Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coveragethe P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.

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Fetal and Neonatal Levels of Omega-3: Effects on Neurodevelopment, Nutrition, and Growth

The Scientific World JOURNAL ◽

10.1100/2012/202473 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 17

Author(s):

Juliana Rombaldi Bernardi ◽

Renata de Souza Escobar ◽

Charles Francisco Ferreira ◽

Patrícia Pelufo Silveira

Keyword(s):

Fatty Acids ◽

Brain Development ◽

Neural Development ◽

Stress Responses ◽

Large Scale ◽

Developmental Stages ◽

Critical Periods ◽

Omega 3 ◽

Dietary Nutrients

Nutrition in pregnancy, during lactation, childhood, and later stages has a fundamental influence on overall development. There is a growing research interest on the role of key dietary nutrients in fetal health. Omega-3 polyunsaturated fatty acids (n-3 LCPUFAs) play an important role in brain development and function. Evidence from animal models of dietary n-3 LCPUFAs deficiency suggests that these fatty acids promote early brain development and regulate behavioral and neurochemical aspects related to mood disorders (stress responses, depression, and aggression and growth, memory, and cognitive functions). Preclinical and clinical studies suggest the role of n-3 LCPUFAs on neurodevelopment and growth. n-3 LCPUFAs may be an effective adjunctive factor for neural development, growth, and cognitive development, but further large-scale, well-controlled trials and preclinical studies are needed to examine its clinical mechanisms and possible benefits. The present paper discusses the use of n-3 LCPUFAs during different developmental stages and the investigation of different sources of consumption. The paper summarizes the role of n-3 LCPUFAs levels during critical periods and their effects on the children’s neurodevelopment, nutrition, and growth.

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Structure and Complexity of a Bacterial Transcriptome

Journal of Bacteriology ◽

10.1128/jb.00122-09 ◽

2009 ◽

Vol 191 (10) ◽

pp. 3203-3211 ◽

Cited By ~ 155

Author(s):

Karla D. Passalacqua ◽

Anjana Varadarajan ◽

Brian D. Ondov ◽

David T. Okou ◽

Michael E. Zwick ◽

...

Keyword(s):

Gene Expression ◽

Bacterial Cell ◽

Large Scale ◽

High Throughput Sequencing ◽

Sequence Data ◽

Transcript Abundance ◽

Growth Conditions ◽

A Genome ◽

Nucleotide Resolution ◽

Bacterial Transcriptome

ABSTRACT Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on absolute abundance all provide valuable insights into gene function and regulation, but none has ever been determined on a genome-wide scale for any bacterium. Indeed, these aspects of the prokaryotic transcriptome have been explored on a large scale in only a few instances, and consequently little is known about the absolute composition of the mRNA population within a bacterial cell. Here we report the use of a high-throughput sequencing-based approach in assembling the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome under a variety of growth conditions and showed that the data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the sequence data identified previously nonannotated regions with significant transcriptional activity and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance and suggest that there is significant transcriptional heterogeneity within a clonal, synchronized bacterial population. Overall, our results offer an unprecedented view of gene expression and regulation in a bacterial cell.

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Lack of DNA helicase Pif1 disrupts zinc and iron homoeostasis in yeast

Biochemical Journal ◽

10.1042/bj20101032 ◽

2010 ◽

Vol 432 (3) ◽

pp. 595-608 ◽

Cited By ~ 4

Author(s):

María Guirola ◽

Lina Barreto ◽

Ayelen Pagani ◽

Miriam Romagosa ◽

Antonio Casamayor ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Responses ◽

Nuclear Dna ◽

Transcriptional Profiling ◽

Growth Conditions ◽

Protective Role ◽

Dna Helicase ◽

Dna Integrity ◽

Zinc Tolerance ◽

Genes Encoding

The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1Δ strain is tolerant to zinc overload. In the present study we demonstrate that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1Δ cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1Δ cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1Δ cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild-type cells. Coincidently, pif1Δ mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1Δ cells contain normal amounts of the Aco1 (yeast aconitase) protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as a nucleoid protein and that this triggers a domino effect on iron homoeostasis resulting in increased zinc tolerance.

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Transcriptional Responses of Paxillus involutus and Betula pendula During Formation of Ectomycorrhizal Root Tissue

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2004.17.2.202 ◽

2004 ◽

Vol 17 (2) ◽

pp. 202-215 ◽

Cited By ~ 75

Author(s):

Tomas Johansson ◽

Antoine Le Quéré ◽

Dag Ahren ◽

Bengt Söderström ◽

Rikard Erlandsson ◽

...

