scholarly journals Energetic Evolution of Cellular Transportomes

2017 ◽  
Author(s):  
Behrooz Darbani ◽  
Douglas B. Kell ◽  
Irina Borodina
Keyword(s):  
Ion Channels ◽  
Bacterial Species ◽  
Living Cells ◽  
Energetic Efficiency ◽  
Cellular Functions ◽  
Transporter Proteins ◽  
Genome Wide Analysis ◽  
Solute Carriers ◽  
Genome Wide ◽  
A Genome

ABSTRACTTransporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, includingNeorickettsia risticiiandNeorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.

scholarly journals A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4

2021 ◽  
Vol 37 (4) ◽  
pp. 389-395
Author(s):  
Da-Ran Kim ◽  
Youn-Sig Kwak
Keyword(s):  
Bacterial Species ◽  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Plant Diseases ◽  
Local Alignment ◽  
Plant Tissues ◽  
Biosynthetic Gene ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.

scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

scholarly journals A Genome‐Wide Analysis of Placental Epigenetic Markers in Response to Maternal Choline Supplementation

2017 ◽  
Vol 31 (S1) ◽  
Author(s):  
Sze Ting (Cecilia) Kwan ◽  
Minghui Wang ◽  
Julia H King ◽  
Jian Yan ◽  
Xinyin Jiang ◽  
...  
Keyword(s):  
Epigenetic Markers ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2409
Author(s):  
Weiwei Liu ◽  
Yingjie Sun ◽  
Xusheng Qiu ◽  
Chunchun Meng ◽  
Cuiping Song ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Virus Infection ◽  
Immune Gene ◽  
Genome Wide Analysis ◽  
Pathogen Invasion ◽  
Avian Virus ◽  
Genome Wide ◽  
A Genome ◽  
Model Animal ◽  
Alternative Splicing Events

The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host–virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.

scholarly journals sPepFinder expedites genome-wide identification of small proteins in bacteria

2020 ◽  
Author(s):  
Lei Li ◽  
Yanjie Chao
Keyword(s):  
De Novo ◽  
Bacterial Species ◽  
Computational Prediction ◽  
Ribosome Profiling ◽  
Support Vector ◽  
Initiation Rate ◽  
E Coli ◽  
Small Proteins ◽  
Genome Wide ◽  
A Genome

ABSTRACTSmall proteins shorter than 50 amino acids have been long overlooked. A number of small proteins have been identified in several model bacteria using experimental approaches and assigned important functions in diverse cellular processes. The recent development of ribosome profiling technologies has allowed a genome-wide identification of small proteins and small ORFs (smORFs), but our incomplete understanding of small proteins hinders de novo computational prediction of smORFs in non-model bacterial species. Here, we have identified several sequence features for smORFs by a systematic analysis of all the known small proteins in E. coli, among which the translation initiation rate is the strongest determinant. By integrating these features into a support vector machine learning model, we have developed a novel sPepFinder algorithm that can predict conserved smORFs in bacterial genomes with a high accuracy of 92.8%. De novo prediction in E. coli has revealed several novel smORFs with evidence of translation supported by ribosome profiling. Further application of sPepFinder in 549 bacterial species has led to the identification of > 100,000 novel smORFs, many of which are conserved at the amino acid and nucleotide levels under purifying selection. Overall, we have established sPepFinder as a valuable tool to identify novel smORFs in both model and non-model bacterial organisms, and provided a large resource of small proteins for functional characterizations.

scholarly journals Correction: A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

PLoS Genetics ◽  
2012 ◽  
Vol 8 (5) ◽  
Author(s):  
Olin K. Silander ◽  
Nela Nikolic ◽  
Alon Zaslaver ◽  
Anat Bren ◽  
Ilya Kikoin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome
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