Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

PeerJ ◽

10.7717/peerj.9861 ◽

2020 ◽

Vol 8 ◽

pp. e9861

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis E. Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Marine Bacteria ◽

Evolutionary History ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Demethylation Pathway ◽

History Of ◽

New Gene ◽

Enzymatic Adaptation

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

10.1101/288530 ◽

2018 ◽

Author(s):

Mónica Lopes-Marques ◽

André M. Machado ◽

Raquel Ruivo ◽

Elza Fonseca ◽

Estela Carvalho ◽

...

Keyword(s):

Gene Family ◽

Metabolic Pathways ◽

Evolutionary History ◽

Gene Families ◽

Gene Repertoire ◽

Physiological Processes ◽

Complex Lipid ◽

History Of ◽

Enzyme Families ◽

Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

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Deep Ancestry of Orthologs and a Theoretical, Gradualist Perspective for the Formation of the LUCA’s (Last Universal Common Ancestor) Genome

10.20944/preprints201808.0330.v1 ◽

2018 ◽

Author(s):

Francisco Prosdocimi ◽

Sávio Torres de Farias

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Deep Understanding ◽

Sister Group ◽

Recent Common Ancestor ◽

Evolutionary Relationships ◽

Universal Common Ancestor ◽

History Of ◽

Group Relationships ◽

Level Of Understanding

Genes and gene trees have been extensively used to study the evolutionary relationships among populations, species, families and higher systematic clades of organisms. This brought modern Biology into a sophisticated level of understanding about the evolutionary relationships and diversification patterns that happened along the entire history of organismal evolution in Earth. Genes however have not been placed in the center of questions when one aims to unravel the evolutionary history of genes themselves. Thus, we still ignore whether Insulin share a more recent common ancestor to Hexokinase or DNA polymerase. This brought modern Genetics into a very poor level of understanding about sister group relationships that happened along the entire evolutionary history of genes. Many conceptual challenges must be overcome to allow this broader comprehension about gene evolution. Here we aim to clear the intellectual path in order to provide a fertile research program that will help geneticists to understand the deep ancestry and sister group relationships among different gene families (or orthologs). We aim to propose methods to study gene formation starting from the establishment of the genetic code in pre-cellular organisms like the FUCA (First Universal Common Ancestor) until the formation of the highly complex genome of LUCA (Last UCA), that harbors hundreds of genes families working coordinated into a cellular organism. The deep understanding of ancestral relationships among orthologs will certainly inspire biotechnological and biomedical approaches and allow a deep understanding about how Darwinian molecular evolution operates inside cells and before the appearance of cellular organisms.

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Structure and evolutionary history of a large family of NLR proteins in the zebrafish

10.1101/022061 ◽

2015 ◽

Author(s):

Kerstin Howe ◽

Philipp H Schiffer ◽

Julia Zielinski ◽

Thomas Wiehe ◽

Gavin K Laird ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Large Family ◽

Gene Families ◽

Immune Recognition ◽

Chromosome 4 ◽

New Family ◽

History Of ◽

Evolutionary Trajectories ◽

B30.2 Domain

NACHT- and Leucine-Rich-Repeat-containing domain (NLR) proteins act as cytoplasmic sensors for pathogen- and danger-associated molecular patterns and are found throughout the plant and animal kingdoms. In addition to having a small set of conserved NLRs, the genomes in some animal lineages contain massive expansions of this gene family. One of these arose in fishes, after the creation of a gene fusion that combined the core NLR domains with another domain used for immune recognition, the PRY/SPRY or B30.2 domain. We have analysed the expanded NLR gene family in zebrafish, which contains 368 genes, and studied its evolutionary history. The encoded proteins share a defining overall structure, but individual domains show different evolutionary trajectories. Our results suggest gene conversion homogenizes NACHT and B30.2 domain sequences among different gene subfamilies, however, the functional implications of its action remains unclear. The majority of the genes are located on the long arm of chromosome 4, interspersed with several other large multi-gene families, including a new family encoding proteins with multiple tandem arrays of Zinc fingers. This suggests that chromosome 4 may be a hotspot for rapid evolutionary change in zebrafish.

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Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

10.1101/095679 ◽

2016 ◽

Cited By ~ 5

Author(s):

Thomas D. Otto ◽

Aude Gilabert ◽

Thomas Crellen ◽

Ulrike Böhme ◽

Céline Arnathau ◽

...

Keyword(s):

Evolutionary History ◽

Gene Families ◽

Recent Common Ancestor ◽

Structural Variations ◽

Specific Sequence ◽

Human Malaria ◽

Repeated Infection ◽

History Of ◽

Underlying Mechanisms ◽

First Time

AbstractPlasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite P. praefalciparum. Little is known about the other gorilla and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species. The completeness of our dataset allows us to conclude that interspecific gene transfers as well as convergent evolution were important in the evolution of these species. Striking copy number and structural variations were observed within gene families and one, stevor shows a host specific sequence pattern. The complete genome sequence of the closest ancestor of P. falciparum enables us to estimate confidently for the first time the timing of the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. falciparum that made it the only member of the Laverania able to infect and spread in humans.

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iHam and pyHam: visualizing and processing hierarchical orthologous groups

Bioinformatics ◽

10.1093/bioinformatics/bty994 ◽

2018 ◽

Vol 35 (14) ◽

pp. 2504-2506 ◽

Cited By ~ 8

Author(s):

Clément-Marie Train ◽

Miguel Pignatelli ◽

Adrian Altenhoff ◽

Christophe Dessimoz

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Gene Families ◽

Comparative Genomic ◽

Last Common Ancestor ◽

Analysis Method ◽

Ancestral Gene ◽

Genomic Analyses ◽

History Of ◽

Multiple Species

Abstract Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.

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Faculty Opinions recommendation of Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1128831.585916 ◽

2009 ◽

Author(s):

Vitaly Citovsky

Keyword(s):

Evolutionary History ◽

Functional Divergence ◽

Histone Demethylase ◽

Evolutionary Patterns ◽

History Of

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The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽

10.1139/cjb-2013-0063 ◽

2013 ◽

Vol 91 (9) ◽

pp. 605-613 ◽

Cited By ~ 6

Author(s):

Claudia Ciotir ◽

Chris Yesson ◽

Joanna Freeland

Keyword(s):

Great Lakes ◽

Evolutionary History ◽

Common Ancestor ◽

Recent Common Ancestor ◽

Great Lakes Region ◽

Conservation Value ◽

Most Recent Common Ancestor ◽

Disjunct Populations ◽

Management Plans ◽

Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

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