scholarly journals Discovery of UPSTREAM OF FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) in Gladiolus ×hybridus, G. dalenii

2021 ◽  
Author(s):  
Jaser Aljaser ◽  
Neil O Anderson ◽  
Andrzej Noyszewski
Keyword(s):  
Amino Acid ◽  
Gene Sequence ◽  
Amino Acid Identity ◽  
Musa Acuminata ◽  
Ananas Comosus ◽  
Flowering Locus C ◽  
Acid Identity ◽  
Gladiolus Hybridus ◽  
Flowering Pathway ◽  
Flowering Locus

Gladiolus is a geophytic floricultural crop, cultivated for cut flower and garden ornamental uses. Ornamental geophytes such as gladiolus, lily, tulip and daffodil are examples of floral crops that are currently being investigated to understand the flowering pathway. While the environmental and hormonal factors leading to flowering are established in Arabidopsis. However, the lack of genetic regulation is poorly understood. Thus, the importance of such an ornamental crop that relies on flowers (flowering) for economic purposes encourages researchers to discover the flowering genes to breed vigorous flowering cultivars. The understanding of the flowering mechanisms in the flowering pathway is also paramount. Herein we show the discovery of UPSTREAM OF FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) genes in Gladiolus ×hybridus and G. dalenii. The UFC gene is adjacent to FLOWERING LOCUS C (FLC) which is a floral repressor in many temperate species. FLX gene upregulates FRIGIDA (FRI) which upregulates FLC expression. The discovery of both genes is a step forward in finding the FLC gene in gladiolus, provided they are linked. Seventeen gladiolus genotypes, consisting of early flowering and commercial cultivars, have the UFC gene, consisting of four exons in two allelic forms. The UFC gene sequenced when translated into amino acid sequence and set in pair-alignment to other species, has up to 57% in amino acid identity to Musa acuminata. The UFC protein ranges in identity with pair-alignment to other species, reaching up to 57% in amino acid identity to Musa acuminata. The FLX gene in gladiolus has 3/5 (60%) exons in relative to Ananas comosus, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the three exons shows up over all ~65% identity of FLX to Ananas comosus. The UFC protein consists of a conserved domain, DUF966, which is higher in identity and pair-alignment, with up to 86% identity in Elaeis guineensis. The discovered FLX gene in gladiolus has 3/5 (60%) exons, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the 3 exons shows up to ~65% of identity of FLX to Ananas comosus. These discovered two genes in gladiolus provide insight to further our understanding of the flowering and vernalization response in ornamental geophytes.

scholarly journals Discovery of UPSTREAM of FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) in Gladiolus ×Hybridus, G. Dalenii

2021 ◽  
Author(s):  
Jaser A. Aljaser ◽  
Neil Anderson ◽  
Andrzej Noyszewski
Keyword(s):  
Amino Acid ◽  
Genetic Research ◽  
Amino Acid Identity ◽  
Ananas Comosus ◽  
Flowering Locus C ◽  
Acid Identity ◽  
Flowering Genes ◽  
Gladiolus Hybridus ◽  
Flowering Pathway ◽  
Flowering Locus

