Transcriptomic Responses of Rhizobium phaseoli to Root Exudates Reflect Its Capacity to Colonize Maize and Common Bean in an Intercropping System

Corn and common bean have been cultivated together in Mesoamerica for thousands of years in an intercropping system called “milpa,” where the roots are intermingled, favoring the exchange of their microbiota, including symbionts such as rhizobia. In this work, we studied the genomic expression of Rhizobium phaseoli Ch24-10 (by RNA-seq) after a 2-h treatment in the presence of root exudates of maize and bean grown in monoculture and milpa system under hydroponic conditions. In bean exudates, rhizobial genes for nodulation and degradation of aromatic compounds were induced; while in maize, a response of genes for degradation of mucilage and ferulic acid was observed, as well as those for the transport of sugars, dicarboxylic acids and iron. Ch24-10 transcriptomes in milpa resembled those of beans because they both showed high expression of nodulation genes; some genes that were expressed in corn exudates were also induced by the intercropping system, especially those for the degradation of ferulic acid and pectin. Beans grown in milpa system formed nitrogen-fixing nodules similar to monocultured beans; therefore, the presence of maize did not interfere with Rhizobium–bean symbiosis. Genes for the metabolism of sugars and amino acids, flavonoid and phytoalexin tolerance, and a T3SS were expressed in both monocultures and milpa system, which reveals the adaptive capacity of rhizobia to colonize both legumes and cereals. Transcriptional fusions of the putA gene, which participates in proline metabolism, and of a gene encoding a polygalacturonase were used to validate their participation in plant–microbe interactions. We determined the enzymatic activity of carbonic anhydrase whose gene was also overexpressed in response to root exudates.

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Comprehensive Analysis of Transcriptomics and Metabolomics between the Heads and Tails of Angelica Sinensis: Genes Related to Phenylpropanoid Biosynthesis Pathway

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323999201103221952 ◽

2020 ◽

Vol 23 ◽

Author(s):

Jie Yang ◽

Chi Zhang ◽

Wei-Hong Li ◽

Tian-Er Zhang ◽

Guang-Zhong Fan ◽

...

Keyword(s):

Ferulic Acid ◽

Metabolic Regulation ◽

Comprehensive Analysis ◽

Angelica Sinensis ◽

Rna Seq ◽

Targeted Metabolomics ◽

Kegg Pathways ◽

Qrt Pcr ◽

Phenylpropanoid Biosynthesis ◽

Combined Strategy

Background:: In Traditional Chinese Medicine (TCM), the heads and tails of Angelica sinensis (Oliv.) Diels (AS) is used in treating different diseases due to their different pharmaceutical efficacies. The underline mechanisms, however, have not been fully explored. Objective:: Novel mechanisms responsible for the discrepant activities between AS heads and tails were explored by a combined strategy of transcriptomes and metabolomics. Method:: Six pairs of the heads and tails of AS roots were collected in Min County, China. Total RNA and metabolites, which were used for RNA-seq and untargeted metabolomics analysis, were respectively isolated from each AS sample (0.1 g) by Trizol and methanol reagent. Subsequently, differentially expressed genes (DEGs) and discrepant pharmaceutical metabolites were identified for comparing AS heads and tails. Key DEGs and metabolites were quantified by qRT-PCR and targeted metabolomics experiment. Results:: Comprehensive analysis of transcriptomes and metabolomics results suggested that five KEGG pathways with significant differences included 57 DEGs. Especially, fourteen DEGs and six key metabolites were relation to the metabolic regulation of Phenylpropanoid biosynthesis (PB) pathway. Results of qRT-PCR and targeted metabolomics indicated that higher levels of expression of crucial genes in PB pathway, such as PAL, CAD, COMT and peroxidase in the tail of AS were positively correlated with levels of ferulic acid-related metabolites. The average content of ferulic acid in tails (569.58162.39 nmol/g) was higher than those in the heads (168.73  67.30 nmol/g) (P˂0.01); Caffeic acid in tails (3.82  0.88 nmol/g) vs heads (1.37  0.41 nmol/g) (P˂0.01), and Cinnamic acid in tails (0.24  0.09 nmol/g) vs heads (0.14  0.02 nmol/g) (P˂0.05). Conclusion:: Our work demonstrated that overexpressed genes and accumulated metabolites derived from PB pathway might be responsible for the discrepant pharmaceutical efficacies between AS heads and tails.