Keyword(s):

Stress Responses ◽

Betula Pendula ◽

Sequence Similarity ◽

Root Tissue ◽

Cdna Libraries ◽

Paxillus Involutus ◽

Transcriptional Responses ◽

Fungal Partner ◽

Genes Encoding ◽

Sequence Similarities

In order to obtain information on genes specifically expressed in the ectomycorrhizal symbiosis, 3,555 expressed sequence tags (ESTs) were analyzed from a cDNA library constructed from ectomycorrhiza formed between the basidiomycete Paxillus involutus and birch (Betula pendula). cDNA libraries from saprophytically growing fungus (3,964 ESTs) and from axenic plants (2,532 ESTs) were analyzed in parallel. By clustering all the EST obtained, a nonredundant set of 2,284 unique transcripts of either fungal or plant origin were identified. The expression pattern of these genes was analyzed using cDNA microarrays. The analyses showed that the plant and fungus responded to the symbiosis by altering the expression levels of a number of enzymes involved in carbon metabolism. Several plant transcripts with sequence similarities to genes encoding enzymes in the tricarboxylic cycle and electron transport chain were down regulated as compared with the levels in free-living roots. In the fungal partner, a number of genes encoding enzymes in the lipid and secondary metabolism were down regulated in mycorrhiza as compared with the saprophytically growing mycelium. A substantial number of the ESTs analyzed displayed significant sequence similarities to proteins involved in biotic stress responses, but only a few of them showed differential expression in the mycorrhizal tissue, including plant and fungal metal-lothioneins and a plant defensin homologue. Several of the genes that were differentially expressed in the mycorrhizal root tissue displayed sequence similarity to genes that are known to regulate growth and development of plant roots and fungal hyphae, including transcription factors and Rho-like GTPases.

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Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

Genome Research ◽

10.1101/gr.145701 ◽

2001 ◽

Vol 11 (2) ◽

pp. 281-289

Author(s):

Hideaki Konno ◽

Yoshifumi Fukunishi ◽

Kazuhiro Shibata ◽

Masayoshi Itoh ◽

Piero Carninci ◽

...

Keyword(s):

Cdna Library ◽

Large Scale ◽

Sequence Data ◽

Full Length ◽

Cdna Libraries ◽

Full Length Cdna ◽

Link Type ◽

Computer Based ◽

End Sequences ◽

Press Time

We developed computer-based methods for constructing a nonredundant mouse full-length cDNA library. Our cDNA library construction process comprises assessment of library quality, sequencing the 3′ ends of inserts and clustering, and completing a re-array to generate a nonredundant library from a redundant one. After the cDNA libraries are generated, we sequence the 5′ ends of the inserts to check the quality of the library; then we determine the sequencing priority of each library. Selected libraries undergo large-scale sequencing of the 3′ ends of the inserts and clustering of the tag sequences. After clustering, the nonredundant library is constructed from the original libraries, which have redundant clones. All libraries, plates, clones, sequences, and clusters are uniquely identified, and all information is saved in the database according to this identifier. At press time, our system has been in place for the past two years; we have clustered 939,725 3′ end sequences into 127,385 groups from 227 cDNA libraries/sublibraries (seehttp://genome.gse.riken.go.jp/).[The sequence data described in this paper have been submitted to the DDBJ data library under accession nos. AV00011–AV175734, AV204013–AV382295, andBB561685–BB609425.]

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Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max

BMC Genomics ◽

10.1186/s12864-020-07130-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Gracia Zabala ◽

Anupreet Kour ◽

Lila O. Vodkin

Keyword(s):

Seed Coat ◽

Developmental Stages ◽

Sequence Data ◽

Acc Oxidase ◽

Germplasm Collection ◽

Cdna Libraries ◽

Small Ring ◽

Recurrent Parent ◽

Expression Of Genes ◽

Hormone Balance

Abstract Background To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region. Results RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10–25, 25–50 and 50–100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, iiR t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, iiR T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value < 0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes. Conclusions We present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.

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Dynamic Planning of Bicycle Stations in Dockless Public Bicycle-sharing System Using Gated Graph Neural Network

ACM Transactions on Intelligent Systems and Technology ◽

10.1145/3446342 ◽

2021 ◽

Vol 12 (2) ◽

pp. 1-22

Author(s):

Jianguo Chen ◽

Kenli Li ◽

Keqin Li ◽

Philip S. Yu ◽

Zeng Zeng

Keyword(s):