Abstract Background. Gladiolus is a geophytic floricultural crop cultivated for cut flower and garden ornamental uses. Monocotyledonous flower crops have few, if any, flowering genes identified. Ornamental geophytes such as gladiolus, lily, tulip and daffodil are examples of floral crops that are currently being investigated to understand the flowering pathway. While the flower genes and environmental / hormonal factors leading to flowering are established in Arabidopsis, the lack of identified flowering genes in economically important ornamental geophytic crops, such as gladiolus, is critical to further genetic research. Thus, the importance of such an ornamental crop that relies on flowers (flowering) for economic purposes encourages researchers to discover the flowering genes to breed vigorous, flowering cultivars. The understanding of the flowering mechanisms in the flowering pathway is also of paramount importance. Results. Herein we show the discovery of UPSTREAM OF FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) genes in Gladiolus ×hybridus and G. dalenii. The UFC gene is adjacent to FLOWERING LOCUS C (FLC) which is a floral repressor in many temperate species. The FLX gene upregulates FRIGIDA (FRI) which upregulates FLC expression. Discovery of both genes is a step forward in finding the FLC gene in gladiolus, provided they are linked. Seventeen gladiolus genotypes, consisting of early flowering and commercial cultivars, were discovered to possess the UFC gene, consisting of four exons in two allelic forms. The sequenced UFC gene, when translated into its amino acid sequence and set in pair-alignment to other species, has up to 57% in amino acid identity to Musa acuminata. The UFC protein ranges in identity with pair-alignment to other monocot species, also with 57% amino acid identity to M. acuminata. The FLX gene in gladiolus has 3/5 (60%) exons in common relative to Ananas comosus, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the three exons shows an overall ~65% identity of FLX to A. comosus. The UFC protein consists of a conserved domain, DUF966, which is higher in identity (86%) and pair-alignment with Elaeis guineensis. Conclusions. The two newly-discovered genes in gladiolus, UFC and FLX, provide insight to further our understanding of the flowering mechanism, flowering pathway genes, and vernalization response in ornamental geophytes. This knowledge will be valuable for gladiolus breeders and geneticists to finding the FLC gene, identify segregating seedlings for both UFC and FLX, and aid in marker assisted selection for flowering gene expression.

Trypanosoma cruziexoantigen is a member of a 160 kDa gene family

Parasitology ◽  
1995 ◽  
Vol 110 (1) ◽  
pp. 61-69 ◽  
Author(s):  
E. E. Jazin ◽  
E. J. Bontempi ◽  
D. O. Sanchez ◽  
L. Åslund ◽  
J. Henriksson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
Gene Sequence ◽  
Surface Antigens ◽  
Amino Acid Identity ◽  
Amino Acid Motif ◽  
Chronic Stage ◽  
Acid Identity ◽  
Trypomastigote Form ◽  
Related Group

During the chronic stage of Chagas disease a 160 kDa antigen appears in the blood of patients and remains detectable many years after the onset of the disease. This antigen is secreted by the trypomastigote form of the parasite while it is undetectable in the epimastigote form. We report here that the chronic 160 kDa exoantigen is encoded by a gene family (CEA 160 family). We describe the cloning and partial nucleotide sequence of a gene (CEA 160–1) belonging to the CEA160 family. Comparison of the gene sequence with other sequences present in the databases revealed homologies with severalTrypanosoma cruzisurface antigens. Highest amino acid identity (59%) was with members of a family containing epitopes that mimic nervous tissues (Van Voorhiset al.1993). Another related group (18–22% amino acid identity) comprises proteins of 85 or 160 kDa sharing an amino acid motif that is conserved among bacterial neuraminidases (Foutset al.1991; Pollevicket al.1991; Kahnet al.1991; Takle & Cross, 1991; Francoet al.1993). The amino acid identities with the different antigens were not homogeneously distributed. Regions of higher identity (40–60%) were grouped in the central region of each protein.

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

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.

Characterization and Induction of Two Cytochrome P450 Genes, CYP6AE28 and CYP6AE30, in Cnaphalocrocis medinalis: Possible Involvement in Metabolism of Rice Allelochemicals

2010 ◽  
Vol 65 (11-12) ◽  
pp. 719-725 ◽  
Author(s):  
Xiaoli Liu ◽  
Jun Chen ◽  
Zhifan Yang
Keyword(s):  
Amino Acid ◽  
Rice Variety ◽  
Amino Acid Identity ◽  
Cnaphalocrocis Medinalis ◽  
Amino Acid Residues ◽  
Acid Identity ◽  
Rice Leaf Folder ◽  
Cytochrome P450 Genes ◽  
Molecular Masses ◽  
Lepidoptera Pyralidae