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AP2M1 Supports TGF-β Signals to Promote Collagen Expression by Inhibiting Caveolin Expression

International Journal of Molecular Sciences ◽

10.3390/ijms22041639 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1639

Author(s):

Saerom Lee ◽

Ga-Eun Lim ◽

Yong-Nyun Kim ◽

Hyeon-Sook Koo ◽

Jaegal Shim

Keyword(s):

Rna Seq ◽

Gene Encoding ◽

Caveolin 1 ◽

Collagen Expression ◽

Disease States ◽

Tumor Growth Factor ◽

Complex Process ◽

Collagen Protein ◽

Complex Regulation ◽

Collagen Genes

The extracellular matrix (ECM) is important for normal development and disease states, including inflammation and fibrosis. To understand the complex regulation of ECM, we performed a suppressor screening using Caenorhabditis elegans expressing the mutant ROL-6 collagen protein. One cuticle mutant has a mutation in dpy-23 that encodes the μ2 adaptin (AP2M1) of clathrin-associated protein complex II (AP-2). The subsequent suppressor screening for dpy-23 revealed the lon-2 mutation. LON-2 functions to regulate body size through negative regulation of the tumor growth factor-beta (TGF-β) signaling pathway responsible for ECM production. RNA-seq analysis showed a dominant change in the expression of collagen genes and cuticle components. We noted an increase in the cav-1 gene encoding caveolin-1, which functions in clathrin-independent endocytosis. By knockdown of cav-1, the reduced TGF-β signal was significantly restored in the dpy-23 mutant. In conclusion, the dpy-23 mutation upregulated cav-1 expression in the hypodermis, and increased CAV-1 resulted in a decrease of TβRI. Finally, the reduction of collagen expression including rol-6 by the reduced TGF-β signal influenced the cuticle formation of the dpy-23 mutant. These findings could help us to understand the complex process of ECM regulation in organism development and disease conditions.

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Indigenous rhizobial strains SEMIA 4108 and SEMIA 4107 for common bean inoculation: A biotechnological tool for cleaner and more sustainable agriculture

Experimental Agriculture ◽

10.1017/s0014479721000041 ◽

2021 ◽

pp. 1-11

Author(s):

Bruno Britto Lisboa ◽

Thomas Müller Schmidt ◽

Arthur Henrique Ely Thomé ◽

Raul Antonio Sperotto ◽

Camila Gazolla Volpiano ◽

...

Keyword(s):

Grain Yield ◽

Common Bean ◽

Field Experiments ◽

Rhizobium Phaseoli ◽

Productivity Losses ◽

Bean Plants ◽

Rrna Sequencing ◽

Low Efficiency ◽

Type Strains ◽

Common Bean Plants

Summary Inoculation of symbiotic N2-fixing rhizobacteria (rhizobia) in legumes is an alternative to reduce synthetic N fertiliser input to crops. Even though common bean benefits from the biological N2 fixation carried out by native rhizobia isolates, the low efficiency of this process highlights the importance of screening new strains for plant inoculation. Two rhizobial strains (SEMIA 4108 and SEMIA 4107) previously showed great potential to improve the growth of common beans under greenhouse conditions. Thus, this study evaluated the growth and grain yield of common bean plants inoculated with those strains in field experiments. The rhizobial identification was performed by 16S rRNA sequencing and the phylogeny showed that SEMIA 4108 and SEMIA 4107 are closely related to Rhizobium phaseoli, within a clade containing other 18 Rhizobium spp. type strains. Common bean plants inoculated with SEMIA 4107 showed similar productivity to N-fertilised (N+) plants in the first experiment (2016/17) and higher productivity in the second experiment (2018/19). The development of inoculated plants was different from that observed for N+. Nonetheless, comparing inoculated treatments with N-fertilised control, no yield or productivity losses at the end of the growing process were detected. Our results showed that inoculation of the rhizobial isolates SEMIA 4108 and SEMIA 4107 improved the growth and grain yield of common bean plants. The observed agronomical performance confirms that both strains were effective and can sustain common bean growth without nitrogen fertilisation under the edaphoclimatic conditions of this study.

