scholarly journals Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 587
Author(s):  
Pascal Sirand-Pugnet ◽  
Damien Brégeon ◽  
Laure Béven ◽  
Catherine Goyenvalle ◽  
Alain Blanchard ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Horizontal Transfer ◽  
Common Ancestor ◽  
23S Rrna ◽  
Reductive Evolution ◽  
Base Modification ◽  
Chemical Solutions ◽  
Enzyme Families

The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup use the ancestral tetrahydrofolate-dependent TrmFO enzyme to catalyze the formation of m5U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m5U1939 formation in 23S rRNA. RlmFO has replaced the S-adenosyl-L-methionine (SAM)-enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m5U-modifying enzymes that is highly dynamic and has undergone horizontal transfer.

scholarly journals Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

2020 ◽  
Author(s):  
Pascal Sirand-Pugnet ◽  
Damien Brégeon ◽  
Laure Beven ◽  
Catherine Goyenvalle ◽  
Alain Blanchard ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Horizontal Transfer ◽  
Functional Annotation ◽  
Common Ancestor ◽  
Structural Information ◽  
Empirical Testing ◽  
Reductive Evolution ◽  
Base Modification ◽  
Chemical Solutions ◽  
Enzyme Families

The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup, use the ancestral tetrahydrofolate-dependent TrmFO enzyme, to catalyze the formation of m5U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m5U1939 formation in 23S RNA. RlmFO has replaced the S-adenosyl-l-methionine (SAM)-enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m5U modifying enzymes that is highly dynamic and has undergone horizontal transfer. This emphasizes the necessity for combining bioinformatics predictions with empirical testing and structural information to get a reliable functional annotation of these enzymes.

scholarly journals A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System in Rhodobacter sphaeroides

2007 ◽  
Vol 189 (8) ◽  
pp. 3208-3216 ◽  
Author(s):  
Sebastian Poggio ◽  
Cei Abreu-Goodger ◽  
Salvador Fabela ◽  
Aurora Osorio ◽  
Georges Dreyfus ◽  
...  
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Horizontal Transfer ◽  
Common Ancestor ◽  
Growth Conditions ◽  
The Other ◽  
Anaerobic Growth ◽  
Entire Cell ◽  
Complete Set ◽  
Rotating Structure ◽  
Flagellar Genes

ABSTRACT Bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. Approximately 40 proteins are required for the assembly and functionality of this structure. Rhodobacter sphaeroides has two flagellar systems. One of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. In this work we found that the second flagellar system of R. sphaeroides can be expressed and produces a functional flagellum. In many bacteria with two flagellar systems, one is required for swimming, while the other allows movement in denser environments by producing a large number of flagella over the entire cell surface. In contrast, the second flagellar system of R. sphaeroides produces polar flagella that are required for swimming. Expression of the second set of flagellar genes seems to be positively regulated under anaerobic growth conditions. Phylogenic analysis suggests that the flagellar system that was initially characterized was in fact acquired by horizontal transfer from a γ-proteobacterium, while the second flagellar system contains the native genes. Interestingly, other α-proteobacteria closely related to R. sphaeroides have also acquired a set of flagellar genes similar to the set found in R. sphaeroides, suggesting that a common ancestor received this gene cluster.

Inhibition of bacterial translation and growth by peptide nucleic acids targeted to domain II of 23S rRNA

2007 ◽  
Vol 13 (4) ◽  
pp. 220-226 ◽  
Author(s):  
Huang Xue-Wen ◽  
Pan Jie ◽  
An Xian-Yuan ◽  
Zhuge Hong-Xiang
Keyword(s):  
Nucleic Acids ◽  
Peptide Nucleic Acids ◽  
23S Rrna ◽  
Bacterial Translation

scholarly journals The Common Ancestor of Deinococcus Species was Rod-Shaped

2018 ◽  
Vol 11 (1) ◽  
pp. 252-258 ◽  
Author(s):  
Yusuke Morita ◽  
Hiromi Nishida
Keyword(s):  
Horizontal Transfer ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Thermus Thermophilus ◽  
Spherical Shape ◽  
Evolutionary Relationships ◽  
The Common ◽  
Formation System

