Protein Ubiquitination

A special issue of Cells (ISSN 2073-4409).

Deadline for manuscript submissions: closed (15 March 2014) | Viewed by 168262

Special Issue Editor

Plant Stress Physiology, School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
Interests: ubiquitin proteasome pathway; E3 ligases; stress physiology; vitamin B6 metabolism
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Special Issue Information

Dear Colleagues,

Since the discovery of the ubiquitin proteasome pathway in the late 1970’s, tremendous progress has been accomplished in understanding its mechanism, and revealing its conserved nature across the different eukaryotic kingdoms. The pathway functions as one of the major regulatory switches in the cell and affects a broad range of processes such as cell division, transcriptional activity, stress responses and transport processes. Although the pathway is often mainly connected with degradation of ubiquitylated proteins, it also has major impact in controlling activity and subcellular localization of proteins, independently of proteolysis.
This Special Issue will provide an Open Access opportunity to publish research work and review articles related to the ubiquitin proteasome pathway, and to offer comprehensive new insights into current developments of this exciting and important research field.

Dr. Hanjo Hellmann
Guest Editor

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Keywords

  • ubiquitin
  • ubiquitin chain
  • Sumo
  • 26S proteasome
  • protein stability
  • protein localization
  • E3 ligases
  • cellular regulation
  • signal transduction
  • development

Published Papers (14 papers)

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Research

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2690 KiB  
Article
Yeast Irc22 Is a Novel Dsk2-Interacting Protein that Is Involved in Salt Tolerance
by Takashi Ishii, Minoru Funakoshi, Hideki Kobayashi and Takeshi Sekiguchi
Cells 2014, 3(2), 180-198; https://doi.org/10.3390/cells3020180 - 27 Mar 2014
Cited by 6 | Viewed by 7661
Abstract
The yeast ubiquitin-like and ubiquitin-associated protein Dsk2 is one of the ubiquitin receptors that function in the ubiquitin-proteasome pathway. We screened the Dsk2-interacting proteins in Saccharomyces cerevisiae by a two-hybrid assay and identified a novel Dsk2-interacting protein, Irc22, the gene locus of which [...] Read more.
The yeast ubiquitin-like and ubiquitin-associated protein Dsk2 is one of the ubiquitin receptors that function in the ubiquitin-proteasome pathway. We screened the Dsk2-interacting proteins in Saccharomyces cerevisiae by a two-hybrid assay and identified a novel Dsk2-interacting protein, Irc22, the gene locus of which has previously been described as YEL001C, but the function of which is unknown. IRC22/YEL001C encodes 225 amino acid residues with a calculated molecular weight of 25 kDa. The Irc22 protein was detected in yeast cells. IRC22 was a nonessential gene for yeast growth, and its homologs were found among ascomycetous yeasts. Irc22 interacted with Dsk2 in yeast cells, but not with Rad23 and Ddi1. Ubiquitin-dependent degradation was impaired mildly by over-expression or disruption of IRC22. Compared with the wild-type strain, dsk2D exhibited salt sensitivity while irc22D exhibited salt tolerance at high temperatures. The salt-tolerant phenotype that was observed in irc22D disappeared in the dsk2Dirc22D double disruptant, indicating that DSK2 is positively and IRC22 is negatively involved in salt stress tolerance. IRC22 disruption did not affect any responses to DNA damage and oxidative stress when comparing the irc22D and wild-type strains. Collectively, these results suggest that Dsk2 and Irc22 are involved in salt stress tolerance in yeast. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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Review

