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Article ; Online: Unique properties of Coronaviridae single-pass transmembrane domain regions as an adaptation to diverse membrane systems.

Kubiszewski-Jakubiak, Szymon / Worch, Remigiusz

2022 Volume 570, Page(s) 1–8

Abstract: Enveloped viruses such as Coronaviridae (CoV) enter the host cell by fusing the viral envelope directly with the plasma membrane (PM) or with the membrane of the endosome. Replication of the CoV genome takes place in membrane compartments formed by ... ...

Abstract	Enveloped viruses such as Coronaviridae (CoV) enter the host cell by fusing the viral envelope directly with the plasma membrane (PM) or with the membrane of the endosome. Replication of the CoV genome takes place in membrane compartments formed by rearrangement of the endoplasmic reticulum (ER) membrane network. Budding of these viruses occurs from the ER-Golgi intermediate compartment (ERGIC). The relationship between proteins and various membranes is crucial for the replication cycle of CoVs. The role of transmembrane domains (TMDs) and pre-transmembrane domains (pre-TMD) of viral proteins in this process is gaining more recognition. Here we present a thorough analysis of physico-chemical parameters, such as accessible surface area (ASA), average hydrophobicity (H
MeSH term(s)	Cell Membrane/metabolism ; Coronaviridae ; Endoplasmic Reticulum/metabolism ; Humans ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Protein Domains ; Viral Proteins/metabolism
Chemical Substances	Membrane Proteins ; Viral Proteins
Language	English
Publishing date	2022-03-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2022.03.002
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Article: Unique properties of Coronaviridae single-pass transmembrane domain regions as an adaptation to diverse membrane systems

Kubiszewski-Jakubiak, Szymon / Worch, Remigiusz

Virology. 2022 May, v. 570

2022

Abstract	Enveloped viruses such as Coronaviridae (CoV) enter the host cell by fusing the viral envelope directly with the plasma membrane (PM) or with the membrane of the endosome. Replication of the CoV genome takes place in membrane compartments formed by rearrangement of the endoplasmic reticulum (ER) membrane network. Budding of these viruses occurs from the ER-Golgi intermediate compartment (ERGIC). The relationship between proteins and various membranes is crucial for the replication cycle of CoVs. The role of transmembrane domains (TMDs) and pre-transmembrane domains (pre-TMD) of viral proteins in this process is gaining more recognition. Here we present a thorough analysis of physico-chemical parameters, such as accessible surface area (ASA), average hydrophobicity (Hₐᵥ), and contribution of specific amino acids in TMDs and pre-TMDs of single-span membrane proteins of human viruses. We focus on unique properties of these elements in CoV and postulate their role in adaptation to diverse host membranes and regulation of retention of membrane proteins during replication.
Keywords	Coronaviridae ; endoplasmic reticulum ; genome ; humans ; hydrophobicity ; plasma membrane ; surface area ; virology
Language	English
Dates of publication	2022-05
Size	p. 1-8.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2022.03.002
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Article ; Online: Influenza A H1 and H3 Transmembrane Domains Interact Differently with Each Other and with Surrounding Membrane Lipids.

Kubiszewski-Jakubiak, Szymon / Worch, Remigiusz

Viruses

2020 Volume 12, Issue 12

Abstract: Hemagglutinin (HA) is a class I viral membrane fusion protein, which is the most abundant transmembrane protein on the surface of influenza A virus (IAV) particles. HA plays a crucial role in the recognition of the host cell, fusion of the viral envelope ...

Abstract	Hemagglutinin (HA) is a class I viral membrane fusion protein, which is the most abundant transmembrane protein on the surface of influenza A virus (IAV) particles. HA plays a crucial role in the recognition of the host cell, fusion of the viral envelope and the host cell membrane, and is the major antigen in the immune response during the infection. Mature HA organizes in homotrimers consisting of a sequentially highly variable globular head and a relatively conserved stalk region. Every HA monomer comprises a hydrophilic ectodomain, a pre-transmembrane domain (pre-TMD), a hydrophobic transmembrane domain (TMD), and a cytoplasmic tail (CT). In recent years the effect of the pre-TMD and TMD on the structure and function of HA has drawn some attention. Using bioinformatic tools we analyzed all available full-length amino acid sequences of HA from 16 subtypes across various host species. We calculated several physico-chemical parameters of HA pre-TMDs and TMDs including accessible surface area (ASA), average hydrophobicity (H
MeSH term(s)	Hemagglutinin Glycoproteins, Influenza Virus/chemistry ; Influenza A virus/chemistry ; Membrane Lipids/chemistry ; Phylogeny ; Protein Domains ; Protein Multimerization
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus ; Membrane Lipids
Language	English
Publishing date	2020-12-17
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12121461
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Design and Structure of Outer Membrane Receptors from Peroxisomes, Mitochondria, and Chloroplasts.

