Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast

Deori, Nayan Moni; Nagotu, Shirisha

doi:10.1007/s00294-022-01254-y

Cited by 3 publications

(1 citation statement)

References 124 publications

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“…More specifically, Pex30p localizes to the ER, enriched at the site of pre-peroxisome vesicle formation, and regulates the tubular structure. Pex11p is responsible for membrane elongation of pre-existing peroxisomes (Deori and Nagotu 2022). Since non-WGD orthologs show interactions with some of these proteins, the detection of specific protein-protein interactions for KAFR0C02290 (B) and KAFR0K00320 (A) with them may indicate slight changes of function.…”

Section: Resultsmentioning

confidence: 99%

Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event

Evans-Yamamoto,

Dubé,

Saha

et al. 2023

Preprint

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Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast familySaccharomycetaceae,HRR25is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy inS. cerevisiaewhere it is now essential, but has been maintained as pairs in at least 7 species post WGD. InS. cerevisiae,HRR25encodes the casein kinase (CK) 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicatedHRR25ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay inS. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis inN. castellishows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate thatHRR25orthologs are undergoing gradual nonfunctionalization.

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Section: Resultsmentioning

confidence: 99%

Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event

Evans-Yamamoto,

Dubé,

Saha

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event

Evans-Yamamoto,

Dubé,

Saha

et al. 2023

Molecular Biology and Evolution

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Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in S. cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post WGD. In S. cerevisiae, HRR25 encodes the casein kinase (CK) 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis in N. castelli shows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.

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Gluing yeast peroxisomes – composition and function of membrane contact sites

Boer

Klei

2023

Journal of Cell Science

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Membrane contact sites are defined as regions of close proximity between two membranes; this association is mediated by protein–protein and/or protein–lipid interactions. Contact sites are often involved in lipid transport, but also can perform other functions. Peroxisomal membrane contact sites have obtained little attention compared to those of other cell organelles. However, recent studies resulted in a big leap in our knowledge of the occurrence, composition and function of peroxisomal contact sites. Studies in yeast strongly contributed to this progress. In this Review, we present an overview of our current knowledge on peroxisomal membrane contact sites in various yeast species, including Hansenula polymorpha, Saccharomyces cerevisiae, Pichia pastoris and Yarrowia lipolytica. Yeast peroxisomes form contacts with almost all other cellular organelles and with the plasma membrane. The absence of a component of a yeast peroxisomal contact site complex results in a range of peroxisomal phenotypes, including metabolic and biogenesis defects and alterations in organelle number, size or position.

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Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast

Cited by 3 publications

References 124 publications

Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event

Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event

Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event

Gluing yeast peroxisomes – composition and function of membrane contact sites

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