scholarly journals A second eukaryotic group with mitochondrion-encoded tmRNA

RNA Biology ◽  
2013 ◽  
Vol 10 (7) ◽  
pp. 1117-1124 ◽  
Author(s):  
Mohamed Hafez ◽  
Gertraud Burger ◽  
Sergey V. Steinberg ◽  
Franz Lang
Keyword(s):  
Eukaryotic Group

UDP-glucose dehydrogenase: structure and function of a potential drug target

2010 ◽  
Vol 38 (5) ◽  
pp. 1378-1385 ◽  
Author(s):  
Sigrid Egger ◽  
Apirat Chaikuad ◽  
Kathryn L. Kavanagh ◽  
Udo Oppermann ◽  
Bernd Nidetzky
Keyword(s):  
Sequence Comparison ◽  
Drug Target ◽  
Glucuronic Acid ◽  
Glucose Dehydrogenase ◽  
Enzymatic Reaction ◽  
Cysteine Residue ◽  
Structure And Function ◽  
Eukaryotic Group ◽  
And Function ◽  
Covalent Catalysis

Biosynthesis of the glycosaminoglycan precursor UDP-α-D-glucuronic acid occurs through a 2-fold oxidation of UDP-α-D-glucose that is catalysed by UGDH (UDP-α-D-glucose 6-dehydrogenase). Structure–function relationships for UGDH and proposals for the enzymatic reaction mechanism are reviewed in the present paper, and structure-based sequence comparison is used for subclassification of UGDH family members. The eukaryotic group of enzymes (UGDH-II) utilize an extended C-terminal domain for the formation of complex homohexameric assemblies. The comparably simpler oligomerization behaviour of the prokaryotic group of enzymes (UGDH-I), in which dimeric forms prevail, is traced back to the lack of relevant intersubunit contacts and trimmings within the C-terminal region. The active site of UGDH contains a highly conserved cysteine residue, which plays a key role in covalent catalysis. Elevated glycosaminoglycan formation is implicated in a variety of human diseases, including the progression of tumours. The inhibition of synthesis of UDP-α-D-glucuronic acid using UGDH antagonists might therefore be a useful strategy for therapy.

scholarly journals Characterization of Bicistronic Transcription in Budding Yeast

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Baojun Wu ◽  
Murray P. Cox
Keyword(s):  
Secondary Structure ◽  
Gc Content ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Mrna Transcript ◽  
Stable Secondary Structure ◽  
Intergenic Spacers ◽  
Eukaryotic Group ◽  
Basic Features

ABSTRACT Bicistronic transcripts (operon-like transcripts) have occasionally been reported in eukaryotes, including unicellular yeasts, plants, and humans, despite the fact that they lack trans-splice mechanisms. However, the characteristics of eukaryotic bicistronic transcripts are poorly understood, except for those in nematodes. Here, we describe the genomic, transcriptomic, and ribosome profiling features of bicistronic transcripts in unicellular yeasts. By comparing the expression level of bicistronic transcripts with their monocistronic equivalents, we identify two main categories of bicistronic transcripts: highly and lowly expressed. These two categories exhibit quite different features. First, highly expressed bicistronic transcripts have higher conservation within and between strains and shorter intergenic spacers with higher GC content and less stable secondary structure. Second, genes in highly expressed bicistronic transcripts have lower translation efficiency, with the second gene showing statistically significant lower translation efficiency than the first. Finally, the genes found in these highly expressed bicistronic transcripts tend to be younger, with more recent origins. Together, these results suggest that bicistronic transcripts in yeast are heterogeneous. We further propose that at least some highly expressed bicistronic transcripts appear to play a role in modulating monocistronic translation. IMPORTANCE Operons, where a single mRNA transcript encodes multiple adjacent proteins, are a widespread feature of bacteria and archaea. In contrast, the genes of eukaryotes are generally considered monocistronic. However, a number of studies have revealed the presence of bicistronic transcripts in eukaryotes, including humans. The basic features of these transcripts are largely unknown in eukaryotes, especially in organisms lacking trans-splice mechanisms. Our analyses characterize bicistronic transcripts in one such eukaryotic group, yeasts. We show that highly expressed bicistronic transcripts have unusual features compared to lowly expressed bicistronic transcripts, with several features influencing translational modulation.