Panigrahi, Rashmi / Kubiszewski-Jakubiak, Szymon / Whelan, James / Vrielink, Alice

Structure (London, England : 1993)

2015 Volume 23, Issue 10, Page(s) 1783–1800

Abstract: The eukaryotic cell is defined by compartments that allow specialization of function. This compartmental structure generates a new concept in cell biology compared with the simpler prokaryotic cell structure, namely the specific targeting of proteins to ... ...

Abstract	The eukaryotic cell is defined by compartments that allow specialization of function. This compartmental structure generates a new concept in cell biology compared with the simpler prokaryotic cell structure, namely the specific targeting of proteins to intracellular compartments. Protein targeting is achieved by the action of specialized signals on proteins destined for organelles that are recognized by cognate receptors. An understanding of the specificity of targeting signal recognition leading to import requires an understanding of the receptor structures. Here, we focus on the structures of receptors of different import machineries located on the outer membrane of three organelles: peroxisomes, mitochondria, and chloroplasts. This review provides an overview of the structural features of outer membrane import receptors that recognize targeting signals. Finally, we briefly discuss combinatorial approaches that might aid in understanding the structural factors mediating receptor targeting signal recognition.
MeSH term(s)	Cell Compartmentation ; Chloroplasts/metabolism ; Chloroplasts/ultrastructure ; Eukaryotic Cells/cytology ; Eukaryotic Cells/metabolism ; Gene Expression ; Humans ; Intracellular Membranes/metabolism ; Intracellular Membranes/ultrastructure ; Mitochondria/metabolism ; Mitochondria/ultrastructure ; Models, Molecular ; Peroxisomes/metabolism ; Peroxisomes/ultrastructure ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Protein Sorting Signals ; Protein Transport ; Receptors, Cytoplasmic and Nuclear/chemistry ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Signal Transduction
Chemical Substances	Plant Proteins ; Protein Sorting Signals ; Receptors, Cytoplasmic and Nuclear
Language	English
Publishing date	2015-10-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2015.08.005
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Article: Evidence for interactions between the mitochondrial import apparatus and respiratory chain complexes via Tim21-like proteins in Arabidopsis.

Murcha, Monika W / Kubiszewski-Jakubiak, Szymon / Wang, Yan / Whelan, James

Frontiers in plant science

2014 Volume 5, Page(s) 82

Abstract: The mitochondrial import machinery and the respiratory chain complexes of the inner membrane are highly interdependent for the efficient import and assembly of nuclear encoded respiratory chain components and for the generation of a proton motive force ... ...

Abstract	The mitochondrial import machinery and the respiratory chain complexes of the inner membrane are highly interdependent for the efficient import and assembly of nuclear encoded respiratory chain components and for the generation of a proton motive force essential for protein translocation into or across the inner membrane. In plant and non-plant systems functional, physical, and evolutionary associations have been observed between proteins of the respiratory chain and protein import apparatus. Here we identify two novel Tim21-like proteins encoded by At2g40800 and At3g56430 that are imported into the mitochondrial inner membrane. We propose that Tim21-like proteins may associate with respiratory chain Complex I, III, in addition to the TIM17:23 translocase of the inner membrane. These results are discussed further with regards to the regulation of mitochondrial activity and biogenesis.
Language	English
Publishing date	2014-03-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2014.00082
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Article ; Online: Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%.

Vallarino, José G / Kubiszewski-Jakubiak, Szymon / Ruf, Stephanie / Rößner, Margit / Timm, Stefan / Bauwe, Hermann / Carrari, Fernando / Rentsch, Doris / Bock, Ralph / Sweetlove, Lee J / Fernie, Alisdair R

Scientific reports

2020 Volume 10, Issue 1, Page(s) 17219

Abstract: The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given ... ...

Abstract	The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.
MeSH term(s)	Amino Acids/metabolism ; Biological Transport ; Carbohydrate Metabolism ; Carbon/metabolism ; Crop Production/methods ; Fruit/growth & development ; Fruit/physiology ; Genetic Engineering/methods ; Lycopersicon esculentum/genetics ; Lycopersicon esculentum/metabolism ; Lycopersicon esculentum/physiology ; Nitrogen/metabolism ; Plants, Genetically Modified/genetics ; Plants, Genetically Modified/metabolism ; Plants, Genetically Modified/physiology
Chemical Substances	Amino Acids ; Carbon (7440-44-0) ; Nitrogen (N762921K75)
Language	English
Publishing date	2020-10-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-73709-6
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Article ; Online: MPIC: a mitochondrial protein import components database for plant and non-plant species.

