scholarly journals A distinct pathway for tetrahymanol synthesis in bacteria

2015 ◽  
Vol 112 (44) ◽  
pp. 13478-13483 ◽  
Author(s):  
Amy B. Banta ◽  
Jeremy H. Wei ◽  
Paula V. Welander
Keyword(s):  
Tetrahymena Pyriformis ◽  
Ring Expansion ◽  
Bacterial Genomes ◽  
Water Column Stratification ◽  
Expression Studies ◽  
Aerobic Methanotrophs ◽  
Biochemical Mechanisms ◽  
Ancient Ecosystems ◽  
Eukaryotic Genomes ◽  
Bacterial Domain

Tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate Tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. Bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. Here we couple comparative genomics with genetic and lipid analyses to link a protein of unknown function to tetrahymanol synthesis in bacteria. This tetrahymanol synthase (Ths) is found in a variety of bacterial genomes, including aerobic methanotrophs, nitrite-oxidizers, and sulfate-reducers, and in a subset of aquatic and terrestrial metagenomes. Thus, the potential to produce tetrahymanol is more widespread in the bacterial domain than previously thought. However, Ths is not encoded in any eukaryotic genomes, nor is it homologous to eukaryotic squalene-tetrahymanol cyclase, which catalyzes the cyclization of squalene directly to tetrahymanol. Rather, heterologous expression studies suggest that bacteria couple the cyclization of squalene to a hopene molecule by squalene-hopene cyclase with a subsequent Ths-dependent ring expansion to form tetrahymanol. Thus, bacteria and eukaryotes have evolved distinct biochemical mechanisms for producing tetrahymanol.

scholarly journals The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity

2020 ◽  
Vol 48 (11) ◽  
pp. 6170-6183 ◽  
Author(s):  
Ketty Pernod ◽  
Laure Schaeffer ◽  
Johana Chicher ◽  
Eveline Hok ◽  
Christian Rick ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Bacterial Genomes ◽  
Eukaryotic Translation ◽  
Eukaryotic Ribosome ◽  
Translation Fidelity ◽  
Translation Systems ◽  
Eukaryotic Genomes ◽  
Paralysis Virus ◽  
Decoding Fidelity

Abstract Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.

scholarly journals The Azurin Coding Gene: Origin and Phylogenetic Distribution

2021 ◽  
Vol 10 (1) ◽  
pp. 9
Author(s):  
Leandro Gammuto ◽  
Carolina Chiellini ◽  
Marta Iozzo ◽  
Renato Fani ◽  
Giulio Petroni
Keyword(s):  
Anticancer Activity ◽  
Bacterial Genomes ◽  
Patchy Distribution ◽  
Vertical Inheritance ◽  
Bacterial Phyla ◽  
Conserved Domain ◽  
Domains Of Life ◽  
Gene Origin ◽  
Bacterial Domain ◽  
Cancer Diseases

Azurin is a bacterial-derived cupredoxin, which is mainly involved in electron transport reactions. Interest in azurin protein has risen in recent years due to its anticancer activity and its possible applications in anticancer therapies. Nevertheless, the attention of the scientific community only focused on the azurin protein found in Pseudomonas aeruginosa (Proteobacteria, Gammaproteobacteria). In this work, we performed the first comprehensive screening of all the bacterial genomes available in online repositories to assess azurin distribution in the three domains of life. The Azurin coding gene was not detected in the domains Archaea and Eucarya, whereas it was detected in phyla other than Proteobacteria, such as Bacteroidetes, Verrucomicrobia and Chloroflexi, and a phylogenetic analysis of the retrieved sequences was performed. Observed patchy distribution and phylogenetic data suggest that once it appeared in the bacterial domain, the azurin coding gene was lost in several bacterial phyla and/or anciently horizontally transferred between different phyla, even though a vertical inheritance appeared to be the major force driving the transmission of this gene. Interestingly, a shared conserved domain has been found among azurin members of all the investigated phyla. This domain is already known in P. aeruginosa as p28 domain and its importance for azurin anticancer activity has been widely explored. These findings may open a new and intriguing perspective in deciphering the azurin anticancer mechanisms and to develop new tools for treating cancer diseases.

