In silico/computational analysis of mevalonate pyrophosphate decarboxylase gene families in Campanulids

Abstract Mevalonate pyrophosphate decarboxylase (MPD) is a key enzyme in terpenoid biosynthesis. MPD plays an important role in the upstream regulation of secondary plant metabolism. However, studies on the MPD gene are relatively very few despite its importance in plant metabolism. Currently, no systematic analysis has been conducted on the MPD gene in plants under the order Apiales, which comprises important medicinal plants such as Panax ginseng and Panax notoginseng. This study sought to explore the structural characteristics of the MPD gene and the effect of adaptive evolution on the gene by comparing and analyzing MPD gene sequences of different campanulids species. For that, phylogenetic and adaptive evolution analyses were carried out using sequences for 11 Campanulids species. MPD sequence characteristics of each species were then analyzed, and the collinearity analysis of the genes was performed. As a result, a total of 21 MPD proteins were identified in 11 Campanulids species through BLAST analysis. Phylogenetic analysis, physical and chemical properties prediction, gene family analysis, and gene structure prediction showed that the MPD gene has undergone purifying selection and exhibited highly conserved structure. Analysis of physicochemical properties further showed that the MPD protein was a hydrophilic protein without a transmembrane region. Moreover, collinearity analysis in Apiales showed that MPD gene on chromosome 2 of D. carota and chromosome 1 of C. sativum were collinear. The findings showed that MPD gene is highly conserved. This may be a common characteristic of all essential enzymes in the biosynthesis pathways of medicinal plants. Notably, MPD gene is significantly affected by environmental factors which subsequently modulate its expression. The current study’s findings provide a basis for follow-up studies on MPD gene and key enzymes in other medicinal plants.

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Exhaustive exploration of the conformational landscape of small cyclic peptides using a robotics approach

10.1101/338483 ◽

2018 ◽

Author(s):

Maud Jusot ◽

Dirk Stratmann ◽

Marc Vaisset ◽

Jacques Chomilier ◽

Juan Cortés

Keyword(s):

Structure Prediction ◽

Cyclic Peptides ◽

Structural Characteristics ◽

Chemical Properties ◽

Computational Design ◽

Complete Characterization ◽

Conformational Space ◽

Drug Candidate ◽

Implicit Solvent ◽

Dynamics Simulations

Small cyclic peptides represent a promising class of therapeutic molecules with unique chemical properties. However, the poor knowledge of their structural characteristics makes their computational design and structure prediction a real challenge. In order to better describe their conformational space, we developed a method, named EGSCyP, for the exhaustive exploration of the energy landscape of small head-to-tail cyclic peptides. The method can be summarized by (i) a global exploration of the conformational space based on a mechanistic representation of the peptide and the use of robotics-based algorithms to deal with the closure constraint, (ii) an all-atom refinement of the obtained conformations. EGSCyP can handle D-form residues and N-methylations. Two strategies for the side-chains placement were implemented and compared. To validate our approach, we applied it to a set of three variants of cyclic RGDFV pentapeptides, including the drug candidate Cilengitide. A comparative analysis was made with respect to replica exchange molecular dynamics simulations in implicit solvent. It results that the EGSCyP method provides a very complete characterization of the conformational space of small cyclic pentapeptides.

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Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽

10.1093/genetics/142.3.1021 ◽

1996 ◽

Vol 142 (3) ◽

pp. 1021-1031 ◽

Cited By ~ 3

Author(s):

Jianping Hu ◽

Beth Anderson ◽

Susan R Wessler

Keyword(s):

Gene Family ◽

Gene Families ◽

Chromosome 1 ◽

R Gene ◽

R Genes ◽

Helix Loop Helix ◽

Isolation And Characterization ◽

Undetermined Function ◽

Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

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Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus)

BMC Genomics ◽

10.1186/s12864-017-3983-0 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 7

Author(s):

Guangshuai Liu ◽

Honghai Zhang ◽

Guolei Sun ◽

Chao Zhao ◽

Shuai Shang ◽

...

Keyword(s):

Adaptive Evolution ◽

Canis Lupus ◽

Peripheral Blood ◽

Gene Families ◽

Mhc I ◽

Blood Transcriptome

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ETHNOBOTANICAL STUDY OF MEDICINAL PLANTS USED IN TRADITIONAL MEDICINE IN THE PROVINCE OF SIDI KACEM, MOROCCO

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2017.v10i1.14326 ◽

2016 ◽

Vol 10 (1) ◽

pp. 121 ◽

Cited By ~ 1

Author(s):

Fouzia Rhazi Filali ◽

Fatima-zahra Ennacirie ◽

Abdelilah Rahou

Keyword(s):