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8072 KiB  
Review
Versatile Roles of K63-Linked Ubiquitin Chains in Trafficking
by Zoi Erpapazoglou, Olivier Walker and Rosine Haguenauer-Tsapis
Cells 2014, 3(4), 1027-1088; https://doi.org/10.3390/cells3041027 - 12 Nov 2014
Cited by 135 | Viewed by 14056
Abstract
Modification by Lys63-linked ubiquitin (UbK63) chains is the second most abundant form of ubiquitylation. In addition to their role in DNA repair or kinase activation, UbK63 chains interfere with multiple steps of intracellular trafficking. UbK63 chains decorate many plasma membrane proteins, providing a [...] Read more.
Modification by Lys63-linked ubiquitin (UbK63) chains is the second most abundant form of ubiquitylation. In addition to their role in DNA repair or kinase activation, UbK63 chains interfere with multiple steps of intracellular trafficking. UbK63 chains decorate many plasma membrane proteins, providing a signal that is often, but not always, required for their internalization. In yeast, plants, worms and mammals, this same modification appears to be critical for efficient sorting to multivesicular bodies and subsequent lysosomal degradation. UbK63 chains are also one of the modifications involved in various forms of autophagy (mitophagy, xenophagy, or aggrephagy). Here, in the context of trafficking, we report recent structural studies investigating UbK63 chains assembly by various E2/E3 pairs, disassembly by deubiquitylases, and specifically recognition as sorting signals by receptors carrying Ub-binding domains, often acting in tandem. In addition, we address emerging and unanticipated roles of UbK63 chains in various recycling pathways that function by activating nucleators required for actin polymerization, as well as in the transient recruitment of signaling molecules at the plasma or ER membrane. In this review, we describe recent advances that converge to elucidate the mechanisms underlying the wealth of trafficking functions of UbK63 chains. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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2252 KiB  
Review
Regulation of TGF-β Superfamily Signaling by SMAD Mono-Ubiquitination
by Feng Xie, Zhengkui Zhang, Hans Van Dam, Long Zhang and Fangfang Zhou
Cells 2014, 3(4), 981-993; https://doi.org/10.3390/cells3040981 - 15 Oct 2014
Cited by 58 | Viewed by 13357
Abstract
TGF-β(transforming growth factor-β) superfamily signaling mediators are important regulators of diverse physiological and pathological events. TGF-β signals are transduced by transmembrane type I and type II serine/threonine kinase receptors and their downstream effectors, the SMAD(drosophila mothers against decapentaplegic protein) proteins. Numerous studies have [...] Read more.
TGF-β(transforming growth factor-β) superfamily signaling mediators are important regulators of diverse physiological and pathological events. TGF-β signals are transduced by transmembrane type I and type II serine/threonine kinase receptors and their downstream effectors, the SMAD(drosophila mothers against decapentaplegic protein) proteins. Numerous studies have already demonstrated crucial regulatory roles for modification of TGF-β pathway components by poly-ubiquitination. Recently, several studies also uncovered mono-ubiquitination of SMADs as a mechanism for SMAD activation or inactivation. Mono-ubiquitination and subsequent deubiquitination of SMAD proteins accordingly play important roles in the control of TGF-β superfamily signaling. This review highlights the major pathways regulated by SMAD mono-ubiquitination. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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4984 KiB  
Review
Bacterial Effectors and Their Functions in the Ubiquitin-Proteasome System: Insight from the Modes of Substrate Recognition
by Minsoo Kim, Ryota Otsubo, Hanako Morikawa, Akira Nishide, Kenji Takagi, Chihiro Sasakawa and Tsunehiro Mizushima
Cells 2014, 3(3), 848-864; https://doi.org/10.3390/cells3030848 - 18 Aug 2014
Cited by 59 | Viewed by 9541
Abstract
Protein ubiquitination plays indispensable roles in the regulation of cell homeostasis and pathogenesis of neoplastic, infectious, and neurodegenerative diseases. Given the importance of this modification, it is to be expected that several pathogenic bacteria have developed the ability to utilize the host ubiquitin [...] Read more.
