scholarly journals Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids

2020 ◽  
Author(s):  
Ryo Harada ◽  
Yuji Inagaki
Keyword(s):  
Dna Replication ◽  
Common Ancestor ◽  
Dna Polymerases ◽  
Mitochondrial Genomes ◽  
Large Contribution ◽  
Evolutionary Trend ◽  
Evolutionary Origins ◽  
Dna Replication And Repair ◽  
Specific Affinity ◽  
The Common

AbstractMitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as “PolIBCD+”) have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via non-vertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.

scholarly journals Origins of Flagellar Gene Operons and Secondary Flagellar Systems

2007 ◽  
Vol 189 (19) ◽  
pp. 7098-7104 ◽  
Author(s):  
Renyi Liu ◽  
Howard Ochman
Keyword(s):  
Genetic Basis ◽  
Common Ancestor ◽  
Evolutionary Trend ◽  
Flagellar Gene ◽  
Bacterial Evolution ◽  
Bacterial Phyla ◽  
New Genes ◽  
Gene Complexes ◽  
The Common ◽  
Flagellar Genes

ABSTRACT Forty-one flagellated species representing 11 bacterial phyla were used to investigate the origin of secondary flagellar systems and the structure and formation of flagellar gene operons over the course of bacterial evolution. Secondary (i.e., lateral) flagellar systems, which are harbored by five of the proteobacterial species considered, originated twice, once in the alphaproteobacterial lineage and again in the common ancestor of the Beta- and Gammaproteobacteria. The order and organization of flagellar genes have undergone extensive shuffling and rearrangement among lineages, and based on the phylogenetic distributions of flagellar gene complexes, the flagellar gene operons existed as small, usually two-gene units in the ancestor of Bacteria and have expanded through the recruitment of new genes and fusion of gene units. In contrast to the evolutionary trend towards larger flagellar gene complexes, operon structures have been highly disrupted through gene disassociation and rearrangements in the Epsilon- and Alphaproteobacteria. These results demonstrate that the genetic basis of this ancient and structurally conserved organelle has been subject to many lineage-specific modifications.

scholarly journals Archaeal DNA polymerases: new frontiers in DNA replication and repair

2018 ◽  
Vol 2 (4) ◽  
pp. 503-516 ◽  
Author(s):  
Christopher D.O. Cooper
Keyword(s):  
Dna Repair ◽  
Dna Replication ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Dna Amplification ◽  
Model Systems ◽  
Genome Replication ◽  
Sequencing Technologies ◽  
Dna Replication And Repair ◽  
Polymerase Chain

Archaeal DNA polymerases have long been studied due to their superior properties for DNA amplification in the polymerase chain reaction and DNA sequencing technologies. However, a full comprehension of their functions, recruitment and regulation as part of the replisome during genome replication and DNA repair lags behind well-established bacterial and eukaryotic model systems. The archaea are evolutionarily very broad, but many studies in the major model systems of both Crenarchaeota and Euryarchaeota are starting to yield significant increases in understanding of the functions of DNA polymerases in the respective phyla. Recent advances in biochemical approaches and in archaeal genetic models allowing knockout and epitope tagging have led to significant increases in our understanding, including DNA polymerase roles in Okazaki fragment maturation on the lagging strand, towards reconstitution of the replisome itself. Furthermore, poorly characterised DNA polymerase paralogues are finding roles in DNA repair and CRISPR immunity. This review attempts to provide a current update on the roles of archaeal DNA polymerases in both DNA replication and repair, addressing significant questions that remain for this field.

scholarly journals Evolution, Diversification, and Biogeography of Grasshoppers (Orthoptera: Acrididae)

2018 ◽  
Vol 2 (4) ◽  
Author(s):  
Hojun Song ◽  
Ricardo Mariño-Pérez ◽  
Derek A Woller ◽  
Maria Marta Cigliano
Keyword(s):  
South America ◽  
Common Ancestor ◽  
Taxonomic Revision ◽  
Valid Species ◽  
Mitochondrial Genomes ◽  
Behavioral Diversity ◽  
The Family ◽  
The Common ◽  
Biogeographical Analysis ◽  
Forest Habitats

