scholarly journals Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245600
Author(s):  
Zezhen Du ◽  
Suren Deng ◽  
Zixuan Wu ◽  
Chuang Wang
Keyword(s):  
Bioinformatics Analysis ◽  
Sequence Similarity ◽  
Motif Analysis ◽  
Systematic Classification ◽  
Diverse Range ◽  
Haloacid Dehalogenase ◽  
Genome Wide ◽  
Pi Starvation ◽  
Had Superfamily ◽  
Pi Stress

The HAD superfamily is named after the halogenated acid dehalogenase found in bacteria, which hydrolyses a diverse range of organic phosphate substrates. Although certain studies have shown the involvement of HAD genes in Pi starvation responses, systematic classification and bioinformatics analysis of the HAD superfamily in plants is lacking. In this study, 41 and 40 HAD genes were identified by genomic searching in rice and Arabidopsis, respectively. According to sequence similarity, these proteins are divided into three major groups and seven subgroups. Conserved motif analysis indicates that the majority of the identified HAD proteins contain phosphatase domains. A further structural analysis showed that HAD proteins have four conserved motifs and specified cap domains. Fewer HAD genes show collinearity relationships in both rice and Arabidopsis, which is consistent with the large variations in the HAD genes. Among the 41 HAD genes of rice, the promoters of 28 genes contain Pi-responsive cis-elements. Mining of transcriptome data and qRT-PCR results showed that at least the expression of 17 HAD genes was induced by Pi starvation in shoots or roots. These HAD proteins are predicted to be involved in intracellular or extracellular Po recycling under Pi stress conditions in plants.

A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity

2019 ◽  
Vol 75 (8) ◽  
pp. 743-752
Author(s):  
Petra Havlickova ◽  
Vitezslav Brinsa ◽  
Jiri Brynda ◽  
Petr Pachl ◽  
Tatyana Prudnikova ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Thermophilic Enzyme ◽  
Haloacid Dehalogenase ◽  
Computational Docking ◽  
Cell Parameters ◽  
X Ray Crystallography ◽  
The Family ◽  
Had Superfamily ◽  
Characteristic Features ◽  
Hydrolysis Of

The haloacid dehalogenase (HAD) superfamily is one of the largest known groups of enzymes and the majority of its members catalyze the hydrolysis of phosphoric acid monoesters into a phosphate ion and an alcohol. Despite the fact that sequence similarity between HAD phosphatases is generally very low, the members of the family possess some characteristic features, such as a Rossmann-like fold, HAD signature motifs or the requirement for Mg2+ ion as an obligatory cofactor. This study focuses on a new hypothetical HAD phosphatase from Thermococcus thioreducens. The protein crystallized in space group P21212, with unit-cell parameters a = 66.3, b = 117.0, c = 33.8 Å, and the crystals contained one molecule in the asymmetric unit. The protein structure was determined by X-ray crystallography and was refined to 1.75 Å resolution. The structure revealed a putative active site common to all HAD members. Computational docking into the crystal structure was used to propose substrates of the enzyme. The activity of this thermophilic enzyme towards several of the selected substrates was confirmed at temperatures of 37°C as well as 60°C.

scholarly journals Genome-wide identification and expression analysis of Raffinose synthetase family in cotton

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruifeng Cui ◽  
Xiaoge Wang ◽  
Waqar Afzal Malik ◽  
Xuke Lu ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Plant Leaves ◽  
Motif Analysis ◽  
Expression Levels ◽  
Genome Wide ◽  
Salt And Drought Stress ◽  
Key Genes ◽  
Stress Gene

Abstract Background The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resistance to abiotic stress in plants, specifically in the Gossypium species. Results In this study, we identified 74 RAFS genes from G. hirsutum, G. barbadense, G. arboreum and G. raimondii by using a series of bioinformatic methods. Phylogenetic analysis showed that the RAFS gene family in the four Gossypium species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the RAFS gene structure was relatively conservative. Promoter analysis for cis-regulatory elements showed that some RAFS genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of RAFS under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of RAFS genes in Gossypium species. Transcriptome analysis suggested that RAFS genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that GhRFS2A-GhRFS6A, GhRFS6D, GhRFS7D and GhRFS8A-GhRFS11A were key genes, with high expression levels under salt, drought, cold and heat stress. Conclusion The findings may provide insights into the evolutionary relationships and expression patterns of RAFS genes in Gossypium species and a theoretical basis for the identification of stress resistance materials in cotton.

scholarly journals Diversity of GPI-anchored fungal adhesins

2020 ◽  
Vol 401 (12) ◽  
pp. 1389-1405
Author(s):  
Lars-Oliver Essen ◽  
Marian Samuel Vogt ◽  
Hans-Ulrich Mösch
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Bioinformatics Analysis ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Growth Forms ◽  
Similarity Networks ◽  
Fungal Adhesins ◽  
Sequence Similarity Networks ◽  
Successful Colonization

