A genome-wide analysis of pentatricopeptide repeat (PPR) protein-encoding genes in four Gossypium species with an emphasis on their expression in floral buds, ovules, and fibers in upland cotton

2019 ◽  
Vol 295 (1) ◽  
pp. 55-66 ◽  
Author(s):  
Zongfu Han ◽  
Yuxiang Qin ◽  
Xihua Li ◽  
Jiwen Yu ◽  
Ruzhong Li ◽  
...  
Keyword(s):  
Upland Cotton ◽  
Pentatricopeptide Repeat ◽  
Genome Wide Analysis ◽  
Floral Buds ◽  
Ppr Protein ◽  
Gossypium Species ◽  
Genome Wide ◽  
A Genome ◽  
Protein Encoding ◽  
Encoding Genes

scholarly journals Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Eric G. Matson ◽  
Adam Z. Rosenthal ◽  
Xinning Zhang ◽  
Jared R. Leadbetter
Keyword(s):  
Protein Synthesis ◽  
Large Body ◽  
Transcriptional Responses ◽  
Translational Coupling ◽  
Genome Wide ◽  
A Genome ◽  
Protein Encoding ◽  
Termite Gut ◽  
Inhibiting Protein ◽  
Encoding Genes

ABSTRACTWhen prokaryotic cells acquire mutations, encounter translation-inhibiting substances, or experience adverse environmental conditions that limit their ability to synthesize proteins, transcription can become uncoupled from translation. Such uncoupling is known to suppress transcription of protein-encoding genes in bacteria. Here we show that the trace element selenium controls transcription of the gene for the selenocysteine-utilizing enzyme formate dehydrogenase (fdhFSec) through a translation-coupled mechanism in the termite gut symbiontTreponema primitia, a member of the bacterial phylumSpirochaetes. We also evaluated changes in genome-wide transcriptional patterns caused by selenium limitation and by generally uncoupling translation from transcription via antibiotic-mediated inhibition of protein synthesis. We observed that inhibiting protein synthesis inT. primitiainfluences transcriptional patterns in unexpected ways. In addition to suppressing transcription of certain genes, the expected consequence of inhibiting protein synthesis, we found numerous examples in which transcription of genes and operons is truncated far downstream from putative promoters, is unchanged, or is even stimulated overall. These results indicate that gene regulation in bacteria allows for specific post-initiation transcriptional responses during periods of limited protein synthesis, which may depend both on translational coupling and on unclassified intrinsic elements of protein-encoding genes.IMPORTANCEA large body of literature demonstrates that the coupling of transcription and translation is a general and essential method by which bacteria regulate gene expression levels. However, the potential role of noncanonical amino acids in regulating transcriptional output via translational control remains, for the most part, undefined. Furthermore, the genome-wide transcriptional state in response to translational decoupling is not well quantified. The results presented here suggest that the noncanonical amino acid selenocysteine is able to tune transcription of an important metabolic gene via translational coupling. Furthermore, a genome-wide analysis reveals that transcriptional decoupling produces a wide-ranging effect and that this effect is not uniform. These results exemplify how growth conditions that impact translational processivity can rapidly feed back on transcriptional productivity of prespecified groups of genes, providing bacteria with an efficient response to environmental changes.

scholarly journals A genome-wide resource of cell cycle and cell shape genes of fission yeast

Open Biology ◽  
2013 ◽  
Vol 3 (5) ◽  
pp. 130053 ◽  
Author(s):  
Jacqueline Hayles ◽  
Valerie Wood ◽  
Linda Jeffery ◽  
Kwang-Lae Hoe ◽  
Dong-Uk Kim ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Fission Yeast ◽  
Cell Shape ◽  
Cell Cycle Progression ◽  
Cycle Progression ◽  
Gene Deletions ◽  
Genome Wide ◽  
A Genome ◽  
Protein Encoding ◽  
Encoding Genes

To identify near complete sets of genes required for the cell cycle and cell shape, we have visually screened a genome-wide gene deletion library of 4843 fission yeast deletion mutants (95.7% of total protein encoding genes) for their effects on these processes. A total of 513 genes have been identified as being required for cell cycle progression, 276 of which have not been previously described as cell cycle genes. Deletions of a further 333 genes lead to specific alterations in cell shape and another 524 genes result in generally misshapen cells. Here, we provide the first eukaryotic resource of gene deletions, which describes a near genome-wide set of genes required for the cell cycle and cell shape.

