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Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.

Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN - BMC Evol. Biol. (2015)

Bottom Line: Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes.Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species.We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA. rhermans@uwyo.edu.

ABSTRACT

Background: Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes.

Results: Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint.

Conclusions: We expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control.

No MeSH data available.


Related in: MedlinePlus

Gene evolution within the fungal species tree. Shown is the NCBI fungal species tree annotated with inferred gene duplication and lateral transfer events following gene tree/species tree reconciliation. Duplication events marked as paralog/xenolog were ambiguous and not obviously differentiable between being a gene duplication event and a lateral transfer event. The numbered branches within the figure indicate the following duplication and lateral transfer events: 1) Branch: Fungi [URA1 – Paralog(2), URA6 – Paralog(3), URA6 – Paralog/Xenolog(3), YNK1 – Paralog, YNK1 – Paralog/Xenolog], 2) Branch: Rhizophagus irregulare [URA5/10 – Paralog], 3) Branch: Mortierella [URA7 – Paralog, YNK1 – Paralog], 4) Branch: Mucorales [URA7 – Paralog], 5) Mucorineae [URA2 – Paralog, URA7 – Paralog], 6) Branch: Rhizopus microsporus [URA1 – Paralog, URA7 – Paralog, YNK1 – Paralog], 7) Branch: Rhizopus delemar [URA2 – Paralog], 8) Branch: Encephalitozoon intestinalis [URA7 – Paralog], 9) Branch: Pucciniales [URA6 – Paralog], 10) Branch: Filobasidiella/Cryptococcus neoformans species complex [URA5/10 – Paralog(5)], 11) Branch: Ceriporiopsis [URA1 – Paralog], 12) Branch: Fomitopsis pinicola [URA7 – Paralog], 13) Branch: Paxillus involutus [YNK1 – Paralog], 14) Branch: Laccaria bicolor [URA5/10 – Paralog], 15) Branch: Taphrinomycotina [YNK1 – Xenolog], 16) Branch: Millerozyma farinosa [YNK1 – Paralog], 17) Branch: Saccharomycetacea [URA1 – Xenolog, URA5/10 – Paralog(2), URA7 – Paralog], 18) Branch: Pezizomycotina [URA3 – Paralog], 19) Pleosporineae [URA7 – Paralog], 20) Branch: Botryosphaeriaceae [URA3 – Paralog], 21) Branch: Leotiomyceta [URA3 – Paralog/Xenolog, URA7 – Paralog, URA7 – Paralog/Xenolog], 22) Branch: Blumeria graminis f. sp. Hordei DH14 [URA5/10 – Paralog], 23) Branch: Sordariomycetes [URA7 – Paralog], 24) Branch: Hypocreales [URA7 – Paralog], 25) Branch: Fusarium [URA7 – Paralog(3)], 26) Branch: Fusarium verticillioides [URA7 – Paralog], 27) Branch: Fusarium sambucinum species complex [URA7 – Paralog], 28) Branch: Fusarium oxysporum FOSC 3-a [URA7 – Paralog], 29) Branch: Fusarium oxysporum f. sp. Vasinfectum 25433 [URA7 – Paralog]. An expandable pdf version of Fig. 2 is also found within the supplementary materials
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Fig2: Gene evolution within the fungal species tree. Shown is the NCBI fungal species tree annotated with inferred gene duplication and lateral transfer events following gene tree/species tree reconciliation. Duplication events marked as paralog/xenolog were ambiguous and not obviously differentiable between being a gene duplication event and a lateral transfer event. The numbered branches within the figure indicate the following duplication and lateral transfer events: 1) Branch: Fungi [URA1 – Paralog(2), URA6 – Paralog(3), URA6 – Paralog/Xenolog(3), YNK1 – Paralog, YNK1 – Paralog/Xenolog], 2) Branch: Rhizophagus irregulare [URA5/10 – Paralog], 3) Branch: Mortierella [URA7 – Paralog, YNK1 – Paralog], 4) Branch: Mucorales [URA7 – Paralog], 5) Mucorineae [URA2 – Paralog, URA7 – Paralog], 6) Branch: Rhizopus microsporus [URA1 – Paralog, URA7 – Paralog, YNK1 – Paralog], 7) Branch: Rhizopus delemar [URA2 – Paralog], 8) Branch: Encephalitozoon intestinalis [URA7 – Paralog], 9) Branch: Pucciniales [URA6 – Paralog], 10) Branch: Filobasidiella/Cryptococcus neoformans species complex [URA5/10 – Paralog(5)], 11) Branch: Ceriporiopsis [URA1 – Paralog], 12) Branch: Fomitopsis pinicola [URA7 – Paralog], 13) Branch: Paxillus involutus [YNK1 – Paralog], 14) Branch: Laccaria bicolor [URA5/10 – Paralog], 15) Branch: Taphrinomycotina [YNK1 – Xenolog], 16) Branch: Millerozyma farinosa [YNK1 – Paralog], 17) Branch: Saccharomycetacea [URA1 – Xenolog, URA5/10 – Paralog(2), URA7 – Paralog], 18) Branch: Pezizomycotina [URA3 – Paralog], 19) Pleosporineae [URA7 – Paralog], 20) Branch: Botryosphaeriaceae [URA3 – Paralog], 21) Branch: Leotiomyceta [URA3 – Paralog/Xenolog, URA7 – Paralog, URA7 – Paralog/Xenolog], 22) Branch: Blumeria graminis f. sp. Hordei DH14 [URA5/10 – Paralog], 23) Branch: Sordariomycetes [URA7 – Paralog], 24) Branch: Hypocreales [URA7 – Paralog], 25) Branch: Fusarium [URA7 – Paralog(3)], 26) Branch: Fusarium verticillioides [URA7 – Paralog], 27) Branch: Fusarium sambucinum species complex [URA7 – Paralog], 28) Branch: Fusarium oxysporum FOSC 3-a [URA7 – Paralog], 29) Branch: Fusarium oxysporum f. sp. Vasinfectum 25433 [URA7 – Paralog]. An expandable pdf version of Fig. 2 is also found within the supplementary materials

