scholarly journals Comparative Analysis of Latex Transcriptome Reveals Putative Molecular Mechanisms Underlying Super Productivity of Hevea brasiliensis

PLoS ONE ◽  
2013 ◽  
Vol 8 (9) ◽  
pp. e75307 ◽  
Author(s):  
Chaorong Tang ◽  
Xiaohu Xiao ◽  
Heping Li ◽  
Yujie Fan ◽  
Jianghua Yang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Hevea Brasiliensis ◽  
Molecular Mechanisms

scholarly journals Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 674
Author(s):  
Tomoko Yamaguchi ◽  
Yukio Kurihara ◽  
Yuko Makita ◽  
Emiko Okubo-Kurihara ◽  
Ami Kageyama ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Natural Rubber ◽  
Hevea Brasiliensis ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Cultured Cells ◽  
Early Stage ◽  
Rubber Biosynthesis ◽  
On The Road

Natural rubber is the main component of latex obtained from laticifer cells of Hevea brasiliensis. For improving rubber yield, it is essential to understand the genetic molecular mechanisms responsible for laticifer differentiation and rubber biosynthesis. Jasmonate enhances both secondary laticifer differentiation and rubber biosynthesis. Here, we carried out time-course RNA-seq analysis in suspension-cultured cells treated with methyljasmonic acid (MeJA) to characterize the gene expression profile. Gene Ontology (GO) analysis showed that the term “cell differentiation” was enriched in upregulated genes at 24 h after treatment, but inversely, the term was enriched in downregulated genes at 5 days, indicating that MeJA could induce cell differentiation at an early stage of the response. Jasmonate signaling is activated by MYC2, a basic helix–loop–helix (bHLH)-type transcription factor (TF). The aim of this work was to find any links between transcriptomic changes after MeJA application and regulation by TFs. Using an in vitro binding assay, we traced candidate genes throughout the whole genome that were targeted by four bHLH TFs: Hb_MYC2-1, Hb_MYC2-2, Hb_bHLH1, and Hb_bHLH2. The latter two are highly expressed in laticifer cells. Their physical binding sites were found in the promoter regions of a variety of other TF genes, which are differentially expressed upon MeJA exposure, and rubber biogenesis-related genes including SRPP1 and REF3. These studies suggest the possibilities that Hb_MYC2-1 and Hb_MYC2-2 regulate cell differentiation and that Hb_bHLH1 and Hb_bHLH2 promote rubber biosynthesis. We expect that our findings will help to increase natural rubber yield through genetic control in the future.

scholarly journals Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales

Biomolecules ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1523
Author(s):  
Isabelle Anna Zink ◽  
Erika Wimmer ◽  
Christa Schleper
Keyword(s):  
Comparative Analysis ◽  
Molecular Mechanisms ◽  
Model Organisms ◽  
Special Focus ◽  
Natural Environments ◽  
Type I ◽  
Accessory Proteins ◽  
Type Iii

Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.

Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex

Gene ◽  
2015 ◽  
Vol 556 (2) ◽  
pp. 153-162 ◽  
Author(s):  
Fang Wei ◽  
Shiqiao Luo ◽  
Qiankun Zheng ◽  
Jian Qiu ◽  
Wenfeng Yang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Hevea Brasiliensis ◽  
Transcriptome Sequencing

scholarly journals Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants

FEBS Open Bio ◽  
2014 ◽  
Vol 4 (1) ◽  
pp. 496-509 ◽  
Author(s):  
Lyudmyla Dorosh ◽  
Nandhakishore Rajagopalan ◽  
Michele C. Loewen ◽  
Maria Stepanova
Keyword(s):  
Comparative Analysis ◽  
Molecular Mechanisms

scholarly journals Continuous-trait probabilistic model for comparing multi-species functional genomic data

2018 ◽  
Author(s):  
Yang Yang ◽  
Quanquan Gu ◽  
Yang Zhang ◽  
Takayo Sasaki ◽  
Julianna Crivello ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Molecular Mechanisms ◽  
Probabilistic Models ◽  
Phenotypic Diversity ◽  
Genomic Data ◽  
Primate Species ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Continuous Trait ◽  
A Genome

