Treponema denticola biofilm-induced expression of a bacteriophage, toxin–antitoxin systems and transposases

Treponema denticola is an oral spirochaete that has been strongly associated with chronic periodontitis. The bacterium exists as part of a dense biofilm (subgingival dental plaque) accreted to the tooth. To determine T. denticola gene products important for persistence as a biofilm we developed a continuous-culture biofilm model and conducted a genome-wide transcriptomic analysis of biofilm and planktonic cells. A total of 126 genes were differentially expressed with a fold change of 1.5 or greater. This analysis identified the upregulation of putative prophage genes in the T. denticola 35405 genome. Intact bacteriophage particles were isolated from T. denticola and circular phage DNA was detected by PCR analysis. This represents the first, to our knowledge, functional bacteriophage isolated from T. denticola, which we have designated φtd1. In biofilm cells there was also an upregulation of genes encoding several virulence factors, toxin–antitoxin systems and a family of putative transposases. Together, these data indicate that there is a higher potential for genetic mobility in T. denticola when growing as a biofilm and that these systems are important for the biofilm persistence and therefore virulence of this bacterium.

Download Full-text

Gene fitness landscape of group A streptococcus during necrotizing myositis

10.1101/432526 ◽

2018 ◽

Author(s):

Luchang Zhu ◽

Randall J. Olsen ◽

Stephen B. Beres ◽

Jesus M. Eraso ◽

Matthew Ojeda Saavedra ◽

...

Keyword(s):

Fitness Landscape ◽

Group A Streptococcus ◽

Insertion Site ◽

Pcr Analysis ◽

Genome Wide ◽

A Genome ◽

Necrotizing Myositis ◽

Genes Encoding ◽

Isogenic Mutant Strain ◽

Group A

ABSTRACTNecrotizing fasciitis and myositis are devastating infections characterized by high mortality. Group A streptococcus (GAS) is a common cause of these infections, but the molecular pathogenesis is poorly understood. We report a genome-wide analysis using serotype M1 and M28 strains that identified novel GAS genes contributing to necrotizing myositis in nonhuman primates (NHP), a clinically relevant model. Using transposon directed insertion-site sequencing (TraDIS) we identified 126 and 116 GAS genes required for infection by serotype M1 and M28 organisms, respectively. For both M1 and M28 strains, more than 25% of the GAS genes required for necrotizing myositis encode known or putative transporters. Thirteen GAS transporters contributed to both M1 and M28 strain fitness in NHP myositis, including putative importers for amino acids, carbohydrates, and vitamins, and exporters for toxins, quorum sensing peptides, and uncharacterized molecules. Targeted deletion of genes encoding five transporters confirmed that each isogenic mutant strain was significantly impaired in causing necrotizing myositis in NHPs. qRT-PCR analysis showed that these five genes are expressed in infected NHP and human skeletal muscle. Certain substrate-binding lipoproteins of these transporters, such as Spy0271 and Spy1728, were previously documented to be surface-exposed, suggesting that our findings have translational research implications.

Download Full-text

Abstract 5340: Cardiac Resynchronization Therapy Corrects Dyssynchrony-induced Regional Gene Expression Changes on a Genomic Level

Circulation ◽

10.1161/circ.118.suppl_18.s_531 ◽

2008 ◽

Vol 118 (suppl_18) ◽

Author(s):

Andreas S Barth ◽

Takeshi Aiba ◽

Victoria Halperin ◽

Deborah DiSilvestre ◽

Chakir Khalid ◽

...

Keyword(s):

Gene Expression ◽

Cardiac Resynchronization Therapy ◽

Cardiac Resynchronization ◽

Functional Improvement ◽

Large Animal ◽

Atrial Pacing ◽

Resynchronization Therapy ◽

Genome Wide ◽

A Genome ◽

Genes Encoding

Purpose: Cardiac Resynchronization Therapy (CRT) improves symptoms and reduces mortality in patients with heart failure (HF). To characterize the molecular processes associated with functional improvement in CRT, we used a genomic approach in a large animal HF model. Methods: After creation of a left bundle branch block (LBBB), dogs in the HF group were subjected to either rapid atrial pacing with 200 bpm for 6 weeks (dyssynchronous HF, DHF, n=10), or 3 weeks of atrial pacing followed by 3 weeks of biventricular stimulation at 200bpm (CRT, n=9). Control animals without LBBB were not paced (NF, n=11). After 6 weeks, RNA from anterior and lateral regions of the LV was hybridized onto canine 44K arrays. Statistical Analysis of Microarrays (SAM) was used for data analysis. Results: Echocardiographically, CRT led to a significant increase in stroke volume (+27%, p=0.03) which translated into a non-significant increase in EF (DHF 25±4%; CRT 31±3% (p=0.15); NF 67±3%). A multiclass analysis of NF, DHF and CRT animals identified 1050 differentially expressed transcripts between anterior and lateral walls with a false discovery rate of 5%. For all these transcripts, dyssynchrony-induced expression changes were reversed by CRT to levels of NF hearts. As a result, CRT samples clustered with NF rather than DHF samples. Of particular interest were genes encoding for signal transduction pathways and contractile processes. Conclusions: By using a whole genome approach, we demonstrate a profound effect of electrical activation on the regional cardiac transcriptome. This is the first study showing that dyssynchrony-induced gene expression changes can be corrected by CRT on a genome-wide level.

