PVCbase: an integrated web resource for the PVC bacterial proteomes

Bordin, Nicola; González-Sánchez, Juan Carlos; Devos, Damien P.

doi:10.1093/database/bay042

Cited by 14 publications

(15 citation statements)

References 42 publications

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“…A Trp residue is also present at the N terminus of this potential domain and aligns with the classical Trp conserved residue of other Pex reticulonlike domains. (Bordin et al, 2018). The black horizontal lines represent the protein sequence.…”

Section: Protein Sequence and Structure Predictionmentioning

confidence: 99%

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Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

Wu¹,

Boer²,

Krikken³

et al. 2020

Preprint

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Two Hansenula polymorpha ER proteins, Pex24 and Pex32, are tethers at peroxisome-ER contacts and function together with the peroxisomal protein Pex11. Their absence disturbs these contacts leading to multiple peroxisomal defects, which can be restored by an artificial tether. AbstractWe analyzed all four Pex23 family proteins of the yeast Hansenula polymorpha, which localize to the ER. Of these Pex24 and Pex32, but not Pex23 and Pex29, accumulate at peroxisome-ER contacts, where they are important for normal peroxisome biogenesis and proliferation and contribute to organelle positioning and segregation.Upon deletion of PEX24 and PEX32 -and to a lesser extent of PEX23 and PEX29peroxisome-ER contacts are disrupted, concomitant with peroxisomal defects. These defects are suppressed upon introduction of an artificial peroxisome-ER tether.

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Section: Protein Sequence and Structure Predictionmentioning

confidence: 99%

“…Homologous sequences were detected using BLASTP with an e-value of 1e-5 (Altschul et al, 1990). Linear and secondary structure predictions were realized using Foundation (Bordin et al, 2018).…”

Section: In Silico Analysesmentioning

confidence: 99%

Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

Wu¹,

Boer²,

Krikken³

et al. 2020

Preprint

Self Cite

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“…Proteins of the PXMP 2 family. (A) Protein phylogeny and secondary structure features of PXMP 2‐related proteins obtained with Foundation . Nc— Neurospora crassa ; Sc— Saccharomyces cerevisiae ; Hs— Homo sapiens ; Hp— Hansenula polymorpha .…”

Section: Resultsmentioning

confidence: 99%

“…The resulting curated MSA was used to create a phylogenetic tree with phyml 3.1 using the LG matrix, 100 bootstraps, tree and leaves refinement, SPR moves, and amino acid substitution rates determined empirically. Secondary structure, transmembrane helices, and disorder predictions were realized with PSIPRED , TMHMM , and IUP software packages , respectively, and drawn with Foundation (http://pvcbacteria.org/foundation) .…”

Section: Methodsmentioning

confidence: 99%

Hansenula polymorpha Pex37 is a peroxisomal membrane protein required for organelle fission and segregation

et al. 2019

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Here, we describe a novel peroxin, Pex37, in the yeast Hansenula polymorpha. H. polymorpha Pex37 is a peroxisomal membrane protein, which belongs to a protein family that includes, among others, the Neurospora crassa Woronin body protein Wsc, the human peroxisomal membrane protein PXMP2, the Saccharomyces cerevisiae mitochondrial inner membrane protein Sym1, and its mammalian homologue MPV17. We show that deletion of H. polymorpha PEX37 does not appear to have a significant effect on peroxisome biogenesis or proliferation in cells grown at peroxisome‐inducing growth conditions (methanol). However, the absence of Pex37 results in a reduction in peroxisome numbers and a defect in peroxisome segregation in cells grown at peroxisome‐repressing conditions (glucose). Conversely, overproduction of Pex37 in glucose‐grown cells results in an increase in peroxisome numbers in conjunction with a decrease in their size. The increase in numbers in PEX37‐overexpressing cells depends on the dynamin‐related protein Dnm1. Together our data suggest that Pex37 is involved in peroxisome fission in glucose‐grown cells. Introduction of human PXMP2 in H. polymorpha pex37 cells partially restored the peroxisomal phenotype, indicating that PXMP2 represents a functional homologue of Pex37. H.polymorpha pex37 cells did not show aberrant growth on any of the tested carbon and nitrogen sources that are metabolized by peroxisomal enzymes, suggesting that Pex37 may not fulfill an essential function in transport of these substrates or compounds required for their metabolism across the peroxisomal membrane.

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“…Their periplasm can be enlarged to form invaginations into the cytoplasm. They are potential producers of small molecules with interesting bioactivities (Graça et al 2016;Jeske et al 2016;Wiegand et al 2018), possess many giant genes (Kohn et al 2016), and belong to the bacterial phylum with the highest number of predicted genes with unknown function (40-55% of the annotated proteins) (Bordin et al 2018;Overmann et al 2017;Wiegand et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Lignipirellula cremea gen. nov., sp. nov., a planctomycete isolated from wood particles in a brackish river estuary

Peeters

Wiegand

Kallscheuer

et al. 2020

Antonie van Leeuwenhoek

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A novel planctomycetal strain, designated Pla85_3_4T, was isolated from the surface of wood incubated at the discharge of a wastewater treatment plant in the Warnow river near Rostock, Germany. Cells of the novel strain have a cell envelope architecture resembling that of Gram-negative bacteria, are round to pear-shaped (length: 2.2 ± 0.4 µm, width: 1.2 ± 0.3 µm), form aggregates and divide by polar budding. Colonies have a cream colour. Strain Pla85_3_4T grows at ranges of 10–30 °C (optimum 26 °C) and at pH 6.5–10.0 (optimum 7.5), and has a doubling time of 26 h. Phylogenetically, strain Pla85_3_4T (DSM 103796T = LMG 29741T) is concluded to represent a novel species of a novel genus within the family Pirellulaceae, for which we propose the name Lignipirellula cremea gen. nov., sp. nov.

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PVCbase: an integrated web resource for the PVC bacterial proteomes

Cited by 14 publications

References 42 publications

Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

Hansenula polymorpha Pex37 is a peroxisomal membrane protein required for organelle fission and segregation

Lignipirellula cremea gen. nov., sp. nov., a planctomycete isolated from wood particles in a brackish river estuary

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