Protein ubiquitination plays indispensable roles in the regulation of cell homeostasis and pathogenesis of neoplastic, infectious, and neurodegenerative diseases. Given the importance of this modification, it is to be expected that several pathogenic bacteria have developed the ability to utilize the host ubiquitin system for their own benefit. Modulation of the host ubiquitin system by bacterial effector proteins inhibits innate immune responses and hijacks central signaling pathways. Bacterial effectors mimic enzymes of the host ubiquitin system, but may or may not be structurally similar to the mammalian enzymes. Other effectors bind and modify components of the host ubiquitin system, and some are themselves subject to ubiquitination. This review will describe recent findings, based on structural analyses, regarding how pathogens use post-translational modifications of proteins to establish an infection. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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Review
Regulation of Endoplasmic Reticulum-Associated Protein Degradation (ERAD) by Ubiquitin
by Leticia Lemus and Veit Goder
Cells 2014, 3(3), 824-847; https://doi.org/10.3390/cells3030824 - 05 Aug 2014
Cited by 90 | Viewed by 15654
Abstract
Quality control of protein folding inside the endoplasmic reticulum (ER) includes chaperone-mediated assistance in folding and the selective targeting of terminally misfolded species to a pathway called ER-associated protein degradation, or simply ERAD. Once selected for ERAD, substrates will be transported (back) into [...] Read more.
Quality control of protein folding inside the endoplasmic reticulum (ER) includes chaperone-mediated assistance in folding and the selective targeting of terminally misfolded species to a pathway called ER-associated protein degradation, or simply ERAD. Once selected for ERAD, substrates will be transported (back) into the cytosol, a step called retrotranslocation. Although still ill defined, retrotranslocation likely involves a protein conducting channel that is in part formed by specific membrane-embedded E3 ubiquitin ligases. Early during retrotranslocation, reversible self-ubiquitination of these ligases is thought to aid in initiation of substrate transfer across the membrane. Once being at least partially exposed to the cytosol, substrates will become ubiquitinated on the cytosolic side of the ER membrane by the same E3 ubiquitin ligases. Ubiquitin on substrates was originally thought to be a permanent modification that (1) promotes late steps of retrotranslocation by recruiting the energy-providing ATPase Cdc48p/p97 via binding to its associated adaptor proteins and that (2) serves to target substrates to the proteasome. Recently it became evident, however, that the poly-ubiquitin chains (PUCs) on ERAD substrates are often subject to extensive remodeling, or processing, at several stages during ERAD. This review recapitulates the current knowledge and recent findings about PUC processing on ERAD substrates and ubiquitination of ERAD machinery components and discusses their functional consequences. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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646 KiB  
Review
Ubiquitin Signaling: Extreme Conservation as a Source of Diversity
by Alice Zuin, Marta Isasa and Bernat Crosas
Cells 2014, 3(3), 690-701; https://doi.org/10.3390/cells3030690 - 10 Jul 2014
Cited by 60 | Viewed by 7765
Abstract
Around 2 × 103–2.5 × 103 million years ago, a unicellular organism with radically novel features, ancestor of all eukaryotes, dwelt the earth. This organism, commonly referred as the last eukaryotic common ancestor, contained in its proteome the same [...] Read more.
Around 2 × 103–2.5 × 103 million years ago, a unicellular organism with radically novel features, ancestor of all eukaryotes, dwelt the earth. This organism, commonly referred as the last eukaryotic common ancestor, contained in its proteome the same functionally capable ubiquitin molecule that all eukaryotic species contain today. The fact that ubiquitin protein has virtually not changed during all eukaryotic evolution contrasts with the high expansion of the ubiquitin system, constituted by hundreds of enzymes, ubiquitin-interacting proteins, protein complexes, and cofactors. Interestingly, the simplest genetic arrangement encoding a fully-equipped ubiquitin signaling system is constituted by five genes organized in an operon-like cluster, and is found in archaea. How did ubiquitin achieve the status of central element in eukaryotic physiology? We analyze here the features of the ubiquitin molecule and the network that it conforms, and propose notions to explain the complexity of the ubiquitin signaling system in eukaryotic cells. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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940 KiB  
Review
Mechanisms of Generating Polyubiquitin Chains of Different Topology
by Randy Suryadinata, Siti Nur Ain Roesley, George Yang and Boris Šarčević