SummaryA large amount of multi-species functional genomic data from high-throughput assays are becoming available to help understand the molecular mechanisms for phenotypic diversity across species. However, continuous-trait probabilistic models, which are key to such comparative analysis, remain underexplored. Here we develop a new model, called phylogenetic hidden Markov Gaussian processes (Phylo-HMGP), to simultaneously infer heterogeneous evolutionary states of functional genomic features in a genome-wide manner. Both simulation studies and real data application demonstrate the effectiveness of Phylo-HMGP. Importantly, we applied Phylo-HMGP to analyze a new cross-species DNA replication timing (RT) dataset from the same cell type in five primate species (human, chimpanzee, orangutan, gibbon, and green monkey). We demonstrate that our Phylo-HMGP model enables discovery of genomic regions with distinct evolutionary patterns of RT. Our method provides a generic framework for comparative analysis of multi-species continuous functional genomic signals to help reveal regions with conserved or lineage-specific regulatory roles.

scholarly journals Adaptation Insights from Comparative Transcriptome Analysis of Two Opisthopappus Species in the Taihang Mountains

2021 ◽  
Author(s):  
Ning Chen ◽  
Hao Zhang ◽  
En Zang ◽  
Zhi-Xia Liu ◽  
Ya-Fei Lan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Positive Selection ◽  
Molecular Mechanisms ◽  
Rapid Evolution ◽  
Model Systems ◽  
Perennial Herb ◽  
Starch Degradation ◽  
Adaptive Divergence ◽  
Nucleotide Synthesis ◽  
Opisthopappus Taihangensis

Abstract Opisthopappus is a major wild source of Asteraceae with good cold and drought resistance. Two species of this genus (Opisthopappus taihangensis and Opisthopappus longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus revealed a higher expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly regarding monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus, 1203 genes were found that related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Different PSG expressions occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Two PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights as to how the two species adapted to different environments, characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species of Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

scholarly journals CgMFS1, a Major Facilitator Superfamily Transporter, Is Required for Sugar Transport, Oxidative Stress Resistance, and Pathogenicity of Colletotrichum gloeosporioides from Hevea brasiliensis

2021 ◽  
Vol 43 (3) ◽  
pp. 1548-1557
Author(s):  
Na Liu ◽  
Qiannan Wang ◽  
Chaozu He ◽  
Bang An
Keyword(s):  
Oxidative Stress ◽  
Hevea Brasiliensis ◽  
Fungicide Resistance ◽  
Molecular Mechanisms ◽  
Colletotrichum Gloeosporioides ◽  
3D Structure ◽  
Sugar Transport ◽  
Major Facilitator Superfamily ◽  
Diverse Range ◽  
Major Facilitator

Colletotrichum gloeosporioides is the main causal agent of anthracnose in various plant species. Determining the molecular mechanisms underlying the pathogenicity and fungicide resistance of C. gloeosporioides could help build new strategies for disease control. The major facilitator superfamily (MFS) has multiple roles in the transport of a diverse range of substrates. In the present study, an MFS protein CgMFS1 was characterized in C. gloeosporioides. This protein contains seven transmembrane domains, and its predicted 3D structure is highly similar to the reported hexose transporters. To investigate the biological functions of CgMFS1, the gene knock-out mutant ΔCgMFS1 was constructed. A colony growth assay showed that the mutant was remarkably decreased in vegetative growth in minimal medium supplemented with monosaccharides and oligosaccharides as the sole carbon sources, whereas it showed a similar growth rate and colony morphology as wild types when using soluble starch as the carbon source. A stress assay revealed that CgMFS1 is involved in oxidative stress but not in the fungicide resistance of C. gloeosporioides. Furthermore, its pathogenicity was significantly impaired in the mutant, although its appressorium formation was not affected. Our results demonstrate that CgMFS1 is required for sugar transport, resistance to oxidative stress, and the pathogenicity of Colletotrichum gloeosporioides from Hevea brasiliensis.

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