Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

Download Full-text

Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula

PeerJ ◽

10.7717/peerj.8471 ◽

2020 ◽

Vol 8 ◽

pp. e8471 ◽

Cited By ~ 1

Author(s):

Lei Ling ◽

Yue Qu ◽

Jintao Zhu ◽

Dan Wang ◽

Changhong Guo

Keyword(s):

Cicer Arietinum ◽

Medicago Truncatula ◽

Stress Responses ◽

Pcr Analysis ◽

Biotic And Abiotic Stress ◽

Systematic Analysis ◽

Genome Wide ◽

Specific Proteins ◽

Solid Foundation ◽

In Silico Analyses

Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I–VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins.

Download Full-text

Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites

10.1101/199356 ◽

2017 ◽

Author(s):

Lisette Meerstein-Kessel ◽

Robin van der Lee ◽

Will Stone ◽

Kjerstin Lanke ◽

David A Baker ◽

...

Keyword(s):

Transcript Abundance ◽

Data Sets ◽

Asexual Blood Stage ◽

Systematic Analysis ◽

Humoral Immune ◽

Proteomic Data ◽

Genome Wide ◽

Field Samples ◽

Specific Proteins ◽

Specific Antigens

AbstractPlasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available ‘omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated “gold standards” of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P. falciparum genes.To illustrate the utility of the gametocyte score, we explored newly predicted gametocyte-specific genes as potential biomarkers of gametocyte carriage and exposure. We analyzed the humoral immune response in field samples against 30 novel gametocyte-specific antigens and found five antigens to be differentially recognized by gametocyte carriers as compared to malaria-infected individuals without detectable gametocytes. We also validated the gametocyte-specificity of 15 identified gametocyte transcripts on culture material and samples from naturally infected individuals, resulting in eight transcripts that were >1000-fold higher expressed in gametocytes compared to asexual parasites and whose transcript abundance allowed gametocyte detection in naturally infected individuals. Our integrated genome-wide gametocyte-specificity scores provide a comprehensive resource to identify targets and monitor P. falciparum gametocytemia.

Download Full-text

Exploring Gene Function and Drug Action Using Chemogenomic Dosage Assays

Methods in Enzymology - Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems Analysis ◽

10.1016/s0076-6879(10)70010-0 ◽

2010 ◽

pp. 233-255 ◽

Cited By ~ 22

Author(s):

Elke Ericson ◽

Shawn Hoon ◽

Robert P. St.Onge ◽

Guri Giaever ◽

Corey Nislow

Keyword(s):

Gene Function ◽

Drug Action

Download Full-text

Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene function discovery

Nature Precedings ◽

10.1038/npre.2010.5114 ◽

2010 ◽

Author(s):

Ramil Mauleon ◽

Kenneth McNally ◽

Hei Leung ◽

Richard Bruskiewich ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Function ◽

Gene Pools ◽

Novel Gene ◽

Function Discovery

Download Full-text

Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

International Journal of Molecular Sciences ◽

10.3390/ijms21197180 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7180

Author(s):

Hongfeng Wang ◽

Hongjiao Jiang ◽

Yiteng Xu ◽

Yan Wang ◽

Lin Zhu ◽

...

Keyword(s):

Medicago Truncatula ◽

Expression Profiles ◽

Expression Patterns ◽

Ectopic Expression ◽

Feedback Regulation ◽

Specific Expression ◽

Systematic Analysis ◽

Model Legume ◽

Genome Wide ◽

A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

Download Full-text