scholarly journals The birth-and-death evolution of cytochrome P450 genes in bees

2021 ◽  
Author(s):  
Kathy Darragh ◽  
David R Nelson ◽  
Santiago R Ramirez
Keyword(s):  
Multigene Family ◽  
Gene Deletion ◽  
Sequence Divergence ◽  
Cytochrome P450s ◽  
Functional Importance ◽  
High Chemical ◽  
Cytochrome P450 Genes ◽  
Toxin Exposure ◽  
Compound Exposure ◽  
Courtship Displays

The birth-and-death model of multigene family evolution describes how families can expand by duplication and contract by gene deletion and formation of pseudogenes. The phylogenetic stability of a gene is thought to be related to the degree of functional importance. However, it is unclear how much evolution of a gene in a gene family is driven by adaptive versus neutral processes. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Bees have a high toxin exposure due to their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some bees. Here, we describe the P450s of the orchid bee Euglossa dilemma. Orchid bees are a neotropical clade in which males form perfume bouquets used in courtship displays by collecting a diverse set of volatile compounds, resulting in high chemical compound exposure. We conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We do not find a relationship between the ecology of a bee species and its P450 repertoire. Our analyses reveal that P450 clades can be classified into stable and unstable clades, and that genes involved in xenobiotic metabolism are more likely to belong to unstable clades. Furthermore, we find that unstable clades are under more dynamic evolutionary pressures, with signals of adaptive evolution detected, suggesting that both gene duplication and positive selection driving sequence divergence have played a role in the diversification of bee P450s. Our works highlights the complexity of multigene family evolution which does not always follow generalized predictions.

scholarly journals Transcriptome-Based Identification and Molecular Evolution of the Cytochrome P450 Genes and Expression Profiling under Dimethoate Treatment in Amur Stickleback (Pungitius sinensis)

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 873 ◽  
Author(s):  
Jun Cao ◽  
Xiuzhu Cheng
Keyword(s):  
Expression Profiling ◽  
Transcriptome Sequencing ◽  
Cell Metabolism ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Cytochrome P450s ◽  
Cytochrome P450 Genes ◽  
Membrane Bound ◽  
Functional Relevance ◽  
Functional Investigation

Cytochrome P450s (CYPs) are a family of membrane-bound mono-oxygenase proteins, which are involved in cell metabolism and detoxification of various xenobiotic substances. In this study, we identified 58 putative CYP genes in Amur stickleback (Pungitius sinensis) based on the transcriptome sequencing. Conserved motif distribution suggested their functional relevance within each group. Some present recombination events have accelerated the evolution of this gene family. Moreover, a few positive selection sites were identified, which may have accelerated the functional divergence of this family of proteins. Expression patterns of these CYP genes were investigated and indicated that most were affected by dimethoate treatment, suggesting that CYPs were involved in the detoxication of dimethoate. This study will provide a foundation for the further functional investigation of CYP genes in fishes.

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence

1994 ◽  
Vol 14 (6) ◽  
pp. 4203-4215
Author(s):  
R Sweeney ◽  
L Chen ◽  
M C Yao
Keyword(s):  
Large Subunit ◽  
Sequence Divergence ◽  
Variable Region ◽  
Rrna Genes ◽  
Functional Importance ◽  
Functional Feature ◽  
Tertiary Structures ◽  
Unrelated Sequence ◽  
Evolutionarily Conserved ◽  
Large Subunit Rrna

Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably.

scholarly journals An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

1994 ◽  
Vol 14 (6) ◽  
pp. 4203-4215 ◽  
Author(s):  
R Sweeney ◽  
L Chen ◽  
M C Yao
Keyword(s):  
Large Subunit ◽  
Sequence Divergence ◽  
Variable Region ◽  
Rrna Genes ◽  
Functional Importance ◽  
Functional Feature ◽  
Tertiary Structures ◽  
Unrelated Sequence ◽  
Evolutionarily Conserved ◽  
Large Subunit Rrna

Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably.