Download Full-text

Genome-wide screen uncovers novel pathways for tRNA processing and nuclear–cytoplasmic dynamics

Genes & Development ◽

10.1101/gad.269803.115 ◽

2015 ◽

Vol 29 (24) ◽

pp. 2633-2644 ◽

Cited By ~ 2

Author(s):

Jingyan Wu ◽

Alicia Bao ◽

Kunal Chatterjee ◽

Yao Wan ◽

Anita K. Hopper

Keyword(s):

Nuclear Export ◽

Outer Membrane Proteins ◽

Chromatin Modification ◽

Mitochondrial Outer Membrane ◽

Cell Physiology ◽

Gene Products ◽

Ribonucleic Acids ◽

Trna Processing ◽

Genome Wide ◽

Genes Encoding

Transfer ribonucleic acids (tRNAs) are essential for protein synthesis. However, key gene products involved in tRNA biogenesis and subcellular movement remain to be discovered. We conducted the first comprehensive unbiased analysis of the role of nearly an entire proteome in tRNA biology and describe 162 novel and 12 previously known Saccharomyces cerevisiae gene products that function in tRNA processing, turnover, and subcellular movement. tRNA nuclear export is of particular interest because it is essential, but the known tRNA exporters (Los1 [exportin-t] and Msn5 [exportin-5]) are unessential. We report that mutations of CRM1 (Exportin-1), MEX67/MTR2 (TAP/p15), and five nucleoporins cause accumulation of unspliced tRNA, a hallmark of defective tRNA nuclear export. CRM1 mutation genetically interacts with los1Δ and causes altered tRNA nuclear–cytoplasmic distribution. The data implicate roles for the protein and mRNA nuclear export machineries in tRNA nuclear export. Mutations of genes encoding actin cytoskeleton components and mitochondrial outer membrane proteins also cause accumulation of unspliced tRNA, likely due to defective splicing on mitochondria. Additional gene products, such as chromatin modification enzymes, have unanticipated effects on pre-tRNA end processing. Thus, this genome-wide screen uncovered putative novel pathways for tRNA nuclear export and extensive links between tRNA biology and other aspects of cell physiology.

Download Full-text

Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

BMC Genomics ◽

10.1186/s12864-020-07201-w ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Guodong Chen ◽

Jizhong Wang ◽

Xin Qiao ◽

Cong Jin ◽

Weike Duan ◽

...

Keyword(s):

Protein Kinase ◽

Gene Family ◽

Structural Characteristics ◽

Purifying Selection ◽

Related Protein ◽

Rosaceae Species ◽

Genome Wide ◽

A Genome ◽

Genes Encoding ◽

Genome Wide Survey

Abstract Background The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

Download Full-text

Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

10.21203/rs.3.rs-60429/v2 ◽

2020 ◽

Author(s):

Guodong Chen ◽

Jizhong Wang ◽

Xin Qiao ◽

Cong Jin ◽

Weike Duan ◽

...

Keyword(s):

Protein Kinase ◽

Gene Family ◽

Structural Characteristics ◽

Purifying Selection ◽

Related Protein ◽

Rosaceae Species ◽

Genome Wide ◽

A Genome ◽

Genes Encoding ◽

Genome Wide Survey

Abstract Background: The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results: A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear ( Pyrus bretschneideri ) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions: This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

Download Full-text

Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of CAMTA Family Genes in Cucumber (Cucumis sativus L.)

Agronomy ◽

10.3390/agronomy11091827 ◽

2021 ◽

Vol 11 (9) ◽

pp. 1827

Author(s):

Rong Gao ◽

Yanyan Luo ◽

Fahong Yun ◽

Xuetong Wu ◽

Peng Wang ◽

...

Keyword(s):

Stress Response ◽

Growth And Development ◽

Chemical Properties ◽

Pcr Analysis ◽

Transcription Activator ◽

Cucumis Sativus L ◽

Expression Levels ◽

Calmodulin Binding ◽

Genome Wide ◽

A Genome

The calmodulin-binding transcription activator (CAMTA), as one of the most distinctive families of transcription factors, plays an important role in plant growth and development and in the stress response. However, it is currently unknown whether CAMTA exists in cucumbers and what its function is. In this study, we first identified four CAMTA genes in the cucumber genome using a genome-wide search method. Subsequently, we analyzed their physical and chemical properties, gene structure, protein domains, and phylogenetic relationships. The results show that the structure of CsCAMTAs is similar to that of other plants, and a phylogenetic analysis divides them into three groups. The analysis of cis-acting elements shows that most CsCAMTAs contain a variety of hormones and stress-related elements. The RT-PCR analysis shows that CsCAMTAs have different expression levels in different tissues and can be induced by IAA, ABA, MeJA, NaCl, and PEG. Finally, we analyzed the expression pattern of CsCAMTAs’ alternative spliceosomes under salt and drought stress. The results show that the expression levels of the different spliceosomes are affected by the type of stress and the duration of stress. These data indicate that CsCAMTAs participate in growth and development and in the stress response in cucumbers, a finding which lays the foundation for future CsCAMTAs’ functional research.