scholarly journals Genome-wide analysis of NIN-like protein (NLP) family in maize (Zea mays L.) by using bioinformatic methods

2017 ◽  
Vol 1 (T2) ◽  
pp. 39-47
Author(s):  
Bang Phi Cao
Keyword(s):  
Zea Mays ◽  
Zea Mays L ◽  
Whole Genome ◽  
Genome Wide Analysis ◽  
Expression Of Genes ◽  
Genome Wide ◽  
A Genome ◽  
Nitrate Signaling ◽  
Duplication Events ◽  
Encoding Genes

The NIN-like proteins (NLP) belong to RWP-RK transcription factor family and possess the similarity characteristics of NIN (Nodules INception). The NLPs regulate the expression of genes which are involved in nitrate signaling in plants. In this work, we have performed a genome-wide analysis of the NLP gene family in maize (Zea mays L.) through the bioinformatic methods. We identified a total of nine NLP encoding genes in whole genome of maize. The genomic sequences of these genes were from 2855 to 8092 nucleotides in length and contained three or four introns. Their predicted protein sizes ranged in size from 786 to 945 amino acids. The theoretical isoelectric point values of most deduced protein were less than 7. The maize NLP proteins possessed conserved regions of plant NLP at N-terminal as well as at C-terminal including the RWP-RK and PB1 domains. Based on the phylogenic analysis, we detected three current whole-genome gene duplication events which occurred in maize genome apter speciation point. All of NLP genes expressed in tissues at different development stages, from germinating seed to maturation seed were examined. The ZmNLP5, ZmNLP6 and ZmNLP7 were weakly expressed in comparison to others genes in most examined tissues.

A Genome-Wide Analysis of the Gene Expression and Alternative Splicing Events in a Whole-Body Hypoxic Preconditioning Mouse Model

2021 ◽  
Vol 46 (5) ◽  
pp. 1101-1111
Author(s):  
Jun Li ◽  
Hongyu Zhao ◽  
Yongqiang Xing ◽  
Tongling Zhao ◽  
Lu Cai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Mouse Model ◽  
Hypoxic Preconditioning ◽  
Whole Body ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Alternative Splicing Events

scholarly journals Cysteine-Rich Hydrophobin Gene Family: Genome Wide Analysis, Phylogeny and Transcript Profiling in Cordyceps militaris

2021 ◽  
Vol 22 (2) ◽  
pp. 643
Author(s):  
Xiao Li ◽  
Fen Wang ◽  
Yanyan Xu ◽  
Guijun Liu ◽  
Caihong Dong
Keyword(s):  
Life Cycle ◽  
Pathogenic Fungi ◽  
Class Ii ◽  
Cordyceps Militaris ◽  
Transcript Profiling ◽  
Saprotrophic Fungi ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Encoding Genes

Hydrophobins are a family of small secreted proteins found exclusively in fungi, and they play various roles in the life cycle. In the present study, genome wide analysis and transcript profiling of the hydrophobin family in Cordyceps militaris, a well-known edible and medicinal mushroom, were studied. The distribution of hydrophobins in ascomycetes with different lifestyles showed that pathogenic fungi had significantly more hydrophobins than saprotrophic fungi, and class II members accounted for the majority. Phylogenetic analysis of hydrophobin proteins from the species of Cordyceps s.l. indicated that there was more variability among the class II members than class I. Only a few hydrophobin-encoding genes evolved by duplication in Cordyceps s.l., which was inconsistent with the important role of gene duplication in basidiomycetes. Different transcript patterns of four hydrophobin-encoding genes during the life cycle indicated the possible different functions for each. The transcripts of Cmhyd2, 3 and 4 can respond to light and were related with the photoreceptors. CmQHYD, with four hydrophobin II domains, was first found in C. militaris, and multi-domain hydrophobins were only distributed in the species of Cordycipitaceae and Clavicipitaceae. These results could be helpful for further function research of hydrophobins and could provide valuable information for the evolution of hydrophobins.

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.

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