scholarly journals mosaicFlye: Resolving long mosaic repeats using long error-prone reads

2020 ◽  
Author(s):  
Anton Bankevich ◽  
Pavel Pevzner
Keyword(s):  
Human Chromosome ◽  
Human Genome ◽  
Genome Assembly ◽  
Chromosome 6 ◽  
Segmental Duplications ◽  
Bacterial Genomes ◽  
Long Read ◽  
Human Chromosome 6 ◽  
Genome Assemblies ◽  
Eukaryotic Genomes

AbstractLong-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e., repeats that are spanned by some reads) in various genomes. However, the problem of resolving unbridged repeats (such as long segmental duplications in the human genome) remains largely unsolved, making it a major obstacle towards achieving the goal of complete genome assemblies. Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of bacterial genomes and metagenomes. We describe the mosaicFlye algorithm for resolving complex unbridged repeats based on differences between various repeat copies and show how it improves assemblies of the human genome as well as bacterial genomes and metagenomes. In particular, we show that mosaicFlye results in a complete assembly of both arms of the human chromosome 6.

Codon Signature Extremes In Eukaryote genomes

2006 ◽  
Vol 52 (3-4) ◽  
pp. 281-297 ◽  
Author(s):  
Samuel Karlin ◽  
Dorit Carmelli
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Mammalian Species ◽  
Life Domains ◽  
Codon Site ◽  
Bacterial Genomes ◽  
Noncoding Regions ◽  
Genome Wide ◽  
Eukaryotic Genomes

Twenty-one complete eukaryotic genomes are compared for codon signature biases. The codon signature refers to the dinucleotide relative abundance values at codon sites {1, 2}, {2, 3}, and {3, 4} (4 = 1 of the next codon site). The genomes under study include human, mouse, chicken, three invertebrates, one plant species, eight fungi, and six protists. The dinucleotide CpG is significantly underrepresented at all contiguous codon sites and drastically suppressed in noncoding regions in mammalian species, in yeast-like genomes, in the dicot Arabidopsis thaliana, but not in the filamentous fungi Neurospora crassa and Asperigillus fumigatus, and in the protist Entamoeba histolytica. The dinucleotide TpA, probably due to DNA structural weaknesses, is underrepresented genome-wide and significantly underrepresented in the codon signature for all contiguous codon sites in mammals, inverterbrates, plants, and fungi, but somewhat restricted to codon sites {1, 2} among protists helping in avoidance of stop codons. The amino acid Ser, not of abundance in bacterial genomes, generally ranks among the two most used amino acids among eukaryotes ostensibly resulting from greater activity in the nucleus. The observed differences are linked to specifics of methylation, context-dependent mutation, DNA repair, and replication. For example, the amino acid Leu is broadly abundant in all life domains generally resulting from extra occurrences of the codon TTR, R purine. The malarial protist Plasmodium falciparum shows many codon signature extremes.

scholarly journals Antibiotic Resistance and Epigenetics: More to It than Meets the Eye

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Dipannita Ghosh ◽  
Balaji Veeraraghavan ◽  
Ravikrishnan Elangovan ◽  
Perumal Vivekanandan
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Epigenetic Inheritance ◽  
Epigenetic Mechanisms ◽  
Bacterial Genomes ◽  
Genetic Changes ◽  
Inappropriate Use ◽  
Transient Nature ◽  
History Of ◽  
Biochemical Mechanisms

ABSTRACT The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.

scholarly journals Genomic GC content drifts slowly downward in most bacterial genomes

2020 ◽  
Author(s):  
Bert Ely
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Bacterial Genomes ◽  
Base Pairs ◽  
Wide Range ◽  
Biased Gene Conversion ◽  
Prokaryotic Genomes ◽  
Genome Content ◽  
Genomic Gc Content ◽  
Eukaryotic Genomes

AbstractIn every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is slowly declining in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing at a slow rate. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genome content as well.

scholarly journals Genomic GC content drifts downward in most bacterial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0244163
Author(s):  
Bert Ely
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Bacterial Genomes ◽  
Evolutionary Time ◽  
Base Pairs ◽  
Wide Range ◽  
Biased Gene Conversion ◽  
Prokaryotic Genomes ◽  
Genomic Gc Content ◽  
Eukaryotic Genomes