Cells 2014, 3(3), 674-689; https://doi.org/10.3390/cells3030674 - 01 Jul 2014
Cited by 98 | Viewed by 11798
Abstract
Ubiquitination is an important post-translational process involving attachment of the ubiquitin molecule to lysine residue/s on a substrate protein or on another ubiquitin molecule, leading to the formation of protein mono-, multi- or polyubiquitination. Protein ubiquitination requires a cascade of three enzymes, where [...] Read more.
Ubiquitination is an important post-translational process involving attachment of the ubiquitin molecule to lysine residue/s on a substrate protein or on another ubiquitin molecule, leading to the formation of protein mono-, multi- or polyubiquitination. Protein ubiquitination requires a cascade of three enzymes, where the interplay between different ubiquitin-conjugating and ubiquitin-ligase enzymes generates diverse ubiquitinated proteins topologies. Structurally diverse ubiquitin conjugates are recognized by specific proteins with ubiquitin-binding domains (UBDs) to target the substrate proteins of different pathways. The mechanism/s for generating the different ubiquitinated proteins topologies is not well understood. Here, we will discuss our current understanding of the mechanisms underpinning the generation of mono- or polyubiquitinated substrates. In addition, we will discuss how linkage-specific polyubiquitin chains through lysines-11, -48 or -63 are formed to target proteins to different fates by binding specific UBD proteins. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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638 KiB  
Review
The Challenge of Producing Ubiquitinated Proteins for Structural Studies
by Serena Faggiano and Annalisa Pastore
Cells 2014, 3(2), 639-656; https://doi.org/10.3390/cells3020639 - 12 Jun 2014
Cited by 16 | Viewed by 8272
Abstract
Protein ubiquitination is an important post-translational modification involved in several essential signalling pathways. It has different effects on the target protein substrate, i.e., it can trigger the degradation of the protein in the proteasome, change the interactions of the modified protein with [...] Read more.
Protein ubiquitination is an important post-translational modification involved in several essential signalling pathways. It has different effects on the target protein substrate, i.e., it can trigger the degradation of the protein in the proteasome, change the interactions of the modified protein with its partners, or affect its localization and activity. In order to understand the molecular mechanisms underlying the consequences of protein ubiquitination, scientists have to face the challenging task of producing ubiquitinated proteins for structural characterization with X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy. These techniques require milligrams of homogeneous samples of high purity. The strategies proposed so far for the production of ubiquitinated proteins can be divided into two groups, i.e., chemical (or non-enzymatic) and enzymatic methodologies. In this review, we summarize the still very sparse examples available in the literature that describe successful production of ubiquitinated proteins amenable for biochemical and structural studies, and discuss advantages and disadvantages of the techniques proposed. We also give a perspective of the direction in which the field might evolve. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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982 KiB  
Review
The Ufm1 Cascade
by Jens Daniel and Eva Liebau
Cells 2014, 3(2), 627-638; https://doi.org/10.3390/cells3020627 - 11 Jun 2014
Cited by 70 | Viewed by 9160
Abstract
The ubiquitin-fold modifier 1 (Ufm1) is a posttranslational modifier that belongs to the ubiquitin-like protein (UBL) family. Ufm1 is present in nearly all eukaryotic organisms, with the exception of fungi. It resembles ubiquitin in its ability to be ligated to other proteins, as [...] Read more.
The ubiquitin-fold modifier 1 (Ufm1) is a posttranslational modifier that belongs to the ubiquitin-like protein (UBL) family. Ufm1 is present in nearly all eukaryotic organisms, with the exception of fungi. It resembles ubiquitin in its ability to be ligated to other proteins, as well as in the mechanism of ligation. While the Ufm1 cascade has been implicated in endoplasmic reticulum functions and cell cycle control, its biological role still remains poorly understood. In this short review, we summarize the current state of Ufm1 research and its potential role in human diseases, like diabetes, ischemic heart disease and cancer. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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451 KiB  