Abstract The grasshopper family Acrididae is one of the most diverse lineages within Orthoptera, including more than 6,700 valid species distributed worldwide. Grasshoppers are dominant herbivores, which have diversified into grassland, desert, semi-aquatic, alpine, and tropical forest habitats, and exhibit a wide array of morphological, ecological, and behavioral diversity. Nevertheless, the phylogeny of Acrididae as a whole has never been proposed. In this study, we present the first comprehensive phylogeny of Acrididae based on mitochondrial genomes and nuclear genes to test monophyly of the family and different subfamilies as well as to understand the evolutionary relationships among them. We recovered the monophyletic Acrididae and identified four major clades as well as several well-characterized subfamilies, but we also found that paraphyly is rampant across many subfamilies, highlighting the need for a taxonomic revision of the family. We found that Acrididae originated in the Paleocene of the Cenozoic period (59.3 million years ago) and, because the separation of South America and Africa predates the origin of the family, we hypothesize that the current cosmopolitan distribution of Acrididae was largely achieved by dispersal. We also inferred that the common ancestor of modern grasshoppers originated in South America, contrary to a popular belief that they originated in Africa, based on a biogeographical analysis. We estimate that there have been a number of colonization and recolonization events between the New World and the Old World throughout the diversification of Acrididae, and, thus, the current diversity in any given region is a reflection of this complex history.

Functions of DNA Polymerases α, β and γ in DNA Replication and Repair

1980 ◽  
pp. 33-51
Author(s):  
Miria Stefanini ◽  
Anna I. Scovassi ◽  
Umberto Bertazzoni
Keyword(s):  
Dna Replication ◽  
Dna Polymerases ◽  
Dna Replication And Repair

scholarly journals Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts

2020 ◽  
Vol 7 (2) ◽  
pp. 191887 ◽  
Author(s):  
Hong Zou ◽  
Ivan Jakovlić ◽  
Dong Zhang ◽  
Cong-Jie Hua ◽  
Rong Chen ◽  
...  
Keyword(s):  
Gene Order ◽  
Replication Origin ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Taxon Sampling ◽  
Mitochondrial Genomes ◽  
Long Branch Attraction ◽  
Strand Asymmetry ◽  
Complete Exclusion ◽  
The Common

The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.

PrimPol (Primase/Polymerase), replicating enzyme – A mini review

2020 ◽  
Vol 2 (4) ◽  
pp. 89-92
Author(s):  
Muhammad Amir ◽  
Sabeera Afzal ◽  
Alia Ishaq
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Genetic Information ◽  
Nuclear Dna ◽  
De Novo ◽  
Dna Polymerases ◽  
Test Site ◽  
Mitochondrial Dna Replication ◽  
Dna Template ◽  
Preliminary Phase

Polymerases were revealed first in 1970s. Most important to the modest perception the enzyme responsible for nuclear DNA replication that was pol , for DNA repair pol and for mitochondrial DNA replication pol  DNA construction and renovation done by DNA polymerases, so directing both the constancy and discrepancy of genetic information. Replication of genome initiate with DNA template-dependent fusion of small primers of RNA. This preliminary phase in replication of DNA demarcated as de novo primer synthesis which is catalyzed by specified polymerases known as primases. Sixteen diverse DNA-synthesizing enzymes about human perspective are devoted to replication, reparation, mutilation lenience, and inconsistency of nuclear DNA. But in dissimilarity, merely one DNA polymerase has been called in mitochondria. It has been suggest that PrimPol is extremely acting the roles by re-priming DNA replication in mitochondria to permit an effective and appropriate way replication to be accomplished. Investigations from a numeral of test site have significantly amplified our appreciative of the role, recruitment and regulation of the enzyme during DNA replication. Though, we are simply just start to increase in value the versatile roles that play PrimPol in eukaryote.

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