A second locus for the 5S multigene family in Secale L.: sequence divergence in two lineages of the family

Genome ◽  
1989 ◽  
Vol 32 (3) ◽  
pp. 456-467 ◽  
Author(s):  
P. Reddy ◽  
R. Appels
Keyword(s):  
Restriction Endonuclease ◽  
Multigene Family ◽  
Sequence Divergence ◽  
Restriction Endonuclease Analysis ◽  
Length Variation ◽  
Repeat Units ◽  
Dna Repeat ◽  
Nucleotide Sequence Alignment ◽  
5S Dna ◽  
Chromosome 1R

The 5S RNA genes in Secale sp. are arranged as tandem arrays of a 460- and 480-bp repeating sequence. These size classes were initially discovered by restriction endonuclease analysis using BamHI and subsequently by DNA sequencing of cloned units. The length variation between short and long units originated from major deletion–insertion events in the noncoding spacer region of the 5S DNA repeat units. In situ hybridization with [3H]cRNA and biotin-labelled probes synthesized from both the short and long 5S DNA units of S. cereale localized the sites on chromosome 1R and a new site on a chromosome identified as 5R. We propose that the chromosome 1R locus, which has been mapped previously, be named 5SDna-R1 and the second locus, reported in the present paper, be referred to as 5SDna-R2. A preferential hybridization of a probe from the long unit to the 5SDna-R2 locus and of a probe from the short unit to the 5SDna-R1 locus is reported. The clustering of long units in the 5SDna-R2 locus was confirmed by restriction endonuclease digestion of DNA from rye chromosome 5R additions to wheat. Nucleotide sequence alignment of 5S DNA repeat units from a number of Secale species, using both phenetic and cladistic computer programmes, demonstrated that two clear lineages corresponding to the long and short units existed in this genus. The different Secale species could not be unambiguously differentiated using the 5S DNA sequences.Key words: Secale, 5S multigene family, restriction mapping, molecular evolution.

scholarly journals African Swine Fever Virus Multigene Family 360 Genes Affect Virus Replication and Generalization of Infection in Ornithodoros porcinus Ticks

2004 ◽  
Vol 78 (5) ◽  
pp. 2445-2453 ◽  
Author(s):  
T. G. Burrage ◽  
Z. Lu ◽  
J. G. Neilan ◽  
D. L. Rock ◽  
L. Zsak
Keyword(s):  
Host Range ◽  
Virus Replication ◽  
Multigene Family ◽  
Deletion Mutant ◽  
Gene Deletion ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Reproductive Organs ◽  
Fever Virus ◽  
Growth Defect

ABSTRACT Recently, we reported that African swine fever virus (ASFV) multigene family (MGF) 360 and 530 genes are significant swine macrophage host range determinants that function by promoting infected-cell survival. To examine the function of these genes in ASFV's arthropod host, Ornithodoros porcinus porcinus, an MGF360/530 gene deletion mutant (Pr4Δ35) was constructed from an ASFV isolate of tick origin, Pr4. Pr4Δ35 exhibited a significant growth defect in ticks. The deletion of six MGF360 and two MGF530 genes from Pr4 markedly reduced viral replication in infected ticks 100- to 1,000-fold. To define the minimal set of MGF360/530 genes required for tick host range, additional gene deletion mutants lacking individual or multiple MGF genes were constructed. The deletion mutant Pr4Δ3-C2, which lacked three MGF360 genes (3HL, 3Il, and 3LL), exhibited reduced viral growth in ticks. Pr4Δ3-C2 virus titers in ticks were significantly reduced 100- to 1,000-fold compared to control values at various times postinfection. In contrast to the parental virus, with which high levels of virus replication were observed in the tissues of infected adults, Pr4Δ3-C2 replication was not detected in the midgut, hemolymph, salivary gland, coxal gland, or reproductive organs at 15 weeks postinfection. These data indicate that ASFV MGF360 genes are significant tick host range determinants and that they are required for efficient virus replication and generalization of infection. The impaired virus replication of Pr4Δ3-C2 in the tick midgut likely accounts for the absence of the generalized infection that is necessary for the natural transmission of virus from ticks to pigs.

scholarly journals Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence

2016 ◽  
Author(s):  
Julian Echave ◽  
Claus O. Wilke
Keyword(s):  
Protein Evolution ◽  
Sequence Divergence ◽  
Future Research ◽  
Evolutionary Sequence ◽  
Functional Importance ◽  
Research Directions ◽  
Biophysical Models ◽  
Future Research Directions ◽  
Protein Biophysics ◽  
Evolution Understanding

AbstractFor decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic mis-folding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field.

scholarly journals The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s

2013 ◽  
Vol 368 (1612) ◽  
pp. 20120474 ◽  
Author(s):  
David R. Nelson ◽  
Jared V. Goldstone ◽  
John J. Stegeman
Keyword(s):  
Cytochrome P450 ◽  
Gene Cluster ◽  
Sequence Divergence ◽  
Cytochrome P450s ◽  
Origin And Evolution ◽  
Trichoplax Adhaerens ◽  
Acropora Digitifera ◽  
Whole Genome Duplications ◽  
Gene Environment ◽  
Genome Duplications

The neighbourhoods of cytochrome P450 ( CYP ) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the ‘cytochrome P450 genesis locus’, where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3, 4, 7, 19, 20, 26, 46, 51, 74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.