AbstractSelective adhesion of fungal cells to one another and to foreign surfaces is fundamental for the development of multicellular growth forms and the successful colonization of substrates and host organisms. Accordingly, fungi possess diverse cell wall-associated adhesins, mostly large glycoproteins, which present N-terminal adhesion domains at the cell surface for ligand recognition and binding. In order to function as robust adhesins, these glycoproteins must be covalently linkedto the cell wall via C-terminal glycosylphosphatidylinositol (GPI) anchors by transglycosylation. In this review, we summarize the current knowledge on the structural and functional diversity of so far characterized protein families of adhesion domains and set it into a broad context by an in-depth bioinformatics analysis using sequence similarity networks. In addition, we discuss possible mechanisms for the membrane-to-cell wall transfer of fungal adhesins by membrane-anchored Dfg5 transglycosidases.

scholarly journals Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

2021 ◽  
Author(s):  
Richard G Dorrell ◽  
Alan Kuo ◽  
Zoltan Fussy ◽  
Elisabeth H Richardson ◽  
Asaf Salamov ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Algal Species ◽  
Gene Families ◽  
The Arctic ◽  
Arctic Water ◽  
Diverse Range ◽  
Binding Domains ◽  
Ice Binding ◽  
Ice Conditions

The Arctic Ocean is being impacted by warming temperatures, increasing freshwater and highly variable ice conditions. The microalgal communities underpinning Arctic marine food webs, once thought to be dominated by diatoms, include a phylogenetically diverse range of small algal species, whose biology remains poorly understood. Here, we present genome sequences of a cryptomonad, a haptophyte, a chrysophyte, and a pelagophyte, isolated from the Arctic water column and ice. Comparing protein family distributions and sequence similarity across a densely-sampled set of algal genomes and transcriptomes, we note striking convergences in the biology of distantly related small Arctic algae, compared to non-Arctic relatives; although this convergence is largely exclusive of Arctic diatoms. Using high-throughput phylogenetic approaches, incorporating environmental sequence data from Tara Oceans, we demonstrate that this convergence was partly explained by horizontal gene transfers (HGT) between Arctic species, in over at least 30 other discrete gene families, and most notably in ice-binding domains (IBD). These Arctic-specific genes have been repeatedly transferred between Arctic algae, and are independent of equivalent HGTs in the Antarctic Southern Ocean. Our data provide insights into the specialised Arctic marine microbiome, and underlines the role of geographically-limited HGT as a driver of environmental adaptation in eukaryotic algae.

scholarly journals Genes and Enzymes of Azetidine-2-Carboxylate Metabolism: Detoxification and Assimilation of an Antibiotic

2008 ◽  
Vol 190 (14) ◽  
pp. 4859-4864 ◽  
Author(s):  
Carol Gross ◽  
Roderick Felsheim ◽  
Lawrence P. Wackett
Keyword(s):  
Specific Activity ◽  
Periplasmic Fraction ◽  
Gene Encoding ◽  
Haloacid Dehalogenase ◽  
Protein Mass ◽  
Protein Mass Spectrometry ◽  
Chaperone Protein ◽  
Marker Proteins ◽  
Had Superfamily ◽  
Cell Fractions

ABSTRACT l-(−)-Azetidine-2-carboxylate (AC) is a toxic, natural product analog of l-proline. This study revealed the genes and biochemical strategy employed by Pseudomonas sp. strain A2C to detoxify and assimilate AC as its sole nitrogen source. The gene region from Pseudomonas sp. strain A2C required for detoxification was cloned into Escherichia coli and sequenced. The 7.0-kb region contained eight identifiable genes. Four encoded putative transporters or permeases for γ-amino acids or drugs. Another gene encoded a homolog of 2-haloacid dehalogenase (HAD). The encoded protein, denoted l-azetidine-2-carboxylate hydrolase (AC hydrolase), was highly overexpressed by subcloning. The AC hydrolase was shown to catalyze azetidine ring opening with the production of 2-hydroxy-4-aminobutyrate. AC hydrolase was further demonstrated to be a new hydrolytic member of the HAD superfamily by showing loss of activity upon changing aspartate-12, the conserved active site nucleophile in this family, to an alanine residue. The presence of a gene encoding a potential export chaperone protein, CsaA, adjacent to the AC hydrolase gene suggested that AC hydrolase might be found inside the periplasm in the native Pseudomonas strain. Periplasmic and cytoplasmic cell fractions from Pseudomonas sp. strain A2C were prepared. A higher specific activity for AC hydrolysis was found in the periplasmic fraction. Protein mass spectrometry further identified AC hydrolase and known periplasmic marker proteins in the periplasmic fraction. A model was proposed in which AC is hydrolyzed in the periplasm and the product of that reaction is transported into and further metabolized in the cytoplasm.

