scholarly journals A Recently Assembled Degradation Pathway for 2,3-Dichloronitrobenzene in Diaphorobacter sp. Strain JS3051

mBio ◽  
2021 ◽  
Author(s):  
Tao Li ◽  
Yi-Zhou Gao ◽  
Jia Xu ◽  
Shu-Ting Zhang ◽  
Yuan Guo ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Degradation Pathway ◽  
Nitroaromatic Compounds ◽  
Naphthalene Dioxygenase ◽  
Evolutionary Mechanisms ◽  
Catabolic Pathways

Because anthropogenic nitroaromatic compounds have entered the biosphere relatively recently, exploration of the recently evolved catabolic pathways can provide clues for adaptive evolutionary mechanisms in bacteria. The concept that nitroarene dioxygenases shared a common ancestor with naphthalene dioxygenase is well established.

Evolution of biosynthetic diversity

2017 ◽  
Vol 474 (14) ◽  
pp. 2277-2299 ◽  
Author(s):  
Anthony J. Michael
Keyword(s):  
Common Ancestor ◽  
Polyamine Metabolism ◽  
Last Common Ancestor ◽  
Protein Fold ◽  
Last Universal Common Ancestor ◽  
Endosymbiotic Gene Transfer ◽  
Evolutionary Mechanisms ◽  
Universal Common Ancestor ◽  
Genes Encoding ◽  
Domains Of Life

Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life. Organisms that live in metabolite-rich environments sometimes lose the pathways that produce those same metabolites. Fusion of different protein domains results in enzymes with novel properties. This review will consider the major evolutionary mechanisms that generate biosynthetic diversity: gene duplication (and gene loss), horizontal and endosymbiotic gene transfer, and gene fusion. It will also discuss mechanisms that lead to convergence as well as divergence. To illustrate these mechanisms, one of the original metabolisms present in the last universal common ancestor will be employed: polyamine metabolism, which is essential for the growth and cell proliferation of archaea and eukaryotes, and many bacteria.

scholarly journals ACPT gene is inactivated in mammalian lineages that lack enamel or teeth

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10219
Author(s):  
Yuan Mu ◽  
Xin Huang ◽  
Rui Liu ◽  
Yulin Gai ◽  
Na Liang ◽  
...  
Keyword(s):  
Fossil Record ◽  
Common Ancestor ◽  
Selective Pressure ◽  
Tooth Enamel ◽  
Sperm Whale ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Baleen Whales ◽  
The Common ◽  
Exon 4

Loss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth/enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and/or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT playing a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals. The results shows that variant ORF-disrupting mutations were detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN/dS values on transitional branches were used to estimate ACPT inactivation records. In the case of aardvark, inactivation of ACPT was estimated at ~23.60–28.32 Ma, which is earlier than oldest aardvark fossil record (Orycteropus minutus, ~19 Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18–11.30 Ma) is later than oldest fossil record, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth/enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.

Phenotypic heterogeneity is an evolutionarily conserved feature of the endothelium

Blood ◽  
2006 ◽  
Vol 109 (2) ◽  
pp. 613-615 ◽  
Author(s):  
Kiichiro Yano ◽  
Daniel Gale ◽  
Steffen Massberg ◽  
Pavan K. Cheruvu ◽  
Rita Monahan-Earley ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Lectin Binding ◽  
Cell Lineage ◽  
Phenotypic Heterogeneity ◽  
Last Common Ancestor ◽  
Functional Heterogeneity ◽  
Evolutionary Mechanisms ◽  
Evolutionarily Conserved ◽  
Vascular Beds ◽  
Ancestral Vertebrate

Abstract Mammalian endothelial cells (ECs) display marked phenotypic heterogeneity. Little is known about the evolutionary mechanisms underlying EC heterogeneity. The last common ancestor of hagfish and gnathostomes was also the last common ancestor of all extant vertebrates, which lived some time more than 500 million years ago. Features of ECs that are shared between hagfish and gnathostomes can be inferred to have already been present in this ancestral vertebrate. The goal of this study was to determine whether the hagfish endothelium displays phenotypic heterogeneity. Electron microscopy of the aorta, dermis, heart, and liver revealed ultrastructural heterogeneity of the endothelium. Immunofluorescent studies demonstrated marked differences in lectin binding between vascular beds. Intravital microscopy of the dermis revealed histamine-induced adhesion of leukocytes in capillaries and postcapillary venules, but no such adhesion in arterioles. Together, these data suggest that structural, molecular, and functional heterogeneity of the endothelium evolved as an early feature of this cell lineage.

scholarly journals ACPT gene is inactivated in mammalian lineages that lack enamel and teeth

2019 ◽  
Author(s):  
Yuan Mu ◽  
Xin Huang ◽  
Rui Liu ◽  
Yulin Gai ◽  
Na Liang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Selective Pressure ◽  
Tooth Enamel ◽  
Sperm Whale ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Baleen Whales ◽  
Single Base ◽  
The Common ◽  
Exon 4

