Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions

2011 ◽  
Vol 39 (1) ◽  
pp. 169-173 ◽  
Author(s):  
Adi Barzel ◽  
Adit Naor ◽  
Eyal Privman ◽  
Martin Kupiec ◽  
Uri Gophna
Keyword(s):  
Homing Endonuclease ◽  
Horizontal Transmission ◽  
Molecular Genetic ◽  
Halophilic Archaea ◽  
Homing Endonucleases ◽  
Protein Coding ◽  
Selfish Genetic Elements ◽  
Fitness Effects ◽  
Endonuclease Domain ◽  
Competition Assays

Inteins are selfish genetic elements that disrupt the sequence of protein-coding genes and are excised post-translationally. Most inteins also contain a HEN (homing endonuclease) domain, which is important for their horizontal transmission. The present review focuses on the evolution of inteins and their nested HENs, and highlights several unsolved questions that could benefit from molecular genetic approaches. Such approaches can be well carried out in halophilic archaea, which are naturally intein-rich and have highly developed genetic tools for their study. In particular, the fitness effects of habouring an intein/HEN can be tested in direct competition assays, providing additional insights that will improve current evolutionary models.

scholarly journals Interplay of population genetics and dynamics in the genetic control of mosquitoes

2014 ◽  
Vol 11 (93) ◽  
pp. 20131071 ◽  
Author(s):  
Nina Alphey ◽  
Michael B. Bonsall
Keyword(s):  
Population Genetics ◽  
Overlapping Generations ◽  
Large Scale ◽  
Genetic Model ◽  
Homing Endonuclease ◽  
Wild Type ◽  
Larval Competition ◽  
Selfish Genetic Elements ◽  
Fitness Effects ◽  
Ecological Aspects

Some proposed genetics-based vector control methods aim to suppress or eliminate a mosquito population in a similar manner to the sterile insect technique. One approach under development in Anopheles mosquitoes uses homing endonuclease genes (HEGs)—selfish genetic elements (inherited at greater than Mendelian rate) that can spread rapidly through a population even if they reduce fitness. HEGs have potential to drive introduced traits through a population without large-scale sustained releases. The population genetics of HEG-based systems has been established using discrete-time mathematical models. However, several ecologically important aspects remain unexplored. We formulate a new continuous-time (overlapping generations) combined population dynamic and genetic model and apply it to a HEG that targets and knocks out a gene that is important for survival. We explore the effects of density dependence ranging from undercompensating to overcompensating larval competition, occurring before or after HEG fitness effects, and consider differences in competitive effect between genotypes (wild-type, heterozygotes and HEG homozygotes). We show that population outcomes—elimination, suppression or loss of the HEG—depend crucially on the interaction between these ecological aspects and genetics, and explain how the HEG fitness properties, the homing rate (drive) and the insect's life-history parameters influence those outcomes.

scholarly journals Complete mitochondrial DNA sequence analysis of Bluespotted seabream, Pagrus caeruleostictus (Perciformes: Sparidae)

2019 ◽  
Author(s):  
Gyamfua Afriyie ◽  
Yusong Guo ◽  
Felix K.A Kuebutornye ◽  
Christian Ayisi Larbi ◽  
Zhongduo Wang
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Molecular Genetic ◽  
Marine Species ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Tropical Regions ◽  
Mitochondrial Dna Sequence ◽  
Rna Genes ◽  
Pagrus Caeruleostictus

Abstract Background Bluespotted seabream, Pagrus caeruleostictus is a benthopelagic marine species found in tropical regions and a member of the family Sparidae and genus Pagrus . In this article, a mitochondrial DNA sequence by high-throughput technique, Illumina Hiseq, was carried out on muscle of the above species and determined the complete mitogenome. Samples were obtained from species collected from the coast of Ghana, West Africa.Results The complete mitochondrial DNA sequence was 16,653 bases pairs in length (GenBank Accession number: MN319701) and comprises of 37 genes; 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a control region as in a typical vertebrate mitochondrial DNA gene. The phylogenetic analysis showed P. caeruleostictus clustered with the clade of P. auriga. Conclusion This research will serve as the foundation for molecular genetic studies of Ghanaian fish species. Moreover, it will contribute to the phylogenetics of class Actinopterygii, order Spariformes, family Sparidae and genus Pagrus.

Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus

2021 ◽  
Author(s):  
Abby M. Korn ◽  
Andrew E. Hillhouse ◽  
Lichang Sun ◽  
Jason J. Gill
Keyword(s):  
Staphylococcus Aureus ◽  
Comparative Genomics ◽  
The United States ◽  
Genomic Diversity ◽  
Homing Endonucleases ◽  
Swine Production ◽  
Protein Coding ◽  
Vertical Inheritance ◽  
Production Environments ◽  
Genes Encoding

The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel S. aureus “jumbo” phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content is similar to known jumbo phages of Bacillus , including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of work: This study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss is an active process in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making them a potential vector for horizontal gene transfer in the environment.

scholarly journals Algal Viruses with Distinct Intraspecies Host Specificities Include Identical Intein Elements

2005 ◽  
Vol 71 (7) ◽  
pp. 3599-3607 ◽  
Author(s):  
Keizo Nagasaki ◽  
Yoko Shirai ◽  
Yuji Tomaru ◽  
Kensho Nishida ◽  
Shmuel Pietrokovski
Keyword(s):  
Dna Polymerase ◽  
Homing Endonuclease ◽  
Sister Group ◽  
Dna Virus ◽  
Single Nucleotide Change ◽  
Double Stranded Dna ◽  
Endonuclease Domain ◽  
Algal Viruses ◽  
Molecular Phylogenetic ◽  
Position Coding

ABSTRACT Heterosigma akashiwo virus (HaV) is a large double-stranded DNA virus infecting the single-cell bloom-forming raphidophyte (golden brown alga) H. akashiwo. A molecular phylogenetic sequence analysis of HaV DNA polymerase showed that it forms a sister group with Phycodnaviridae algal viruses. All 10 examined HaV strains, which had distinct intraspecies host specificities, included an intein (protein intron) in their DNA polymerase genes. The 232-amino-acid inteins differed from each other by no more than a single nucleotide change. All inteins were present at the same conserved position, coding for an active-site motif, which also includes inteins in mimivirus (a very large double-stranded DNA virus of amoebae) and in several archaeal DNA polymerase genes. The HaV intein is closely related to the mimivirus intein, and both are apparently monophyletic to the archaeal inteins. These observations suggest the occurrence of horizontal transfers of inteins between viruses of different families and between archaea and viruses and reveal that viruses might be reservoirs and intermediates in horizontal transmissions of inteins. The homing endonuclease domain of the HaV intein alleles is mostly deleted. The mechanism keeping their sequences basically identical in HaV strains specific for different hosts is yet unknown. One possibility is that rapid and local changes in the HaV genome change its host specificity. This is the first report of inteins found in viruses infecting eukaryotic algae.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI fromChlorella vulgarisin complex with its target DNA

2014 ◽  
Vol 70 (2) ◽  
pp. 256-259 ◽  
Author(s):  
Pilar Redondo ◽  
Nekane Merino ◽  
Maider Villate ◽  
Francisco J. Blanco ◽  
Guillermo Montoya ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Homing Endonuclease ◽  
Homing Endonucleases ◽  
Resolution Limit ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Strand Breaks ◽  
X Ray ◽  
Cell Parameters ◽  
Wide Range

Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of DNA. The engineering of these enzymes provides novel instruments for genome modification in a wide range of fields, including gene targeting, by inducing specific double-strand breaks. I-CvuI is a homing endonuclease from the green algaChlorella vulgaris. This enzyme was purified after overexpression inEscherichia coli. Crystallization experiments of I-CvuI in complex with its DNA target in the presence of Mg2+yielded crystals suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 62.83,b= 83.56,c= 94.40 Å. The self-rotation function and the Matthews coefficient suggested the presence of one protein–DNA complex per asymmetric unit. The crystals diffracted to a resolution limit of 1.9 Å using synchrotron radiation.

scholarly journals Evolution of symbiont transmission in conditional mutualisms in spatially and temporally variable environments

2020 ◽  
Author(s):  
Alexandra Brown ◽  
Erol Akçay
Keyword(s):  
Vertical Transmission ◽  
Horizontal Transmission ◽  
Environmental Variation ◽  
Transmission Mode ◽  
Trade Off ◽  
Symbiotic Relationships ◽  
Physiological Constraints ◽  
Fitness Effects ◽  
Variable Environments ◽  
Symbiont Transmission

AbstractSymbiotic relationships affect the fitness and organismal function of virtually all organisms. In many cases, the fitness effects of symbiosis may be beneficial or harmful depending on the environment. The hosts of such symbionts are favored to acquire them only when the symbiont is beneficial. However, it is not clear whether such selection favors vertical or horizontal transmission, both, or neither. To address this question, we model the evolution of transmission mode in a conditional mutualism experiencing spatial and temporal environmental variation. We find that when symbionts affect host lifespan, but not fecundity, horizontal transmission can contain them to beneficial environments. Vertical transmission can produce symbiont containment when the environmental state is synchronized across locations. We also find an emergent trade-off between horizontal and vertical transmission, suggesting that physiological constraints are not required for the evolution of limits on the total amount of transmission.

Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

1999 ◽  
Vol 65 (12) ◽  
pp. 5586-5589 ◽  
Author(s):  
Ken Takai ◽  
Koki Horikoshi
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Homing Endonuclease ◽  
Open Reading Frames ◽  
Molecular Phylogenetic Analysis ◽  
Homing Endonucleases ◽  
Deep Subsurface ◽  
Molecular Phylogenetic ◽  
Sequence Similarity Analysis

ABSTRACT Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases.

scholarly journals De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Nikolaos Vakirlis ◽  
Omer Acar ◽  
Brian Hsu ◽  
Nelson Castilho Coelho ◽  
S. Branden Van Oss ◽  
...  
Keyword(s):  
Natural Selection ◽  
De Novo ◽  
Natural Populations ◽  
Evolutionary Model ◽  
Transmembrane Domains ◽  
Protein Coding ◽  
Fitness Effects ◽  
Evolutionary Innovation ◽  
Intergenic Regions ◽  
Novel Protein

AbstractRecent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast. Disruption of emerging sequences is generally inconsequential for fitness in the laboratory and in natural populations. Overexpression of emerging sequences, however, is enriched in adaptive fitness effects compared to overexpression of established genes. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich non-genic regions and subsequently accumulate changes molded by natural selection.

scholarly journals An assessment of the immune costs associated with meiotic drive elements in Drosophila

2019 ◽  
Vol 286 (1911) ◽  
pp. 20191534 ◽  
Author(s):  
Jenna Kay Lea ◽  
Robert L. Unckless
Keyword(s):  
Meiotic Drive ◽  
Immune Gene ◽  
Immune Defence ◽  
Deleterious Mutations ◽  
Wild Type ◽  
Selfish Genetic Elements ◽  
Fitness Effects ◽  
Immune Gene Expression ◽  
Chromosomal Inversions ◽  
Segregation Distorter

Most organisms are constantly adapting to pathogens and parasites that exploit their host for their own benefit. Less studied, but perhaps more ubiquitous, are intragenomic parasites or selfish genetic elements. These include transposable elements, selfish B chromosomes and meiotic drivers that promote their own replication without regard to fitness effects on hosts. Therefore, intragenomic parasites are also a constant evolutionary pressure on hosts. Gamete-killing meiotic drive elements are often associated with large chromosomal inversions that reduce recombination between the drive and wild-type chromosomes. This reduced recombination is thought to reduce the efficacy of selection on the drive chromosome and allow for the accumulation of deleterious mutations. We tested whether gamete-killing meiotic drive chromosomes were associated with reduced immune defence against two bacterial pathogens in three species of Drosophila . We found little evidence of reduced immune defence in lines with meiotic drive. One line carrying the Drosophila melanogaster autosomal Segregation Distorter did show reduced defence, but we were unable to attribute that reduced defence to either genotype or immune gene expression differences. Our results suggest that though gamete-killing meiotic drive chromosomes probably accumulate deleterious mutations, those mutations do not result in reduced capacity for immune defence.

scholarly journals Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions

2016 ◽  
Vol 72 (6) ◽  
pp. 473-479 ◽  
Author(s):  
Jesús Prieto ◽  
Pilar Redondo ◽  
Nekane Merino ◽  
Maider Villate ◽  
Guillermo Montoya ◽  
...  
Keyword(s):  
Metal Ion ◽  
Catalytic Mechanism ◽  
Homing Endonuclease ◽  
Homing Endonucleases ◽  
Resolution Limit ◽  
Orthorhombic Space Group ◽  
Cell Parameters ◽  
Anomalous Data ◽  
Wide Range ◽  
Dna Strand

Homing endonucleases are highly specific DNA-cleaving enzymes that recognize and cleave long stretches of DNA. The engineering of these enzymes provides instruments for genome modification in a wide range of fields, including gene targeting. The homing endonuclease I-SceI from the yeastSaccharomyces cerevisiaehas been purified after overexpression inEscherichia coliand its crystal structure has been determined in complex with its target DNA. In order to evaluate the number of ions that are involved in the cleavage process, thus determining the catalytic mechanism, crystallization experiments were performed in the presence of Mn2+, yielding crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 80.11,b= 80.57,c= 130.87 Å, α = β = γ = 90°. The self-rotation function and the Matthews coefficient suggested the presence of two protein–DNA complexes in the asymmetric unit. The crystals diffracted to a resolution limit of 2.9 Å using synchrotron radiation. From the anomalous data, it was determined that three cations are involved in catalysis and it was confirmed that I-SceI follows a two-metal-ion DNA-strand cleavage mechanism.

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