBF0041841GJN) to AAM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. There are no financial, personal, or professional interests that could be construed to have influenced the paper.

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