AbstractLoss of tooth or enamel is widespread in multiple mammal lineages. Although several studies have been reported, the evolutionary mechanisms of tooth / enamel loss are still unclear. Most previous studies have found that some tooth-related genes have been inactivated in toothless and / or enamel-less mammals, such as ENAM, ODAM, C4orf26, AMBN, AMTN, DSPP, etc. Here, we conducted evolutionary analyses on ACPT plays a key role in amelogenesis, to interrogate the mechanisms. We obtained the ACPT sequences from 116 species, including edentulous and enamel-less mammals, then evolutionary analyses were implemented. The results showed that variant ORF-disrupting mutations have been detected in ACPT coding region among nine edentulous baleen whales and three enamel-less taxa (pygmy sperm whale, aardvark, nine-banded armadillo). Furtherly, selective pressure uncovered that the selective constraints have been relaxed among all toothless and enamel-less lineages. Moreover, our results support the hypothesis that mineralized teeth were lost or degenerated in the common ancestor of crown Mysticeti through two shared single-base sites deletion in exon 4 and 5 of ACPT among all living baleen whales. DN / dS values on transitional branches were used to estimate ACPT inactivation times. In the case of aardvark, inactivation of ACPT was estimated at ~23.60-28.32 Ma, which is earlier than the oldest pangolin fossil time (Orycteropus minutus, ~19Ma), suggesting that ACPT inactivation may result in degeneration or loss of enamel. Conversely, the inactivation time of ACPT estimated in armadillo (~10.18-11.30 Ma) is later than the oldest fossil time, suggesting that inactivation of ACPT may result from degeneration or loss of enamel in these mammals. Our findings suggested that different mechanisms of degeneration of tooth / enamel might exist among toothless and enamel-less lineages during evolution. Our study further considered that ACPT is a novel gene for studying tooth evolution.

scholarly journals On the contingent nature of satellite DNA evolution

2021 ◽  
Author(s):  
Juan Pedro M Camacho ◽  
Josefa Cabrero ◽  
Maria Dolores Lopez-Leon ◽  
Maria Martin-Pecina ◽  
Francisco Perfectti ◽  
...  
Keyword(s):  
Concerted Evolution ◽  
Satellite Dna ◽  
Common Ancestor ◽  
Locusta Migratoria ◽  
Recent Common Ancestor ◽  
Evolutionary Mechanisms ◽  
Consensus Sequences ◽  
Most Recent Common Ancestor ◽  
Dna Conformations ◽  
Library Hypothesis

Background: The full catalogue of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. Results: We found that about one-third of their satDNA families (near 60 in every species) showed sequence homology, and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH pattern at both intra- and interspecific levels. We defined indices of homogenization and degeneration, and quantified the level of incomplete library sorting between species. Conclusions: Our analyses revealed that satDNA degenerates through point mutation and rejuvenates through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification, degeneration, and rejuvenation, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.

scholarly journals Lymphatic metastases have more diverse roots than distant metastases

2019 ◽  
Author(s):  
Johannes G. Reiter ◽  
Shriya Nagpal ◽  
Kamila Naxerova
Keyword(s):  
Primary Tumor ◽  
Phylogenetic Diversity ◽  
Common Ancestor ◽  
Distant Metastases ◽  
Mathematical Framework ◽  
Cancer Cell Migration ◽  
Biological Mechanisms ◽  
Evolutionary Mechanisms ◽  
Clinical Behavior ◽  
Lymphatic Metastases

AbstractBoth lymphatic and distant metastases arise through cancer cell migration and colonization of ectopic sites. Nonetheless, the two metastasis types are associated with significantly different clinical outcomes, suggesting that distinct biological mechanisms may drive their formation. Here we show fundamental differences in the seeding patterns of lymphatic and distant metastases. Analyzing the reconstructed phylogenies of human colorectal cancers, we find that distant metastases typically are monophyletic, originating from one common ancestor. Lymphatic metastases, in contrast, are almost exclusively polyphyletic and can be seeded from many primary tumor regions. We develop a rigorous mathematical framework for quantifying the phylogenetic diversity of metastases while accounting for differential lesion sampling among patients. Our results indicate that a smaller fraction of primary tumor cells gives rise to distant metastases than lymphatic metastases. Thus, the two metastasis types exhibit profoundly distinct phylogenetic traits, indicating that different evolutionary mechanisms may drive their formation and influence their clinical behavior.

Additional Dermal Ossifications in the Anuran Skull: Morphological Novelties or Archaic Elements?

2011 ◽  
Vol 4 (1) ◽  
pp. 17-27 ◽  
Author(s):  
Sergei V. Smirnov
Keyword(s):  
Common Ancestor ◽  
The State ◽  
Cranial Morphology ◽  
Anterior Portion ◽  
Bombina Orientalis ◽  
Common Event ◽  
Rostral Portion ◽  
Morphological Novelties ◽  
Dermal Bones

Examination of the cranial morphology in Bombina orientalis (Anura: Discoglossidae) revealed the occurrence of additional dermal bones lying: a) between the nasals and frontoparietals, b) between frontoparietals, and c) on the tectum synoticum behind the frontoparietals. The presence of similar bones as well as extra ossifications lying in the midline in the rostral portion of skull was shown to be a rather common event among anurans. Based on the occurrence of bones with similar topology in crossopterygians and different stegocephalians, it was concluded that extra ossifications sporadically appearing in anurans are more likely to be ancient cranial elements than neomorphs. Additional dermal bones found in the anterior portion of the anuran skull are homologous to the postrostrals of crossopterygians; extra ossifications lying between the frontoparietals correspond to the bones with similar topology sporadically appearing in crossopterygians and stegocephalians; and extra bones situated behind the frontoparietals are homologous to the lateral extrascapulars (postparietals of stegocephalians) and the median extrascapular of crossopterygians. These extra bones were proposed to be inherited from the presumed common ancestor of all Gnathostomes and retained in anurans in the state of latent capacities. The sporadic appearance of these bones in anurans results from the phenotypical realization of these latent capacities.

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