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

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

Open Biology ◽

10.1098/rsob.160009 ◽

2016 ◽

Vol 6 (4) ◽

pp. 160009 ◽

Cited By ~ 56

Author(s):

Kerstin Howe ◽

Philipp H. Schiffer ◽

Julia Zielinski ◽

Thomas Wiehe ◽

Gavin K. Laird ◽

...

Keyword(s):

Adaptive Immune System ◽

Large Family ◽

Immune Recognition ◽

Adaptive Immune ◽

New Family ◽

The Family ◽

History Of ◽

Leucine Rich Repeats ◽

Adaptive Immune Systems ◽

B30.2 Domain

Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.

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

10.1101/766360 ◽

2019 ◽

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis Enrique Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Common Ancestor ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Common Ancestry ◽

Demethylation Pathway ◽

History Of ◽

New Gene

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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Phylogenetic diversification of sirtuin genes with a description of a new family member

10.1101/2020.07.17.209510 ◽

2020 ◽

Author(s):

Juan C. Opazo ◽

Kattina Zavala ◽

Michael W. Vandewege ◽

Federico G. Hoffmann

Keyword(s):

Gene Family ◽

Family Member ◽

Gene Families ◽

Last Common Ancestor ◽

Gene Repertoire ◽

Origin And Evolution ◽

New Family ◽

Wide Range ◽

Evolutionary Context ◽

History Of

AbstractStudying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

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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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A new endemic family of New Zealand passerine birds: adding heat to a biodiversity hotspot

Australian Journal of Zoology ◽

10.1071/zo07007 ◽

2007 ◽

Vol 55 (2) ◽

pp. 73 ◽

Cited By ~ 33

Author(s):

Amy Driskell ◽

Les Christidis ◽

B. J. Gill ◽

Walter E. Boles ◽

F. Keith Barker ◽

...

Keyword(s):

New Zealand ◽

Evolutionary History ◽

Divergence Time ◽

Biodiversity Hotspot ◽

Passerine Birds ◽

New Family ◽

Close Relationship ◽

History Of ◽

Anthornis Melanura ◽

Notiomystis Cincta

The results of phylogenetic analysis of two molecular datasets sampling all three endemic New Zealand ‘honeyeaters’ (Prosthemadera novaeseelandiae, Anthornis melanura and Notiomystis cincta) are reported. The undisputed relatedness of the first two species to other honeyeaters (Meliphagidae), and a close relationship between them, are demonstrated. However, our results confirm that Notiomystis is not a honeyeater, but is instead most closely related to the Callaeidae (New Zealand wattlebirds) represented by Philesturnus carunculatus in our study. An estimated divergence time for Notiomystis and Philesturnus of 33.8 mya (Oligocene) suggests a very long evolutionary history of this clade in New Zealand. As a taxonomic interpretation of these data we place Notiomystis in a new family of its own which takes the name Notiomystidae. We expect this new phylogenetic and taxonomic information to assist policy decisions for the conservation of this rare bird.

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