In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genomic GC content as well.

scholarly journals Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Michael Sheinman ◽  
Ksenia Arkhipova ◽  
Peter F Arndt ◽  
Bas Dutilh ◽  
Rutger Hermsen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Transfer Rate ◽  
Microbial Evolution ◽  
Functional Categories ◽  
Bacterial Genomes ◽  
Long Distance ◽  
Microbial World ◽  
Alignment Free ◽  
Fundamental Process ◽  
Bacterial Domain

Horizontal Gene Transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93 481 bacterial genomes identified 138 273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than 3 orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.

scholarly journals C-4 sterol demethylation enzymes distinguish bacterial and eukaryotic sterol synthesis

2018 ◽  
Vol 115 (23) ◽  
pp. 5884-5889 ◽  
Author(s):  
Alysha K. Lee ◽  
Amy B. Banta ◽  
Jeremy H. Wei ◽  
David J. Kiemle ◽  
Ju Feng ◽  
...  
Keyword(s):  
Heterologous Expression ◽  
Unknown Function ◽  
Bacterial Species ◽  
Sedimentary Rocks ◽  
Sterol Synthesis ◽  
Methylococcus Capsulatus ◽  
Bacterial Genomes ◽  
Separate Pathway ◽  
Phylogenomic Analyses ◽  
Eukaryotic Genomes

Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth’s history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers. Recent studies suggest that bacterial sterol synthesis may be distinct from what is observed in eukaryotes. In particular, phylogenomic analyses of sterol-producing bacteria have failed to identify homologs of several key eukaryotic sterol synthesis enzymes, most notably those required for demethylation at the C-4 position. In this study, we identified two genes of previously unknown function in the aerobic methanotrophic γ-ProteobacteriumMethylococcus capsulatusthat encode sterol demethylase proteins (Sdm). We show that a Rieske-type oxygenase (SdmA) and an NAD(P)-dependent reductase (SdmB) are responsible for converting 4,4-dimethylsterols to 4α-methylsterols. Identification of intermediate products synthesized during heterologous expression of SdmA-SdmB along with13C-labeling studies support a sterol C-4 demethylation mechanism distinct from that of eukaryotes. SdmA-SdmB homologs were identified in several other sterol-producing bacterial genomes but not in any eukaryotic genomes, indicating that these proteins are unrelated to the eukaryotic C-4 sterol demethylase enzymes. These findings reveal a separate pathway for sterol synthesis exclusive to bacteria and show that demethylation of sterols evolved at least twice—once in bacteria and once in eukaryotes.

Albumin-Induced Endocytic Vacuoles in Tetrahymena Pyrijormis

1975 ◽  
Vol 33 ◽  
pp. 694-695
Author(s):  
L. J. Brenner ◽  
D. G. Osborne ◽  
B. L. Schumaker
Keyword(s):  
Electron Microscopy ◽  
Bovine Serum Albumin ◽  
Bovine Serum ◽  
Protein Concentration ◽  
Tetrahymena Pyriformis ◽  
Sequence Of Events ◽  
Cytoplasmic Bodies ◽  
Food Vacuoles ◽  
Mouse Ascites ◽  
Normal Human

Exposure of the ciliate, Tetrahymena pyriformis, strain WH6, to normal human or rabbit sera or mouse ascites fluids induces the formation of large cytoplasmic bodies. By electron microscopy these (LB) are observed to be membrane-bounded structures, generally spherical and varying in size (Fig. 1), which do not resemble the food vacuoles of cells grown in proteinaceous broth. The possibility exists that the large bodies represent endocytic vacuoles containing material concentrated from the highly nutritive proteins and lipoproteins of the sera or ascites fluids. Tetrahymena mixed with bovine serum albumin or ovalbumin solutions having about the same protein concentration (7g/100 ml) as serum form endocytic vacuoles which bear little resemblance to the serum-induced LB. The albumin-induced structures (Fig. 2) are irregular in shape, rarely spherical, and have contents which vary in density and consistency. In this paper an attempt is made to formulate the sequence of events which might occur in the formation of the albumin-induced vacuoles.

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