Origin of the eukaryotic nucleus: eukaryotes and eocytes are genotypically related

1989 ◽  
Vol 35 (1) ◽  
pp. 109-118 ◽  
Author(s):  
James A. Lake
Keyword(s):  
Common Ancestor ◽  
Sulfur Metabolism ◽  
Nuclear Genes ◽  
Rrna Genes ◽  
Last Common Ancestor ◽  
Nucleotide Substitutions ◽  
Eukaryotic Nucleus ◽  
Eukaryotic Group

The origin of the eukaryotic nucleus is difficult to reconstruct. While eukaryotic organelles (chloroplast, mitochondrion) are eubacterial endosymbionts, the source of nuclear genes has been obscured by multiple nucleotide substitutions. Using evolutionary parsimony, a newly developed rate-invariant treeing algorithm, the eukaryotic rRNA genes are shown to have evolved from the eocytes, a group of extremely thermophilic, sulfur-metabolizing, anucleate cells. The deepest bifurcation yet found separates the reconstructed tree into two taxonomic divisions. These are a proto-eukaryotic group (karyotes) and an essentially bacterial one (parkaryotes). Within the precision of the rooting procedure, the tree is not consistent with either the prokaryotic–eukaryotic or the archaebacterial–eubacterial–eukaryotic groupings. It implies that the last common ancestor of extant life, and the early ancestors of eukaryotes, very likely lacked nuclei, metabolized sulfur, and lived at near boiling temperatures.Key words: rRNA, evolution, phylogeny, sulfur metabolism.

scholarly journals Diatom modulation of select bacteria through use of two unique secondary metabolites

2020 ◽  
Vol 117 (44) ◽  
pp. 27445-27455
Author(s):  
Ahmed A. Shibl ◽  
Ashley Isaac ◽  
Michael A. Ochsenkühn ◽  
Anny Cárdenas ◽  
Cong Fei ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Microbial Communities ◽  
Azelaic Acid ◽  
Rosmarinic Acid ◽  
Microbial Consortia ◽  
Beneficial Bacteria ◽  
Bacterial Populations ◽  
Eukaryotic Phytoplankton ◽  
Eukaryotic Group ◽  
Asterionellopsis Glacialis

Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatomAsterionellopsis glacialisto reveal how it modulates its naturally associated bacteria. We show thatA. glacialisreprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world’s oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.

scholarly journals Rapid Turnover of Life-Cycle-Related Genes in the Brown Algae

2018 ◽  
Author(s):  
A.P. Lipinska ◽  
M.L. Serrano-Serrano ◽  
Akira F. Peters ◽  
K. Kogame ◽  
J Mark Cock ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Brown Algae ◽  
Phenotypic Diversity ◽  
Expression Patterns ◽  
Life Cycles ◽  
Sexual Life ◽  
High Turnover ◽  
Life Cycle Stages ◽  
Eukaryotic Group

ABSTRACTBackgroundSexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free living, and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures in each of the life cycle generations. Here, we have analysed the nature and extent of genome-wide generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations, in order to assess the potential role of generation-specific selection in shaping patterns of gene expression and divergence.ResultsWe show that the proportion of the transcriptome that is generation-biased is associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also a key role for newly emerged, lineage-specific genes in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes exhibit changes in their patterns of expression.ConclusionOur analysis uncovers the characteristics, expression patterns and evolution of generation-biased genes and underline the selective forces that shape this previously underappreciated source of phenotypic diversity.

scholarly journals Development of a yeast internal-subunit eGFP labeling strategy and its application in subunit identification in eukaryotic group II chaperonin TRiC/CCT

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Yunxiang Zang ◽  
Huping Wang ◽  
Zhicheng Cui ◽  
Mingliang Jin ◽  
Caixuan Liu ◽  
...  
Keyword(s):  
Eukaryotic Group ◽  
Group Ii ◽  
Group Ii Chaperonin

scholarly journals Intron Losses and Gains in Nematodes: Not Eccentric at All

2021 ◽  
Author(s):  
Ming-Yue Ma ◽  
Ji Xia ◽  
Kunxian Shu ◽  
Deng-Ke Niu
Keyword(s):  
Intron Loss ◽  
Significant Heterogeneity ◽  
Intron Evolution ◽  
High Level Expression ◽  
Spliceosomal Introns ◽  
Coding Sequence ◽  
Extensive Analysis ◽  
Wide Range ◽  
Eukaryotic Group ◽  
High Level

AbstractThe evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes of nematodes, Nematoda seem to be an eccentric group. Taking advantage of the recent accumulation of sequenced genomes, we carried out an extensive analysis on the intron losses and gains using 104 nematodes genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per 1kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, and high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3′-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes. All the results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.

scholarly journals Crystal structure of a eukaryotic group II intron lariat

Nature ◽  
2014 ◽  
Vol 514 (7521) ◽  
pp. 193-197 ◽  
Author(s):  
Aaron R. Robart ◽  
Russell T. Chan ◽  
Jessica K. Peters ◽  
Kanagalaghatta R. Rajashankar ◽  
Navtej Toor
Keyword(s):  
Crystal Structure ◽  
Group Ii Intron ◽  
Eukaryotic Group ◽  
Group Ii
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