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Genetic Analysis of Mutations Affecting pckA Regulation in Rhizobium (Sinorhizobium) meliloti

Genetics ◽

10.1093/genetics/147.4.1521 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1521-1531 ◽

Cited By ~ 2

Author(s):

Magne Østerås ◽

Shelley A P O'Brien ◽

Turlough M Finan

Keyword(s):

Sinorhizobium Meliloti ◽

Phosphoenolpyruvate Carboxykinase ◽

Root Nodules ◽

Genetic Regulation ◽

Carbon Sources ◽

Dicarboxylic Acids ◽

Phenotypic Analysis ◽

Gene Encoding ◽

Type Locus ◽

Rapid Induction

Abstract The enzyme phosphoenolpyruvate carboxykinase (Pck) catalyzes the first step in the gluconeogenic pathway in most organisms. We are examining the genetic regulation of the gene encoding Pck, pckA, in Rhizobium (now Sinorhizobium) meliloti. This bacterium forms N2-fixing root nodules on alfalfa, and the major energy sources supplied to the bacteria within these nodules are C4-dicarboxylic acids such as malate and succinate. R. meliloti cells growing in glucose minimal medium show very low pckA expression whereas addition of succinate to this medium results in a rapid induction of pckA transcription. We identified spontaneous mutations (rpk) that alter the regulation of pckA expression such that pckA is expressed in media containing the non-inducing carbon sources lactose and glucose. Genetic and phenotypic analysis allowed us to differentiate at least four rpk mutant classes that map to different locations on the R. meliloti chromosome. The wild-type locus corresponding to one of these rpk loci was cloned by complementation, and two Tn5 insertions within the insert DNA that no longer complemented the rpk mutation were identified. The nucleotide sequence of this region revealed that both Tn5 insertions lay within a gene encoding a protein homologous to the Ga1R/LacI family of transcriptional regulators that are involved in metabolism.

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Cross-species RNA-seq for deciphering host–microbe interactions

Nature Reviews Genetics ◽

10.1038/s41576-021-00326-y ◽

2021 ◽

Author(s):

Alexander J. Westermann ◽

Jörg Vogel

Keyword(s):

Rna Seq ◽

Microbe Interactions ◽

Host Microbe Interactions

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Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽

10.3390/plants10071465 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1465

Author(s):

Ramon de Koning ◽

Raphaël Kiekens ◽

Mary Esther Muyoka Toili ◽

Geert Angenon

Keyword(s):

Common Bean ◽

Seed Development ◽

Expression Analysis ◽

De Novo ◽

Expression Patterns ◽

Gene Families ◽

Rna Seq ◽

Raffinose Family Oligosaccharides ◽

Specific Expression ◽

Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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A transcription-based mechanism for oncogenic β-catenin-induced lethality in BRCA1/2-deficient cells

Nature Communications ◽

10.1038/s41467-021-25215-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Rebecca A. Dagg ◽

Gijs Zonderland ◽

Emilia Puig Lombardi ◽

Giacomo G. Rossetti ◽

Florian J. Groelly ◽

...

Keyword(s):

Dna Damage ◽

Replication Fork ◽

High Throughput Sequencing ◽

Germline Mutations ◽

Cdk Inhibitor ◽

Rna Seq ◽

Gene Encoding ◽

Origin Firing ◽

Replication Fork Progression ◽

Transcriptional Alterations

AbstractBRCA1 or BRCA2 germline mutations predispose to breast, ovarian and other cancers. High-throughput sequencing of tumour genomes revealed that oncogene amplification and BRCA1/2 mutations are mutually exclusive in cancer, however the molecular mechanism underlying this incompatibility remains unknown. Here, we report that activation of β-catenin, an oncogene of the WNT signalling pathway, inhibits proliferation of BRCA1/2-deficient cells. RNA-seq analyses revealed β-catenin-induced discrete transcriptome alterations in BRCA2-deficient cells, including suppression of CDKN1A gene encoding the CDK inhibitor p21. This accelerates G1/S transition, triggering illegitimate origin firing and DNA damage. In addition, β-catenin activation accelerates replication fork progression in BRCA2-deficient cells, which is critically dependent on p21 downregulation. Importantly, we find that upregulated p21 expression is essential for the survival of BRCA2-deficient cells and tumours. Thus, our work demonstrates that β-catenin toxicity in cancer cells with compromised BRCA1/2 function is driven by transcriptional alterations that cause aberrant replication and inflict DNA damage.