Background:The genusDeinococcusconsists of species in rod-shape (Bacilli) and spherical shape (Cocci).Objective:In this study, we aimed to determine whether the common ancestor ofDeinococcusspecies was rod-shaped or spherical.Methods:We compared the homologs of the proteins related to the rod-shape in bacteria (MreB, MreC, MreD, MrdA, RodA, and RodZ) in variousDeinococcusspecies andThermus thermophilus.Results:The phylogenetic trees based on each protein and the homologs reflected the evolutionary relationships of the species, indicating that the Horizontal transfer of the genes did not occur during theDeinococcusevolution.Conclusion:The ancestor of the genusDeinococcuswas rod-shaped, and the spherical forms appeared when the rod-shaped formation system was lost during evolution and diversification within the genus.

A Newly Isolated Family of Short Interspersed Repetitive Elements (SINEs) in Coregonid Fishes (Whitefish) With Sequences That Are Almost Identical To Those of the SmaI Family of Repeats: Possible Evidence for the Horizontal Transfer of SINEs

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 355-367 ◽  
Author(s):  
Mitsuhiro Hamada ◽  
Yukiharu Kido ◽  
Mikael Himberg ◽  
James D Reist ◽  
Cao Ying ◽  
...  
Keyword(s):  
Horizontal Transfer ◽  
Chum Salmon ◽  
Common Ancestor ◽  
Consensus Sequence ◽  
Pink Salmon ◽  
Repetitive Elements ◽  
Nuclear Genes ◽  
New Family ◽  
High Degree ◽  
Coregonid Fishes

The SmaI family of repeats is present only in the chum salmon and the pink salmon, and it is not present in five other species in the same genus or in other species in closely related genera. In the present study, we showed that another short interspersed repetitive elements (SINEs) family, which is almost identical to the SmaI family, is present in all fishes in the subfamily Coregoninae, being regarded as the most primitive salmonids. This new family of SINEs was designated the SmaI-cor family (SmaI family of repeats in coregonids). The consensus sequence of the SmaI-cor family was found to be 98.6% homologous to that of the SmaI family. Accordingly, it is difficult to explain the high degree of homology between these two families of SINEs by any mechanism other than the horizontal transfer of SINEs. The estimates of the rate of neutral mutation of nuclear genes, comparing chum salmon and European whitefish, confirmed this possibility. Our results strongly suggest that a member(s) of the SmaI-cor family might have been transferred horizontally from one coregonid species to a common ancestor of chum and pink salmon or to these two species independently, to allow subsequent amplification of the SmaI family in their respective genomes.

scholarly journals Phylogenetic Analysis of “Candidatus Phytoplasma australiense” Reveals Distinct Populations in New Zealand

2006 ◽  
Vol 96 (8) ◽  
pp. 838-845 ◽  
Author(s):  
Mark T. Andersen ◽  
Richard D. Newcomb ◽  
Lia W. Liefting ◽  
Ross E. Beever
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Gene Sequence ◽  
Common Ancestor ◽  
Synonymous Substitution ◽  
Geographic Region ◽  
23S Rrna ◽  
Internal Transcribed Spacer Region ◽  
Tuf Gene ◽  
Time Of Divergence