Medicinal Plants ◽

Traditional Medicine ◽

Chemical Properties ◽

Ethnobotanical Study ◽

Ethnobotanical Survey ◽

Cutaneous Infections ◽

Traditional Therapy

ABSTRACTAn ethnobotanical study of medicinal plants was carried in the province of Sidi Kacem (Morocco), whose objective is to make an inventory of medicinalplants used in traditional therapy against respiratory, digestive, and cutaneous infections; also to describe their mode of use practiced by the localpopulation. The tool of the study was a questionnaire completed by 200 citizens of four investigated areas, determined by the stratified samplingtechniques, 40% practiced phytotherapy. The survey consists of a section on the informant, and another is interested in plants used by the population.The analysis of information has established a catalog of 73 species identified with their use of frequencies, partly used and the method of preparation.They belong to 39 families; the most dominant are Lamiaceae, Apiaceae, and Asteraceae. The leaves are the most used part in decoction to treat thethree types of infection mentioned above. These results allow us to create a database about this region’s plants characteristic. They will be useful toestablish further studies on their chemical properties and biological activities.Keywords: Province of Sidi Kacem (Morocco), Phytotherapy, Ethnobotanical survey, Infections, Catalogue of plants.

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Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

10.1101/2020.07.14.20153395 ◽

2020 ◽

Author(s):

Catherine Stein ◽

Penelope Bencheck ◽

Jacquelaine Bartlett ◽

Robert P Igo ◽

Rafal S Sobota ◽

...

Keyword(s):

Genome Wide Association Study ◽

Sub Saharan Africa ◽

Chromosome 1 ◽

Chromosome 2 ◽

Chromosome 5 ◽

Epigenetic Marks ◽

Genome Wide ◽

A Genome ◽

Immunodeficiency Virus ◽

Sub Saharan

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.

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Zoomqa: Residue-Level Single-Model QA Support Vector Machine Utilizing Sequential and 3D Structural Features

10.1101/2021.01.28.428680 ◽

2021 ◽

Author(s):

Kyle Hippe ◽

Cade Lilley ◽

William Berkenpas ◽

Kiyomi Kishaba ◽

Renzhi Cao

Keyword(s):

Protein Complex ◽

Structure Prediction ◽

Tertiary Structure ◽

State Of The Art ◽

Chemical Properties ◽

Structural Features ◽

Residue Level ◽

Support Vector ◽

Single Model

ABSTRACTMotivationThe Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. When predictions are made for proteins of which we do not know the native structure, we run into an issue to tell how good a tertiary structure prediction is, especially the protein binding regions, which are useful for drug discovery. Currently, most methods only evaluate the overall quality of a protein decoy, and few can work on residue level and protein complex. Here we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure / complex prediction at residue level. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius r of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grades their placement within the protein as a whole. Moreover, ZoomQA can evaluate the quality of protein complex, which is unique.ResultsWe benchmark ZoomQA on CASP14, it outperforms other state of the art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features, and shows our method is able to match the performance of other state-of-the-art methods without the use of homology searching against database or PSSM matrix.Availabilityhttp://[email protected]

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Genome-Wide Identification of CBL-CIPK Gene Family in Honeysuckle (Lonicera japonica Thunb.) and Their Regulated Expression Under Salt Stress

Frontiers in Genetics ◽

10.3389/fgene.2021.751040 ◽

2021 ◽

Vol 12 ◽

Author(s):

Luyao Huang ◽

Zhuangzhuang Li ◽

Qingxia Fu ◽

Conglian Liang ◽

Zhenhua Liu ◽

...

Keyword(s):

Salt Stress ◽

Protein Kinases ◽

Stress Responses ◽

Structure Prediction ◽

Functional Divergence ◽

Gene Families ◽

Plant Responses ◽

Interacting Protein ◽

Protein Motifs ◽

Insight Into

In plants, calcineurin B-like proteins (CBLs) are a unique group of Ca2+ sensors that decode Ca2+ signals by activating a family of plant-specific protein kinases known as CBL-interacting protein kinases (CIPKs). CBL-CIPK gene families and their interacting complexes are involved in regulating plant responses to various environmental stimuli. To gain insight into the functional divergence of CBL-CIPK genes in honeysuckle, a total of six LjCBL and 17 LjCIPK genes were identified. The phylogenetic analysis along with the gene structure analysis divided both CBL and CBL-interacting protein kinase genes into four subgroups and validated by the distribution of conserved protein motifs. The 3-D structure prediction of proteins shown that most LjCBLs shared the same Protein Data Bank hit 1uhnA and most LjCIPKs shared the 6c9Da. Analysis of cis-acting elements and gene ontology implied that both LjCBL and LjCIPK genes could be involved in hormone signal responsiveness and stress adaptation. Protein-protein interaction prediction suggested that LjCBL4 is hypothesized to interact with LjCIPK7/9/15/16 and SOS1/NHX1. Gene expression analysis in response to salinity stress revealed that LjCBL2/4, LjCIPK1/15/17 under all treatments gradually increased over time until peak expression at 72 h. These results demonstrated the conservation of salt overly sensitive pathway genes in honeysuckle and a model of Ca2+-LjCBL4/LjSOS3-LjCIPK16/LjSOS2 module-mediated salt stress signaling in honeysuckle is proposed. This study provides insight into the characteristics of the CBL-CIPK gene families involved in honeysuckle salt stress responses, which could serve as a foundation for gene transformation technology, to obtain highly salt-tolerant medicinal plants in the context of the global reduction of cultivated land.