Large Scale ◽

Sequence Data ◽

Location Prediction ◽

City Management ◽

Dynamic Planning ◽

Graph Sequence ◽

Graph Modeling ◽

The Government ◽

Location Clustering ◽

Station Location

Benefiting from convenient cycling and flexible parking locations, the Dockless Public Bicycle-sharing (DL-PBS) network becomes increasingly popular in many countries. However, redundant and low-utility stations waste public urban space and maintenance costs of DL-PBS vendors. In this article, we propose a Bicycle Station Dynamic Planning (BSDP) system to dynamically provide the optimal bicycle station layout for the DL-PBS network. The BSDP system contains four modules: bicycle drop-off location clustering, bicycle-station graph modeling, bicycle-station location prediction, and bicycle-station layout recommendation. In the bicycle drop-off location clustering module, candidate bicycle stations are clustered from each spatio-temporal subset of the large-scale cycling trajectory records. In the bicycle-station graph modeling module, a weighted digraph model is built based on the clustering results and inferior stations with low station revenue and utility are filtered. Then, graph models across time periods are combined to create a graph sequence model. In the bicycle-station location prediction module, the GGNN model is used to train the graph sequence data and dynamically predict bicycle stations in the next period. In the bicycle-station layout recommendation module, the predicted bicycle stations are fine-tuned according to the government urban management plan, which ensures that the recommended station layout is conducive to city management, vendor revenue, and user convenience. Experiments on actual DL-PBS networks verify the effectiveness, accuracy, and feasibility of the proposed BSDP system.

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A Metzincin and TIMP-Like Protein Pair of a Phage Origin Sensitize Listeria monocytogenes to Phage Lysins and Other Cell Wall Targeting Agents

Microorganisms ◽

10.3390/microorganisms9061323 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1323

Author(s):

Etai Boichis ◽

Nadejda Sigal ◽

Ilya Borovok ◽

Anat A. Herskovits

Keyword(s):

Cell Wall ◽

Listeria Monocytogenes ◽

Mammalian Cells ◽

Protein Pair ◽

Growth Conditions ◽

Wall Structure ◽

Antibiotic Resistant ◽

Extracellular Milieu ◽

Virion Release ◽

Genes Encoding

Infection of mammalian cells by Listeria monocytogenes (Lm) was shown to be facilitated by its phage elements. In a search for additional phage remnants that play a role in Lm’s lifecycle, we identified a conserved locus containing two XRE regulators and a pair of genes encoding a secreted metzincin protease and a lipoprotein structurally similar to a TIMP-family metzincin inhibitor. We found that the XRE regulators act as a classic CI/Cro regulatory switch that regulates the expression of the metzincin and TIMP-like genes under intracellular growth conditions. We established that when these genes are expressed, their products alter Lm morphology and increase its sensitivity to phage mediated lysis, thereby enhancing virion release. Expression of these proteins also sensitized the bacteria to cell wall targeting compounds, implying that they modulate the cell wall structure. Our data indicate that these effects are mediated by the cleavage of the TIMP-like protein by the metzincin, and its subsequent release to the extracellular milieu. While the importance of this locus to Lm pathogenicity remains unclear, the observation that this phage-associated protein pair act upon the bacterial cell wall may hold promise in the field of antibiotic potentiation to combat antibiotic resistant bacterial pathogens.

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Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽

10.3390/biom11081153 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1153

Author(s):

Jutta Ludwig-Müller ◽

Roman Rattunde ◽

Sabine Rößler ◽

Katja Liedel ◽

Freia Benade ◽

...

Keyword(s):

Brassica Napus ◽

Expression Patterns ◽

Growth Conditions ◽

Growth Stages ◽

Auxin Response ◽

Time Points ◽

Genes Encoding ◽

Different Temperatures ◽

Indigenous Plant ◽

Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

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Versatile Physiological Functions of Plant GSK3-Like Kinases

Genes ◽

10.3390/genes12050697 ◽

2021 ◽

Vol 12 (5) ◽

pp. 697

Author(s):

Juan Mao ◽

Wenxin Li ◽

Jing Liu ◽

Jianming Li

Keyword(s):

Stress Responses ◽

Glycogen Synthase ◽

Plant Stress ◽

Normal Growth ◽

Growth Conditions ◽

Genetic Studies ◽

Physiological Functions ◽

Environmental Signals ◽

Plant Stress Responses ◽

Diverse Plant

The plant glycogen synthase kinase 3 (GSK3)-like kinases are highly conserved protein serine/threonine kinases that are grouped into four subfamilies. Similar to their mammalian homologs, these kinases are constitutively active under normal growth conditions but become inactivated in response to diverse developmental and environmental signals. Since their initial discoveries in the early 1990s, many biochemical and genetic studies were performed to investigate their physiological functions in various plant species. These studies have demonstrated that the plant GSK3-like kinases are multifunctional kinases involved not only in a wide variety of plant growth and developmental processes but also in diverse plant stress responses. Here we summarize our current understanding of the versatile physiological functions of the plant GSK3-like kinases along with their confirmed and potential substrates.

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