The phytoplasma “Candidatus Phytoplasma australiense” has been reported from New Zealand and Australia, where it has been associated with a range of host plants, especially since the 1970s. Partial tuf gene sequences of 36 New Zealand (NZ) isolates from four different host genera revealed nine different variants, which clustered into two distinct groups without any obvious correlation with host or geographic region. Phylogenetic analysis of these sequences, together with those available from Australian isolates, revealed three distinct clades: one found solely in Australia, one found solely in NZ, and a third with representatives from both countries. These divisions are consistent with differences observed in the 16–23S rRNA internal transcribed spacer region; therefore, we conclude that they represent three distinct subgroups: tuf 1, tuf 2, and tuf 3. We estimated a time of divergence for the three clades based on a synonymous substitution rate calculated by comparing the complete tuf gene sequence from the Loofah witches'-broom phytoplasma and “Candidatus Phytoplasma australiense”. Using a calibration date of 110 million years, the estimated time to a common ancestor for all clades (6 to 9 million years ago) suggests divergence during the Miocene, well after the geological separation of NZ and Australia.

Nano-graphene oxide as a novel platform for monitoring the effect of LNA modification on nucleic acid interactions

The Analyst ◽  
2014 ◽  
Vol 139 (4) ◽  
pp. 714-720 ◽  
Author(s):  
Muhit Rana ◽  
Mustafa Balcioglu ◽  
Neil Robertson ◽  
Mehmet V. Yigit
Keyword(s):  
Graphene Oxide ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Base Modification ◽  
Spectroscopic Information ◽  
Nano Graphene ◽  
Nucleic Acid Interactions

Graphene oxide serves as a stable nano-platform for adsorption of nucleic acids with or without LNA base modification while providing kinetic and spectroscopic information about the interaction.

scholarly journals The Salmon SmaI Family of Short Interspersed Repetitive Elements (SINEs): Interspecific and Intraspecific Variation of the Insertion of SINEs in the Genomes of Chum and Pink Salmon

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 369-380
Author(s):  
Nobuyoshi Takasaki ◽  
Toshifumi Yamaki ◽  
Mitsuhiro Hamada ◽  
Linda Park ◽  
Norihiro Okada
Keyword(s):  
Intraspecific Variation ◽  
Horizontal Transfer ◽  
Chum Salmon ◽  
Common Ancestor ◽  
Pink Salmon ◽  
Repetitive Elements ◽  
Sine Family ◽  
Orthologous Loci ◽  
Insertion Sites ◽  
Interspecific And Intraspecific Variation

The genomes of chum salmon and pink salmon contain a family of short interspersed repetitive elements (SINEs), designated the salmon SmaI family. It is restricted to these two species, a distribution that suggests that this SINE family might have been generated in their common ancestor. When insertions of the SmaI SINEs at 10 orthologous loci of these species were analyzed, however, it was found that there were no shared insertion sites between chum and pink salmon. Furthermore, at six loci where SmaI SINEs have been species-specifically inserted in chum salmon, insertions of SINEs were polymorphic among populations of chum salmon. By contrast, at four loci where SmaI SINEs had been species-specifically inserted in pink salmon, the SINEs were fixed among all populations of pink salmon. The interspecific and intraspecific variation of the SmaI SINEs cannot be explained by the assumption that the SmaI family was amplified in a common ancestor of these two species. To interpret these observations, we propose several possible models, including introgression and the horizontal transfer of SINEs from pink salmon to chum salmon during evolution.

Electron Microscopy of Nucleic Acids

1974 ◽  
Vol 32 ◽  
pp. 302-303
Author(s):  
Norman Davidson
Keyword(s):  
Electron Microscopy ◽  
Nucleic Acids ◽  
Basic Protein ◽  
Molecular Biologist ◽  
Topological Properties ◽  
Protein Film ◽  
Polynucleotide Chain

The basic protein film technique for mounting nucleic acids for electron microscopy has proven to be a general and powerful tool for the working molecular biologist in characterizing different nucleic acids. It i s possible to measure molecular lengths of duplex and single-stranded DNAs and RNAs. In particular, it is thus possible to as certain whether or not the nucleic acids extracted from a particular source are or are not homogeneous in length. The topological properties of the polynucleotide chain (linear or circular, relaxed or supercoiled circles, interlocked circles, etc. ) can also be as certained.

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