scholarly journals Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qing-Lan Li ◽  
Xiang Lin ◽  
Ya-Li Yu ◽  
Lin Chen ◽  
Qi-Xin Hu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Colorectal Cancer Patient ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Motif Analysis ◽  
Single Nucleotide ◽  
Super Enhancer ◽  
Genome Wide ◽  
Functional Factors ◽  
Cancer Tissues

AbstractColorectal cancer is one of the most common cancers in the world. Although genomic mutations and single nucleotide polymorphisms have been extensively studied, the epigenomic status in colorectal cancer patient tissues remains elusive. Here, together with genomic and transcriptomic analysis, we use ChIP-Seq to profile active enhancers at the genome wide level in colorectal cancer paired patient tissues (tumor and adjacent tissues from the same patients). In total, we sequence 73 pairs of colorectal cancer tissues and generate 147 H3K27ac ChIP-Seq, 144 RNA-Seq, 147 whole genome sequencing and 86 H3K4me3 ChIP-Seq samples. Our analysis identifies 5590 gain and 1100 lost variant enhancer loci in colorectal cancer, and 334 gain and 121 lost variant super enhancer loci. Multiple key transcription factors in colorectal cancer are predicted with motif analysis and core regulatory circuitry analysis. Further experiments verify the function of the super enhancers governing PHF19 and TBC1D16 in regulating colorectal cancer tumorigenesis, and KLF3 is identified as an oncogenic transcription factor in colorectal cancer. Taken together, our work provides an important epigenomic resource and functional factors for epigenetic studies in colorectal cancer.

The agent associated with blue dwarf disease in wheat represents a new phytoplasma taxon, ‘Candidatus Phytoplasma tritici’

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Yan Zhao ◽  
Wei Wei ◽  
Robert E. Davis ◽  
Ing-Ming Lee ◽  
Kristi D. Bottner-Parker
Keyword(s):  
Reference Strain ◽  
Sequence Similarity ◽  
Rrna Genes ◽  
Molecular Characteristics ◽  
Plant Host ◽  
Genome Wide ◽  
Significant Divergence ◽  
Pr China ◽  
Identity Score ◽  
Dwarf Disease

Wheat blue dwarf (WBD) is one of the most economically damaging cereal crop diseases in northwestern PR China. The agent associated with the WBD disease is a phytoplasma affiliated with the aster yellows (AY) group, subgroup C (16SrI-C). Since phytoplasma strains within the AY group are ecologically and genetically diverse, it has been conceived that the AY phytoplasma group may consist of more than one species. This communication presents evidence to demonstrate that, while each of the two 16 rRNA genes of the WBD phytoplasma shares >97.5 % sequence similarity with that of the ‘Candidatus Phytoplasma asteris’ reference strain, the WBD phytoplasma clearly represents an ecologically separated lineage: the WBD phytoplasma not only has its unique transmitting vector (Psammotettix striatus) but also elicits a distinctive symptom in its predominant plant host (wheat). In addition, the WBD phytoplasma possesses molecular characteristics that further manifest its significant divergence from ‘Ca. P. asteris’. Such molecular characteristics include lineage-specific antigenic membrane proteins and a lower than 95 % genome-wide average nucleotide identity score with ‘Ca. P. asteris’. These ecological, molecular and genomic evidences justify the recognition of the WBD phytoplasma as a novel taxon, ‘Candidatus Phytoplasma tritici’.

Lentzea tibetensis sp. nov., a novel Actinobacterium with antimicrobial activity isolated from soil of the Qinghai–Tibet Plateau

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Jiao Huang ◽  
Ying Huang
Keyword(s):  
Antimicrobial Activity ◽  
Type Species ◽  
Sequence Similarity ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Pr China ◽  
Qinghai Tibet Plateau

A novel filamentous Actinobacterium, designated strain FXJ1.1311T, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and Fusarium oxysporum. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311T belonged to the genus Lentzea and showed the highest sequence similarity to Lentzea guizhouensis DHS C013T (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea . The genome-wide average nucleotide identity between strain FXJ1.1311T and L. guizhouensis DHS C013T as well as other Lentzea type strains was <82.2 %. Strain FXJ1.1311T also formed a monophyletic line distinct from the known Lentzea species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from L. guizhouensis . Based on the evidence presented here, strain FXJ1.1311T represents a novel species of the genus Lentzea , for which the name Lentzea tibetensis sp. nov. is proposed. The type strain is FXJ1.1311T (=CGMCC 4.7383T=DSM 104975T).

scholarly journals QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Mohamed El-Soda ◽  
Charles Neris Moreira ◽  
Nakai Goredema-Matongera ◽  
Diaan Jamar ◽  
Maarten Koornneef ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Candidate Genes ◽  
Long Distance ◽  
Gene Encoding ◽  
Significant Treatment ◽  
P Deficiency ◽  
Sulphate Concentration ◽  
Genome Wide ◽  
Pi Starvation ◽  
Phosphatase 2A

Abstract Background Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability. Results Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus. Conclusion We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .

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