Download Full-text

High-Throughput GRID Computing for Life Sciences

Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ◽

10.4018/978-1-60566-374-6.ch010 ◽

2011 ◽

pp. 187-205 ◽

Cited By ~ 1

Author(s):

Giulia De Sario ◽

Angelica Tulipano ◽

Giacinto Donvito ◽

Giorgio Maggi

Keyword(s):

Life Sciences ◽

Computational Grid ◽

Data Repository ◽

Sequence Annotation ◽

Gene Products ◽

Grid Infrastructure ◽

Computer Clusters ◽

Genome Wide ◽

A Genome ◽

Full Search

The number of fully sequenced genomes increases daily, producing an exponential explosion of the sequence, annotation and metadata databases. Data analysis on a genome-wide level or investigation within a specific data repository has become a data- and calculation-intensive process occupying single computers and even larger computer clusters for month or even years. In most cases such applications can be subdivided into many independent smaller tasks. The smaller tasks are particularly suited to distribution over a computational GRID infrastructure, which drastically reduces the time to reach the final result. In our analysis of gene ontology data and their associations to gene products of any kind of organism in a search to find gene products with similar functionalities, we developed a system to divide the full search into a large number of jobs and to submit these jobs to the GRID infrastructure as long as all jobs are processed successfully, guaranteeing an analysis of the data without missing any information.

Download Full-text

A Genome-Wide Survey of Genes Encoding Transcription Factors in Japanese Pearl Oyster Pinctada fucata: II. Tbx, Fox, Ets, HMG, NFκ;B, bZIP, and C2H2 Zinc Fingers

ZOOLOGICAL SCIENCE ◽

10.2108/zsj.30.858 ◽

2013 ◽

Vol 30 (10) ◽

pp. 858 ◽

Cited By ~ 7

Author(s):

Hiroyuki Koga ◽

Naoki Hashimoto ◽

Daichi G. Suzuki ◽

Hiroki Ono ◽

Miho Yoshimura ◽

...

Keyword(s):

Transcription Factors ◽

Zinc Fingers ◽

Pearl Oyster ◽

Pinctada Fucata ◽

Genome Wide ◽

A Genome ◽

Genes Encoding ◽

Genome Wide Survey

Download Full-text

Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms19092478 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2478 ◽

Cited By ~ 15

Author(s):

Qinglong Dong ◽

Dingyue Duan ◽

Shuang Zhao ◽

Bingyao Xu ◽

Jiawei Luo ◽

...

Keyword(s):

Drought Tolerance ◽

Gene Family ◽

Transgenic Arabidopsis ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Pcr Analysis ◽

Sequence Alignments ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

Download Full-text

Genome-wide expression analysis identifies core components during iron starvation in hexaploid wheat

10.1101/539098 ◽

2019 ◽

Author(s):

Gazaldeep Kaur ◽

Vishnu Shukla ◽

Anil Kumar ◽

Mandeep Kaur ◽

Parul Goel ◽

...

Keyword(s):

Hexaploid Wheat ◽

Design Strategies ◽

Glutathione S Transferase ◽

Iron Starvation ◽

Wheat Roots ◽

Metal Transporters ◽

Genome Wide ◽

A Genome ◽

Genes Encoding ◽

Yellow Stripe

AbstractIron is one of essential micronutrient for all organisms. Its deficiency causes a severe loss in crops yield. Nevertheless, our current understanding on major crops response to Fe deficiency remains limited. Herein, we investigated the effect of Fe deprivation at both transcriptomic and metabolic levels in hexaploid wheat. A genome-wide gene expression reprogramming was observed with a total of 5854 genes showing differential expression in roots of wheat subjected to Fe-starved medium. Subsequent, analysis revealed a predominance of strategy-II mode of Fe uptake, with induced genome bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc-induced facilitator-like protein was noticed. Our transcriptomic data were in agreement with the GC-MS analysis that showed an enhancement of accumulation of various metabolites such as fumarate, malonate, succinate and xylofuranose, which could be linked for enhancing Fe-mobilization. Interestingly, Fe starvation causes a significant temporal increase of glutathione-S-transferase both at transcriptional and enzymatic activity, which indicate the important role of glutathione in the response to Fe starvation in wheat roots. Taken together, our result provides new insight on wheat response to Fe starvation and lays foundation to design strategies to improve Fe nutrition in crops.

Download Full-text