Two cDNAs specific for P450 genes, CYP6AE28 and CYP6AE30, have been isolated from the rice leaf folder Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae). Both cDNApredicted proteins have 504 amino acid residues in length, but with molecular masses of 60177 Dalton for CYP6AE28 and 60020 Dalton for CYP6AE30, and theoretical pI values of 8.49 for CYP6AE28 and 8.56 for CYP6AE30, respectively. Both putative proteins contain the conserved structural and functional domains characteristic of all CYP6 members. CYP6AE28 and CYP6AE30 show 52% amino acid identity to each other; both of them have 49 - 56% identities with CYP6AE1, Cyp6ae12, and CYP6AE14. Phylogenetic analysis showed that the two P450s are grouped in the lineage containing some of the CYP6AE members, CYP6B P450s and CYP321A1. The transcripts of CYP6AE28 and CYP6AE30 were found to be induced in response to TKM-6, a rice variety with high resistance to C. medinalis. The results suggest that the two P450s may play important roles in adaptation to the host plant rice. This is the first report of P450 genes cloned in C. medinalis

scholarly journals PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Laurent Poirel ◽  
Mattia Palmieri ◽  
Michael Brilhante ◽  
Amandine Masseron ◽  
Vincent Perreten ◽  
...  
Keyword(s):  
Amino Acid ◽  
Pseudomonas Fluorescens ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Chicken Meat ◽  
The Novel ◽  
Content Type ◽  
Acid Identity ◽  
Carbapenem Resistant ◽  
Encoding Genes

ABSTRACT A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola. The blaPFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.

Comparative sequence analysis of morbillivirus receptors and its implication in host range expansion

2019 ◽  
Vol 65 (11) ◽  
pp. 783-794
Author(s):  
Ajay Kumar Yadav ◽  
Kaushal Kishor Rajak ◽  
Mukesh Bhatt ◽  
Ashok Kumar ◽  
Soumendu Chakravarti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Host Range ◽  
Range Expansion ◽  
Small Ruminants ◽  
Amino Acid Identity ◽  
Amino Acid Residues ◽  
Binding Region ◽  
Acid Identity ◽  
Host Range Expansion ◽  
High Amino Acid

SLAM (CD150) and nectin-4 are the major morbillivirus receptors responsible for virus pathogenesis and host range expansion. Recently, morbillivirus infections have been reported in unnatural hosts, including endangered species, posing a threat to their conservation. To understand the host range expansion of morbilliviruses, we generated the full-length sequences of morbillivirus receptors (goat, sheep, and dog SLAM, and goat nectin-4) and tried to correlate their role in determining host tropism. A high level of amino acid identity was observed between the sequences of related species, and phylogenetic reconstruction showed that the receptor sequences of carnivores, marine mammals, and small ruminants grouped separately. Analysis of the ligand binding region (V region; amino acid residues 52–136) of SLAM revealed high amino acid identity between small ruminants and bovine SLAMs. Comparison of canine SLAM with ruminants and non-canids SLAM revealed appreciable changes, including charge alterations. Significant differences between feline SLAM and canine SLAM have been reported. The binding motifs of nectin-4 genes (FPAG motif and amino acid residues 60, 62, and 63) were found to be conserved in sheep, goat, and dog. The differences reported in the binding region may be responsible for the level of susceptibility or resistance of a species to a particular morbillivirus.

scholarly journals Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Sara Kleindienst ◽  
Karuna Chourey ◽  
Gao Chen ◽  
Robert W. Murdoch ◽  
Steven A. Higgins ◽  
...  
Keyword(s):  
Amino Acid ◽  
Reductive Dechlorination ◽  
Bond Cleavage ◽  
Amino Acid Identity ◽  
Methyl Group ◽  
Acid Identity ◽  
Group Transfer ◽  
Degrading Bacterium ◽  
Chlorine Bond ◽  
Methyl Group Transfer

ABSTRACTDichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader “CandidatusDichloromethanomonas elyunquensis” strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM’s genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase ofDehalococcoides mccartyistrain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase ofDehalobactersp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCENaturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader “CandidatusDichloromethanomonas elyunquensis” strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacteriumDehalobacterium formicoaceticumand “CandidatusDichloromethanomonas elyunquensis” strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.

