scholarly journals Reconstructing the Evolutionary History of Nitrogenases: Evidence for Ancestral Molybdenum-Cofactor Utilization

2019 ◽  
Author(s):  
Amanda K. Garcia ◽  
Hanon McShea ◽  
Bryan Kolaczkowski ◽  
Betül Kaçar
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Fixed Nitrogen ◽  
Ancestral Sequences ◽  
Cofactor Biosynthesis ◽  
Ancient Proteins ◽  
History Of ◽  
Femo Cofactor ◽  
Global Biogeochemical Cycles ◽  
Active Site Sequence

ABSTRACTThe nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life’s key biogeochemical innovations. The three isozymes of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active-site sequence features can reliably distinguish extant Mo-nitrogenases from V- and Fe-nitrogenases, and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo-nitrogenases. Taxa representing early-branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo-cofactor in studied organisms, suggesting that early Mo-nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein-level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism-level innovations that characterize the Phanerozoic Eon.

scholarly journals Identification and Characterization of a Novel clcn7 Variant Associated With Osteopetrosis

2020 ◽  
Author(s):  
Dmitrii S. Bug ◽  
Ildar M. Barkhatov ◽  
Yana V. Gudozhnikova ◽  
Artem V. Tishkov ◽  
Natalia V. Petukhova ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Evolutionary History ◽  
Hot Spot ◽  
Phylogenetic Reconstruction ◽  
Novel Variant ◽  
Uncertain Significance ◽  
Precise Diagnosis ◽  
History Of ◽  
Identification And Characterization

Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene in a patient diagnosed with osteopetrosis and provide evidence for its significance (likely deleterious) based on extensive comparative genomics, protein sequence and structure analysis. A set of automated bioinformatics tools used to predict consequences of this variant identified it as deleterious or pathogenic. Structure analysis revealed that the variant is located at the same “hot spot” as the most common CLCN7 mutations causing osteopetrosis. Deep phylogenetic reconstruction showed that not only Leu614Arg, but any non-aliphatic substitutions in this position are evolutionarily intolerant, further supporting the deleterious nature of the variant. The present study provides further evidence that reconstructing a precise evolutionary history of a gene helps predicting phenotypical consequences of variants of uncertain significance.

scholarly journals Structural Changes and Adaptative Evolutionary Constraints In FLOWERING LOCUS T and TERMINAL FLOWER1-Like Genes of Flowering Plants

2021 ◽  
Author(s):  
Deivid Almeida de Jesus ◽  
Darlisson Mesquista Batista ◽  
Shayla Salzman ◽  
Lucas Miguel Carvalho ◽  
Kaue Santana ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Structural Changes ◽  
Protein Structures ◽  
Flowering Phenology ◽  
Flowering Locus T ◽  
Ancestral Sequences ◽  
Terminal Flower 1 ◽  
History Of ◽  
Flowering Locus ◽  
Complex Signaling

Abstract Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. Residues from the P-loop domain of the analyzed FT structures showed predominantly high destabilizing mutations which is consistent with constant selective pressure found for this region. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure experience positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.

Controversies on the evolutionary history of pycnodont fishes – reply to Kriwet 2004

2004 ◽  
Vol 95 (3-4) ◽  
pp. 543-546 ◽  
Author(s):  
Francisco José Poyato-Ariza
Keyword(s):  
Recent Work ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
History Of ◽  
Transformation Series

Criticisms by Kriwet regarding recent work on pycnodont phylogeny are based on the use of additive characters. Therefore, applying transformation series in phylogenetic reconstruction is justified in theory and in practice, and an example of additional ontogenetic evidence supporting character ordering in pycnodonts is provided. Moreover, comments on some pycnodont genera are included, and the accurate taxonomic use of the genera Coelodus and Ocloedus is emphasised.

scholarly journals Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

Nature ◽  
2015 ◽  
Vol 522 (7554) ◽  
pp. 81-84 ◽  
Author(s):  
Frido Welker ◽  
Matthew J. Collins ◽  
Jessica A. Thomas ◽  
Marc Wadsley ◽  
Selina Brace ◽  
...  
Keyword(s):  
Evolutionary History ◽  
South American ◽  
Ancient Proteins ◽  
History Of

scholarly journals Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins

2021 ◽  
Author(s):  
Weijian Guo ◽  
Di Sun ◽  
Yang Cao ◽  
Linlin Xiao ◽  
Xin Huang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Genomic Data ◽  
Sliding Window ◽  
Interspecific Gene Flow ◽  
History Of ◽  
Relationship Of

AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.

scholarly journals Identification and Characterization of a Novel CLCN7 Variant Associated with Osteopetrosis

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1242 ◽  
Author(s):  
Dmitrii S. Bug ◽  
Ildar M. Barkhatov ◽  
Yana V. Gudozhnikova ◽  
Artem V. Tishkov ◽  
Igor B. Zhulin ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Evolutionary History ◽  
Hot Spot ◽  
Phylogenetic Reconstruction ◽  
Novel Variant ◽  
Uncertain Significance ◽  
Precise Diagnosis ◽  
History Of ◽  
Identification And Characterization

Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene in a patient diagnosed with osteopetrosis and provide evidence for its significance (likely deleterious) based on extensive comparative genomics, protein sequence and structure analysis. A set of automated bioinformatics tools used to predict consequences of this variant identified it as deleterious or pathogenic. Structure analysis revealed that the variant is located at the same “hot spot” as the most common CLCN7 mutations causing osteopetrosis. Deep phylogenetic reconstruction showed that not only Leu614Arg, but any non-aliphatic substitutions in this position are evolutionarily intolerant, further supporting the deleterious nature of the variant. The present study provides further evidence that reconstructing a precise evolutionary history of a gene helps in predicting phenotypical consequences of variants of uncertain significance.

scholarly journals Insights Into the Evolutionary History of the Subfamily Orthotrichoideae (Orthotrichaceae, Bryophyta): New and Former Supra-Specific Taxa So Far Obscured by Prevailing Homoplasy

2021 ◽  
Vol 12 ◽  
Author(s):  
Isabel Draper ◽  
Ricardo Garilleti ◽  
Juan Antonio Calleja ◽  
Maren Flagmeier ◽  
Vicente Mazimpaka ◽  
...  
Keyword(s):  
Evolutionary History ◽  
New Genus ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Generic Level ◽  
Evolutionary Patterns ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Epiphytic Communities ◽  
Main Components

Mosses of the subfamily Orthotrichoideae represent one of the main components of the cryptogam epiphytic communities in temperate areas. During the last two decades, this taxonomical group has undergone an extensive revision that has led to its rearrangement at the generic level. However, their phylogenetic relationships and inferences on the evolutionary patterns that have driven the present diversity have little advanced. In this study, we present a dated molecular phylogenetic reconstruction at the subfamily level, including 130 samples that represent the 12 genera currently recognized within the subfamily, and the analysis of four molecular markers: ITS2, rps4, trnG, and trnL-F. We also analyze 13 morphological characters of systematic value to infer their origin and diagnostic utility within the subfamily. The phylogenetic reconstruction yields three main clades within the subfamily, two of which correspond to the tribe Zygodonteae, and one to Orthotricheae. Within Zygodonteae, the genus Zygodon results to be a polyphyletic artificial assembly, and we propose to separate a new genus named Australoria. Conversely, our results do not support the separation of Pentastichella and Pleurorthotrichum at the genus level and we therefore propose to include Pleurorthotrichum in Pentastichella. Regarding Orthotricheae, our analyses clearly allow the distinction of two subtribes: Orthotrichinae and Lewinskyinae. Within the latter, Ulota results a polyphyletic entity, and therefore we propose the segregation of a separate new genus named Atlantichella. Dating analyses allow us to conclude that the split of the tribes within Orthotrichoideae dates from the Middle Jurassic, while the diversification of Orthotrichum and Zygodon probably started during the Late Cretaceous. However, most of the extant genera of this subfamily seem to be younger, and apparently its highest diversification burst took place during the Oligocene. Finally, the analysis of the morphological traits reveals that most of the characters previously used to separate genera and here tested are homoplastic, which has hindered the taxonomical and systematic proposals for decades. However, even if there are no exclusive characters, all of the genera can be defined by the combination of a few characters.

Evidence for local DNA influences on patterns of substitutions in the human α-interferon gene family

1986 ◽  
Vol 28 (4) ◽  
pp. 483-496 ◽  
Author(s):  
G. Brian Golding ◽  
Barry W. Glickman
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Spontaneous Mutation ◽  
Direct Repeat ◽  
Base Substitution ◽  
Human Interferon ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Ancestral Sequences ◽  
History Of

The evolutionary history of genes can be used to examine patterns of spontaneous mutation if the sequences are sufficiently extensive to provide reliable data. Many human α-interferon genes have been sequenced and they form a large multigene family including several pseudogenes. A phylogenetic history for 15 human interferon sequences was reconstructed and their ancestral sequences inferred using a maximum parsimony method. This evolutionary history provided a record of more than 738 spontaneous mutations that have occurred in man's recent evolution. Of these mutations, more than 267 base substitution and deletion–insertion events were analyzed to determine the possible effects of nearby DNA sequences. Many substitutions occur at the end of long runs of identical bases and some dinucleotide pairs may mutate more often than others. Because templating by local DNA sequences has been implicated in prokaryotic mutation, the sequences were also examined for nearby repeats that include the substituted nucleotide and hence are potentially capable of templating the substitution. The majority of sequence alterations examined have either a similar direct repeat or palindrome nearby. Often such templates can account for simultaneous multiple mutations. These results suggest that sequence-directed events may occur occasionally in eukaryotes and that neighbouring DNA sequences can influence both the occurrence and types of mutations in several different ways.Key words: spontaneous mutation, template-directed mutations, phylogenetic history, evolution.

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