Mentions: An examination of the entire URA1 gene family additionally showed four different high confidence duplication events and one potential horizontal gene transfer (HGT) event after being reconciled against the fungal species tree using a soft parsimony-based approach (Fig. 2; Additional file 1: Figure S12).Fig. 2


Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.

Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN - BMC Evol. Biol. (2015)

Gene evolution within the fungal species tree. Shown is the NCBI fungal species tree annotated with inferred gene duplication and lateral transfer events following gene tree/species tree reconciliation. Duplication events marked as paralog/xenolog were ambiguous and not obviously differentiable between being a gene duplication event and a lateral transfer event. The numbered branches within the figure indicate the following duplication and lateral transfer events: 1) Branch: Fungi [URA1 – Paralog(2), URA6 – Paralog(3), URA6 – Paralog/Xenolog(3), YNK1 – Paralog, YNK1 – Paralog/Xenolog], 2) Branch: Rhizophagus irregulare [URA5/10 – Paralog], 3) Branch: Mortierella [URA7 – Paralog, YNK1 – Paralog], 4) Branch: Mucorales [URA7 – Paralog], 5) Mucorineae [URA2 – Paralog, URA7 – Paralog], 6) Branch: Rhizopus microsporus [URA1 – Paralog, URA7 – Paralog, YNK1 – Paralog], 7) Branch: Rhizopus delemar [URA2 – Paralog], 8) Branch: Encephalitozoon intestinalis [URA7 – Paralog], 9) Branch: Pucciniales [URA6 – Paralog], 10) Branch: Filobasidiella/Cryptococcus neoformans species complex [URA5/10 – Paralog(5)], 11) Branch: Ceriporiopsis [URA1 – Paralog], 12) Branch: Fomitopsis pinicola [URA7 – Paralog], 13) Branch: Paxillus involutus [YNK1 – Paralog], 14) Branch: Laccaria bicolor [URA5/10 – Paralog], 15) Branch: Taphrinomycotina [YNK1 – Xenolog], 16) Branch: Millerozyma farinosa [YNK1 – Paralog], 17) Branch: Saccharomycetacea [URA1 – Xenolog, URA5/10 – Paralog(2), URA7 – Paralog], 18) Branch: Pezizomycotina [URA3 – Paralog], 19) Pleosporineae [URA7 – Paralog], 20) Branch: Botryosphaeriaceae [URA3 – Paralog], 21) Branch: Leotiomyceta [URA3 – Paralog/Xenolog, URA7 – Paralog, URA7 – Paralog/Xenolog], 22) Branch: Blumeria graminis f. sp. Hordei DH14 [URA5/10 – Paralog], 23) Branch: Sordariomycetes [URA7 – Paralog], 24) Branch: Hypocreales [URA7 – Paralog], 25) Branch: Fusarium [URA7 – Paralog(3)], 26) Branch: Fusarium verticillioides [URA7 – Paralog], 27) Branch: Fusarium sambucinum species complex [URA7 – Paralog], 28) Branch: Fusarium oxysporum FOSC 3-a [URA7 – Paralog], 29) Branch: Fusarium oxysporum f. sp. Vasinfectum 25433 [URA7 – Paralog]. An expandable pdf version of Fig. 2 is also found within the supplementary materials
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4625875&req=5