scholarly journals Genome of Lumpy Skin Disease Virus

2001 ◽  
Vol 75 (15) ◽  
pp. 7122-7130 ◽  
Author(s):  
E. R. Tulman ◽  
C. L. Afonso ◽  
Z. Lu ◽  
L. Zsak ◽  
G. F. Kutish ◽  
...  
Keyword(s):  
Amino Acid ◽  
Host Range ◽  
Disease Virus ◽  
Skin Disease ◽  
Amino Acid Identity ◽  
Lower Percentage ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus ◽  
Acid Identity ◽  
Viral Virulence

ABSTRACT Lumpy skin disease virus (LSDV), a member of the capripoxvirus genus of the Poxviridae, is the etiologic agent of an important disease of cattle in Africa. Here we report the genomic sequence of LSDV. The 151-kbp LSDV genome consists of a central coding region bounded by identical 2.4 kbp-inverted terminal repeats and contains 156 putative genes. Comparison of LSDV with chordopoxviruses of other genera reveals 146 conserved genes which encode proteins involved in transcription and mRNA biogenesis, nucleotide metabolism, DNA replication, protein processing, virion structure and assembly, and viral virulence and host range. In the central genomic region, LSDV genes share a high degree of colinearity and amino acid identity (average of 65%) with genes of other known mammalian poxviruses, particularly suipoxvirus, yatapoxvirus, and leporipoxviruses. In the terminal regions, colinearity is disrupted and poxvirus homologues are either absent or share a lower percentage of amino acid identity (average of 43%). Most of these differences involve genes and gene families with likely functions involving viral virulence and host range. Although LSDV resembles leporipoxviruses in gene content and organization, it also contains homologues of interleukin-10 (IL-10), IL-1 binding proteins, G protein-coupled CC chemokine receptor, and epidermal growth factor-like protein which are found in other poxvirus genera. These data show that although LSDV is closely related to other members of the Chordopoxvirinae, it contains a unique complement of genes responsible for viral host range and virulence.

scholarly journals 330 Identification and genomic characterization of two novel strains of Prevotella albensis as starch utilizers in the rumen of beef cows

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 132-132
Author(s):  
Venkata Bandarupalli ◽  
Benoit St- Pierre
Keyword(s):  
Amino Acid ◽  
Lactate Dehydrogenase ◽  
Gene Annotation ◽  
Rumen Fluid ◽  
Operational Taxonomic Unit ◽  
Beef Cows ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Acid Identity ◽  
Different Strains

Abstract In cattle fed concentrate diets, rumen amylolytic bacteria digest starch into glucose, which is metabolized for growth. Since metagenomics studies have revealed that uncharacterized ruminal amylolytic bacteria far outnumber known starch utilizers, we have been pursing the identification of novel ruminal amylolytic bacteria. The same Operational Taxonomic Unit (OTU) was enriched independently from the rumen fluid of two beef cows after culturing with starch. Since this identification was performed using the V1–V3 region of the 16S rRNA gene, a metagenomic analysis was conducted to determine whether this OTU represented the same strain or different strains of the same species. A total of 9.25 and 9.16 million sequence reads were respectively generated from a select enriched starch culture from each cow, which had a relative abundance for this OTU of 67.9% and 74.0%, respectively. Contigs were assembled using the publicly available software ABySS, with contigs of at least 2kb in length used for further analysis. Of the enzymes identified by gene annotation of these contigs (using a combination of the online tools RAST and BLASTp), the presence of genes encoding α-amylase and lactate dehydrogenase enzymes further supported this OTU as corresponding to a starch utilizer. The alpha-amylase isoforms from the two rumens differed in amino acid length (538 vs 625) and sequence, with their respective closest affiliation being to an uncultured species of Lachnospiraceae (51% amino acid identity) and to Prevotella albensis (95% amino acid identity), respectively. The lactate dehydrogenase isoforms were also found to be different in length (348 aa vs 335 aa) and sequence (100% amino acid identity to Lactobacillus mucosae and 99% to an uncultured species of the genus Olsonella, respectively). These and other gene comparisons together suggest that two strains of the same starch-utilizing OTU have been identified in the rumen of beef cows.

Sign in / Sign up

Export Citation Format

Share Document