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. 2018 Jan;1866(1):141-154.
doi: 10.1016/j.bbapap.2017.05.003. Epub 2017 May 11.

Cytochrome P450 diversity in the tree of life

David R Nelson  1
Affiliations

Cytochrome P450 diversity in the tree of life

David R Nelson. Biochim Biophys Acta Proteins Proteom. 2018 Jan.

Abstract

Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses. CYPs from the fungi, one of the most diverse groups, are being explored and organized as nearly 800 fungal species are now sequenced. The CYP clan structure in fungi is emerging with 805 CYP families sorting into 32 CYP clans. >3000 bacterial sequences are named, mostly from terrestrial or freshwater sources. Of 18,379 bacterial sequences downloaded from the CYPED database, all are >43% identical to named CYPs. Therefore, they fit in the 602 named P450 prokaryotic families. Diversity in this group is becoming saturated, however 25% of 3305 seawater bacterial P450s did not match known P450 families, indicating marine bacterial CYPs are not as well sampled as land/freshwater based bacterial CYPs. Future sequencing plans of the Genome 10K project, i5k and GIGA (Global Invertebrate Genomics Alliance) are expected to produce more than one million cytochrome P450 sequences by 2020. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Keywords: Bacteria; Biodiversity; Birds; Cytochrome P450; Evolution; Fungi; Insects; Limulus polyphemus; Plants; Tardigrades; Velvet worm.

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Conflict of interest statement

Conflict of interest

The author declares that no conflict of interest exists.

Figures

Figure 1
Figure 1
A schematic tree showing the relationships of the major taxa in the panarthropoda. The chart on the right shows the presence of clans in these groups.
Figure 2
Figure 2
CYPs from the horseshoe crab Limulus polyphemus and a tardigrade Hypsibius dujardini. The spokes are colored to indicate CYP clan and the tip labels are colored blue for tardigrade and orange for the horseshoe crab Limulus. A few other sequences are included to clarify the branching pattern. This is an NJ tree made using CLUSTAL Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/). The tree was drawn in Figtree v1.3.1 and labeled in Adobe Illustrator CC. Tardigrade gene model IDs are given in Suppl. Table S7. Sequences are included in Suppl. Sequence file 1.
Figure 3
Figure 3
House spider tree. The spokes are colored to indicate the four CYP clans. This tree was made as described in Material and Methods. It is a midpoint rooted NJ tree. Sequences used are in Suppl. Sequence File 4. Accession numbers are in Suppl. Table S8.
Figure 4
Figure 4
Distribution of numbers of P450s in 87 panarthropods by phylogeny
Figure 5
Figure 5
Liverwort tree showing representative sequences and featuring Marchantia polymorpha (green labels) and Marchantia paleacea (red labels). The spokes are colored to show CYP clans. Liverworts = Mpa Marchantia paleacea; Mpo Marchantia polymorpha; Me Marchantia emarginata; Pn Porella navicularis; Pp Ptilidium pulcherrimum; Pa Plagiochila asplenoides; Rb Riccia berychiana; Cc Conochephalus conicum; Ply Pallavicinia lyellii; Tl Treubia lacunose; Sch Schistochila sp.; PE Pellia cf. Epiphylla; Other species = Php Physcomitrella patens (moss); Selm Selaginella moellendorffii (lycophyte); Nen Nelumbo nucifera (sacred lotus); Cycas Cycas rumphii (cycad); Met Medicago trucatula; Pinus or Pinu Pinus taeda; Picea Picea glauca; Picsi or Pics Picea sitchensis; Gmax Glycine max (soybeans); rice Oryza sativa; Pop Populus trichocarpa; Antik Antirrhinum kelloggii; Vv Vitis vinifera; Pyrus Pyrus communis (Pear); Gink Ginkgo biloba. Sequences used are in Suppl. Sequence File 5.
Figure 6
Figure 6
Pie chart showing the size of the P450 clans in Liverworts compared to Angiosperms and Hornworts
Figure 7
Figure 7
Distribution of the numbers of P450s in 570 fungi by phylogeny
Figure 8
Figure 8
Sphaerobolus stellatus P450 length of sequences in decreasing order. Sequence lengths were averaged in groups of 20.
Figure 9
Figure 9
Fungal clan tree. The sequences used in this tree are provided in Suppl. Sequence File 2.
Figure 10
Figure 10
Figure 11
Figure 11
See this image and copyright information in PMC

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