Murcha, Monika W / Narsai, Reena / Devenish, James / Kubiszewski-Jakubiak, Szymon / Whelan, James

Plant & cell physiology

2014 Volume 56, Issue 1, Page(s) e10

Abstract: In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to ... ...

Abstract	In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. We have generated the Mitochondrial Protein Import Components (MPIC) Database (DB; http://www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest. The MPIC DB presents an extensive resource facilitating detailed investigation of the mitochondrial protein import machinery and allowing patterns of conservation and divergence to be recognized that would otherwise have been missed. To demonstrate the usefulness of the MPIC DB, we present a comparative analysis of the mitochondrial protein import machinery in plants and non-plant species, revealing plant-specific features that have evolved.
MeSH term(s)	Base Sequence ; Databases, Factual ; Fungi/genetics ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Annotation ; Phaeophyceae/genetics ; Phylogeny ; Plants/genetics ; Protein Transport ; Rhodophyta/genetics
Chemical Substances	Mitochondrial Proteins
Language	English
Publishing date	2014-11-29
Publishing country	Japan
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcu186
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Protein import into plant mitochondria: signals, machinery, processing, and regulation.

Murcha, Monika W / Kmiec, Beata / Kubiszewski-Jakubiak, Szymon / Teixeira, Pedro F / Glaser, Elzbieta / Whelan, James

Journal of experimental botany

2014 Volume 65, Issue 22, Page(s) 6301–6335

Abstract: The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on ... ...

Abstract	The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.
MeSH term(s)	Mitochondria/metabolism ; Plant Proteins/metabolism ; Plants/metabolism ; Protein Processing, Post-Translational ; Protein Transport ; Signal Transduction
Chemical Substances	Plant Proteins
Language	English
Publishing date	2014-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/eru399
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Article ; Online: In vitro RNA uptake studies in plant mitochondria.

Kubiszewski-Jakubiak, Szymon / Megel, Cyrille / Ubrig, Elodie / Salinas, Thalia / Duchêne, Anne-Marie / Maréchal-Drouard, Laurence

Methods in molecular biology (Clifton, N.J.)

2015 Volume 1305, Page(s) 45–60

Abstract: During evolution, most of the ancestral genes from the endosymbiotic α-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. To allow the comeback of proteins and RNAs [in particular transfer RNA (tRNAs)] ...

Abstract	During evolution, most of the ancestral genes from the endosymbiotic α-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. To allow the comeback of proteins and RNAs [in particular transfer RNA (tRNAs)] into the organelle, macromolecule import systems were universally established. While protein import processes have been studied into details, much less is known about tRNA mitochondrial import. In plants, part of the knowledge on the tRNA import process into mitochondria has been acquired thanks to in vitro import assays. Furthermore, the development of in vitro RNA import strategies allowed the study of plant mitochondrial gene expression. The purpose of this chapter is to provide detailed protocols to perform in vitro RNA uptake into potato (Solanum tuberosum) or Arabidopsis (Arabidopsis thaliana) mitochondria as well as approaches to analyze them.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Electrophoresis, Polyacrylamide Gel/methods ; Mitochondria/genetics ; Mitochondria/metabolism ; RNA Transport ; RNA, Plant/genetics ; RNA, Plant/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Solanum tuberosum/genetics ; Solanum tuberosum/metabolism ; Transcription, Genetic
Chemical Substances	RNA, Plant ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-2639-8_4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: MPIC: A Mitochondrial Protein Import Components Database for Plant and Non-Plant Species

Murcha, Monika W / James Devenish / James Whelan / Reena Narsai / Szymon Kubiszewski-Jakubiak

Plant & cell physiology. 2015 Jan., v. 56, no. 1

2015

Abstract	In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. We have generated the Mitochondrial Protein Import Components (MPIC) Database (DB; http://www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest. The MPIC DB presents an extensive resource facilitating detailed investigation of the mitochondrial protein import machinery and allowing patterns of conservation and divergence to be recognized that would otherwise have been missed. To demonstrate the usefulness of the MPIC DB, we present a comparative analysis of the mitochondrial protein import machinery in plants and non-plant species, revealing plant-specific features that have evolved.
Keywords	algae ; Arabidopsis thaliana ; databases ; genome ; Homo sapiens ; humans ; imports ; mitochondria ; Oryza sativa ; protein transport ; rice ; Saccharomyces cerevisiae ; yeasts
Language	English
Dates of publication	2015-01
Size	p. e10.
Publishing place	Japanese Society of Plant Physiologists.
Document type	Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcu186
Database	NAL-Catalogue (AGRICOLA)

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