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Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance

10.1101/2021.12.17.473133 ◽

2021 ◽

Author(s):

Wen Feng ◽

Lei Zhou ◽

Pengju Zhao ◽

Heng Du ◽

Chenguang Diao ◽

...

Keyword(s):

Large Scale ◽

Genetic Resistance ◽

African Swine Fever ◽

Gene Families ◽

Specific Gene ◽

Chromosome 2 ◽

Sequencing Data ◽

Domestic Pig ◽

Phacochoerus Africanus ◽

Contraction And Expansion

As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understanding the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog's genome to adapt the environment. Importantly, the analysis of presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. The Combining with large scale sequencing data of 123 pigs from all over world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

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The Essential Genome of Burkholderia cenocepacia H111

Journal of Bacteriology ◽

10.1128/jb.00260-17 ◽

2017 ◽

Vol 199 (22) ◽

Cited By ~ 7

Author(s):

Steven Higgins ◽

Maria Sanchez-Contreras ◽

Stefano Gualdi ◽

Marta Pinto-Carbó ◽

Aurélien Carlier ◽

...

Keyword(s):

Minimal Medium ◽

Essential Genes ◽

Burkholderia Cenocepacia ◽

Chromosome 1 ◽

Biological Research ◽

Chromosome 2 ◽

Powerful Method ◽

Rich Medium ◽

Content Type ◽

Autonomous Growth

ABSTRACT The study of the minimum set of genes required to sustain life is a fundamental question in biological research. Recent studies on bacterial essential genes suggested that between 350 and 700 genes are essential to support autonomous bacterial cell growth. Essential genes are of interest as potential new antimicrobial drug targets; hence, our aim was to identify the essential genome of the cystic fibrosis (CF) isolate Burkholderia cenocepacia H111. Using a transposon sequencing (Tn-Seq) approach, we identified essential genes required for growth in rich medium under aerobic and microoxic conditions as well as in a defined minimal medium with citrate as a sole carbon source. Our analysis suggests that 398 genes are required for autonomous growth in rich medium, a number that represents only around 5% of the predicted genes of this bacterium. Five hundred twenty-six genes were required to support growth in minimal medium, and 434 genes were essential under microoxic conditions (0.5% O2). A comparison of these data sets identified 339 genes that represent the minimal set of essential genes required for growth under all conditions tested and can be considered the core essential genome of B. cenocepacia H111. The majority of essential genes were found to be located on chromosome 1, and few such genes were located on chromosome 2, where most of them were clustered in one region. This gene cluster is fully conserved in all Burkholderia species but is present on chromosome 1 in members of the closely related genus Ralstonia, suggesting that the transfer of these essential genes to chromosome 2 in a common ancestor contributed toward the separation of the two genera. IMPORTANCE Transposon sequencing (Tn-Seq) is a powerful method used to identify genes that are essential for autonomous growth under various conditions. In this study, we have identified a set of “core essential genes” that are required for growth under multiple conditions, and these genes represent potential antimicrobial targets. We also identified genes specifically required for growth under low-oxygen and nutrient-limited environments. We generated conditional mutants to verify the results of our Tn-Seq analysis and demonstrate that one of the identified genes was not essential per se but was an artifact of the construction of the mutant library. We also present verified examples of genes that were not truly essential but, when inactivated, showed a growth defect. These examples have identified so-far-underestimated shortcomings of this powerful method.

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Two Different Genetic Markers for High and Low Myopia

European Journal of Ophthalmology ◽

10.1177/112067219200200406 ◽

1992 ◽

Vol 2 (4) ◽

pp. 196-199 ◽

Cited By ~ 1

Author(s):

M.V. Olmedo ◽

J.I. Muñoz ◽

M.J. Rodriguez-Cid ◽

A. Carracedo ◽

F.J. Gomez-Ulla ◽

...

Keyword(s):

Acid Phosphatase ◽

High Myopia ◽

Control Population ◽

Chromosome 1 ◽

Chromosome 2 ◽

Significant Difference ◽

Hardy Weinberg Equilibrium ◽

Group 2 ◽

And Control ◽

Group 1

In myopia patients, Rh and acid phosphatase were typed in two groups: group 1 consisted of 214 patients with low myopia (−6 D or less); group 2 of 124 patients with high myopia (more than −6 D). Statistical analysis of the markers showed a good Hardy-Weinberg equilibrium for both groups. In the Rh system there was a significant difference between group 1 and the control population (p < 0.05), but not between group 2 and control (p > 0.1). In the case of ACP there was a significant difference between group 2 and the control population (p < 0.05), but not between group 1 and control (p > 0.25). We conclude that the observed association between myopia and Rh system (chromosome 1) involves low myopia, while the association between myopia and acid phosphatase (chromosome 2) involves high myopia. Further DNA researche will lead to more specific results.

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