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The Bartonella vinsonii subsp. arupensis Immunodominant Surface Antigen BrpA Gene, Encoding a 382-Kilodalton Protein Composed of Repetitive Sequences, Is a Member of a Multigene Family Conserved among Bartonella Species

Infection and Immunity ◽

10.1128/iai.73.5.3128-3136.2005 ◽

2005 ◽

Vol 73 (5) ◽

pp. 3128-3136 ◽

Cited By ~ 14

Author(s):

Robert D. Gilmore ◽

Travis M. Bellville ◽

Steven L. Sviat ◽

Michael Frace

Keyword(s):

Bartonella Henselae ◽

Repetitive Sequences ◽

Expression Library ◽

Gene Encoding ◽

Significant Similarity ◽

Bartonella Quintana ◽

Genomic Expression ◽

Genes Encoding ◽

Multiple Regions ◽

Adhesin Protein

ABSTRACT Bartonella proteins that elicit an antibody response during an infection are poorly defined; therefore, to characterize antigens recognized by the host, a Bartonella genomic expression library was screened with serum from an infected mouse. This process led to the discovery of a Bartonella vinsonii subsp. arupensis gene encoding a 382-kDa protein, part of a gene family encoding large proteins, each containing multiple regions of repetitive segments. The genes were termed brpA to -C (bartonella repeat protein) and bore significant similarity to genes encoding the BadA adhesin protein and members of the variably expressed outer membrane protein family of proteins from Bartonella henselae and Bartonella quintana, respectively.

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Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake

10.1101/2020.05.03.074617 ◽

2020 ◽

Cited By ~ 1

Author(s):

Irina A. Rodionova ◽

Ye Gao ◽

Anand Sastry ◽

Reo Yoo ◽

Dmitry A. Rodionov ◽

...

Keyword(s):

Nitrogen Sources ◽

Gene Arrangement ◽

The Novel ◽

Rna Seq ◽

Gene Encoding ◽

E Coli ◽

Binding Sequence ◽

Predicted Binding Site ◽

Lysr Family ◽

Mg1655 Strain

AbstractThe YdhB transcriptional factor, re-named here AdnB, homologous to the allantoin regulator, AllS, was shown to regulate ydhC gene expression in Escherichia coli, which is divergently transcribed from adnB, and this gene arrangement is conserved in many Protreobacteria. The predicted consensus DNA binding sequence for YdhB is also conserved in Entrobacterial genomes. RNA-seq data confirmed the activation predicted due to the binding of AdnB as shown by Chip-Exo results. Fluorescent polarization experiments revealed binding of YdhB to the predicted binding site upstream of ydhC in the presence of 0.35 mM adenine, but not in its absence. The E. coli MG1655, strain lacking the ydhB gene, showed a lower level of ydhC mRNA in cells grown in M9-glucose supplemented with 2 mM adenosine. Adenosine and adenine are products of purine metabolism and provide sources of ammonium for many organisms. They are utilized under nitrogen starvation conditions as single nitrogen sources. Deletion of either the ydhC or the ydhB gene leads to a substantially decreased growth rate for E. coli in minimal M9 medium with glycerol as the carbon source and adenosine or adenine as the single nitrogen source. The ydhC mutant showed increased resistance to Paromomycine, Sulfathiazole and Sulfamethohazole using Biolog plates. We provide evidence that YdhB, (a novel LysR family regulator) activates expression of the ydhC gene, encoding a novel adenosine/adenine transporter in E. coli. The YdhB binding consensus for different groups of Enterobacteria was predicted.

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