Fig2: Gene evolution within the fungal species tree. Shown is the NCBI fungal species tree annotated with inferred gene duplication and lateral transfer events following gene tree/species tree reconciliation. Duplication events marked as paralog/xenolog were ambiguous and not obviously differentiable between being a gene duplication event and a lateral transfer event. The numbered branches within the figure indicate the following duplication and lateral transfer events: 1) Branch: Fungi [URA1 – Paralog(2), URA6 – Paralog(3), URA6 – Paralog/Xenolog(3), YNK1 – Paralog, YNK1 – Paralog/Xenolog], 2) Branch: Rhizophagus irregulare [URA5/10 – Paralog], 3) Branch: Mortierella [URA7 – Paralog, YNK1 – Paralog], 4) Branch: Mucorales [URA7 – Paralog], 5) Mucorineae [URA2 – Paralog, URA7 – Paralog], 6) Branch: Rhizopus microsporus [URA1 – Paralog, URA7 – Paralog, YNK1 – Paralog], 7) Branch: Rhizopus delemar [URA2 – Paralog], 8) Branch: Encephalitozoon intestinalis [URA7 – Paralog], 9) Branch: Pucciniales [URA6 – Paralog], 10) Branch: Filobasidiella/Cryptococcus neoformans species complex [URA5/10 – Paralog(5)], 11) Branch: Ceriporiopsis [URA1 – Paralog], 12) Branch: Fomitopsis pinicola [URA7 – Paralog], 13) Branch: Paxillus involutus [YNK1 – Paralog], 14) Branch: Laccaria bicolor [URA5/10 – Paralog], 15) Branch: Taphrinomycotina [YNK1 – Xenolog], 16) Branch: Millerozyma farinosa [YNK1 – Paralog], 17) Branch: Saccharomycetacea [URA1 – Xenolog, URA5/10 – Paralog(2), URA7 – Paralog], 18) Branch: Pezizomycotina [URA3 – Paralog], 19) Pleosporineae [URA7 – Paralog], 20) Branch: Botryosphaeriaceae [URA3 – Paralog], 21) Branch: Leotiomyceta [URA3 – Paralog/Xenolog, URA7 – Paralog, URA7 – Paralog/Xenolog], 22) Branch: Blumeria graminis f. sp. Hordei DH14 [URA5/10 – Paralog], 23) Branch: Sordariomycetes [URA7 – Paralog], 24) Branch: Hypocreales [URA7 – Paralog], 25) Branch: Fusarium [URA7 – Paralog(3)], 26) Branch: Fusarium verticillioides [URA7 – Paralog], 27) Branch: Fusarium sambucinum species complex [URA7 – Paralog], 28) Branch: Fusarium oxysporum FOSC 3-a [URA7 – Paralog], 29) Branch: Fusarium oxysporum f. sp. Vasinfectum 25433 [URA7 – Paralog]. An expandable pdf version of Fig. 2 is also found within the supplementary materials
Mentions: An examination of the entire URA1 gene family additionally showed four different high confidence duplication events and one potential horizontal gene transfer (HGT) event after being reconciled against the fungal species tree using a soft parsimony-based approach (Fig. 2; Additional file 1: Figure S12).Fig. 2

Bottom Line: Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes.Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species.We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA. rhermans@uwyo.edu.

ABSTRACT

Background: Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes.

Results: Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint.

Conclusions: We expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control.

No MeSH data available.


Related in: MedlinePlus