Transcriptome-wide identification, characterization, and phylogenomic analysis of cytochrome P450s from Nothapodytes nimmoniana reveal candidate genes involved in the camptothecin biosynthetic pathway

Genome ◽  
2021 ◽  
Vol 64 (1) ◽  
pp. 1-14
Author(s):  
Rucha C. Godbole ◽  
Anupama A. Pable ◽  
Vitthal T. Barvkar
Keyword(s):  
Cytochrome P450 ◽  
Biosynthetic Pathway ◽  
Expression Profiles ◽  
Cytochrome P450s ◽  
Phylogenomic Analysis ◽  
Cytochrome P450 Enzymes ◽  
Nothapodytes Nimmoniana ◽  
Cytochrome P450 Genes ◽  
Root Tissues ◽  
Anticancer Compound

The plant Nothapodytes nimmoniana is an important source of camptothecin (CPT), an anticancer compound widely used in the treatment of colorectal, lung, and ovarian cancers. CPT is biosynthesized by the combination of the seco-iridoid and indole pathways in plants. The majority of the biosynthetic steps and associated genes still remain unknown. Certain reactions in the seco-iridoid pathway are catalyzed by cytochrome P450 enzymes. Hence, identifying transcriptionally active cytochrome P450 genes becomes essential in the elucidation of the CPT biosynthetic pathway. Here, we report the identification of 94 cytochrome P450s from the assembled transcriptomic data from leaf and root tissues of N. nimmoniana. The identified cytochrome P450 genes were full length and possessed all four conserved characteristic signature motifs of cytochrome P450 genes. Phylogenetic analysis of the protein sequences revealed their evolution and diversification and further categorized them into A-type (52.12%) and non-A-type (47.87%) cytochrome P450s. These 94 sequences represent 38 families and 63 subfamilies of cytochrome P450s. We also compared the transcriptional activity of identified cytochrome P450s with the expression of their homologs in the CPT-producing plant Ophiorrhiza pumila. Based on expression profiles and quantitative PCR validation, we propose NnCYP81CB1 and NnCYP89R1 as candidate cytochrome P450 genes involved in camptothecin biosynthesis in N. nimmoniana.

Research advances in cytochrome P450-catalysed pharmaceutical terpenoid biosynthesis in plants

2019 ◽  
Vol 70 (18) ◽  
pp. 4619-4630 ◽  
Author(s):  
Xiaoyan Zheng ◽  
Ping Li ◽  
Xu Lu
Keyword(s):  
Cytochrome P450 ◽  
Cytochrome P450s ◽  
Terpenoid Biosynthesis ◽  
Cytochrome P450 Genes

Advances in the role of cytochrome P450s in pharmaceutical terpenoid biosynthesis are reviewed, and different cloning strategies to identify new cytochrome P450 genes in the biosynthesis of natural terpenoids are summarized.

Membrane microdomains: lessons from microscopy

1995 ◽  
Vol 53 ◽  
pp. 776-777
Author(s):  
J.M. Robinson ◽  
J.M Oliver
Keyword(s):  
Spatial Distribution ◽  
Plasma Membrane ◽  
Epithelial Cells ◽  
Plasma Membranes ◽  
Cell Types ◽  
Imaging Modalities ◽  
Membrane Microdomains ◽  
Membrane Domains ◽  
Lateral Heterogeneity ◽  
Functional Importance

Specialized regions of plasma membranes displaying lateral heterogeneity are the focus of this Symposium. Specialized membrane domains are known for certain cell types such as differentiated epithelial cells where lateral heterogeneity in lipids and proteins exists between the apical and basolateral portions of the plasma membrane. Lateral heterogeneity and the presence of microdomains in membranes that are uniform in appearance have been more difficult to establish. Nonetheless a number of studies have provided evidence for membrane microdomains and indicated a functional importance for these structures.This symposium will focus on the use of various imaging modalities and related approaches to define membrane microdomains in a number of cell types. The importance of existing as well as emerging imaging technologies for use in the elucidation of membrane microdomains will be highlighted. The organization of membrane microdomains in terms of dimensions and spatial distribution is of considerable interest and will be addressed in this Symposium.

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