Review
Role of Ubiquitylation in Controlling Suppressor of Cytokine Signalling 3 (SOCS3) Function and Expression
by Jamie J. L. Williams, Kirsten M. A. Munro and Timothy M. Palmer
Cells 2014, 3(2), 546-562; https://doi.org/10.3390/cells3020546 - 30 May 2014
Cited by 31 | Viewed by 12529
Abstract
The realisation that unregulated activation of the Janus kinase–signal transducer and activator of transcription (JAK–STAT) pathway is a key driver of a wide range of diseases has identified its components as targets for therapeutic intervention by small molecule inhibitors and biologicals. In this [...] Read more.
The realisation that unregulated activation of the Janus kinase–signal transducer and activator of transcription (JAK–STAT) pathway is a key driver of a wide range of diseases has identified its components as targets for therapeutic intervention by small molecule inhibitors and biologicals. In this review, we discuss JAK-STAT signalling pathway inhibition by the inducible inhibitor “suppressor of cytokine signaling 3 (SOCS3), its role in diseases such as myeloproliferative disorders, and its function as part of a multi-subunit E3 ubiquitin ligase complex. In addition, we highlight potential applications of these insights into SOCS3-based therapeutic strategies for management of conditions such as vascular re-stenosis associated with acute vascular injury, where there is strong evidence that multiple processes involved in disease progression could be attenuated by localized potentiation of SOCS3 expression levels. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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475 KiB  
Review
HSV-1 ICP0: An E3 Ubiquitin Ligase That Counteracts Host Intrinsic and Innate Immunity
by Mirna Perusina Lanfranca, Heba H. Mostafa and David J. Davido
Cells 2014, 3(2), 438-454; https://doi.org/10.3390/cells3020438 - 20 May 2014
Cited by 68 | Viewed by 12756
Abstract
The herpes simplex virus type 1 (HSV-1) encoded E3 ubiquitin ligase, infected cell protein 0 (ICP0), is required for efficient lytic viral replication and regulates the switch between the lytic and latent states of HSV-1. As an E3 ubiquitin ligase, ICP0 directs the [...] Read more.
The herpes simplex virus type 1 (HSV-1) encoded E3 ubiquitin ligase, infected cell protein 0 (ICP0), is required for efficient lytic viral replication and regulates the switch between the lytic and latent states of HSV-1. As an E3 ubiquitin ligase, ICP0 directs the proteasomal degradation of several cellular targets, allowing the virus to counteract different cellular intrinsic and innate immune responses. In this review, we will focus on how ICP0’s E3 ubiquitin ligase activity inactivates the host intrinsic defenses, such as nuclear domain 10 (ND10), SUMO, and the DNA damage response to HSV-1 infection. In addition, we will examine ICP0’s capacity to impair the activation of interferon (innate) regulatory mediators that include IFI16 (IFN γ-inducible protein 16), MyD88 (myeloid differentiation factor 88), and Mal (MyD88 adaptor-like protein). We will also consider how ICP0 allows HSV-1 to evade activation of the NF-κB (nuclear factor kappa B) inflammatory signaling pathway. Finally, ICP0’s paradoxical relationship with USP7 (ubiquitin specific protease 7) and its roles in intrinsic and innate immune responses to HSV-1 infection will be discussed. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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258 KiB  
Review
Mcl-1 Ubiquitination: Unique Regulation of an Essential Survival Protein
by Barbara Mojsa, Iréna Lassot and Solange Desagher
Cells 2014, 3(2), 418-437; https://doi.org/10.3390/cells3020418 - 08 May 2014
Cited by 147 | Viewed by 14539
Abstract
Mcl-1 is an anti-apoptotic protein of the Bcl-2 family that is essential for the survival of multiple cell lineages and that is highly amplified in human cancer. Under physiological conditions, Mcl-1 expression is tightly regulated at multiple levels, involving transcriptional, post-transcriptional and post-translational [...] Read more.
Mcl-1 is an anti-apoptotic protein of the Bcl-2 family that is essential for the survival of multiple cell lineages and that is highly amplified in human cancer. Under physiological conditions, Mcl-1 expression is tightly regulated at multiple levels, involving transcriptional, post-transcriptional and post-translational processes. Ubiquitination of Mcl-1, that targets it for proteasomal degradation, allows for rapid elimination of the protein and triggering of cell death, in response to various cellular events. In the last decade, a number of studies have elucidated different pathways controlling Mcl-1 ubiquitination and degradation. Four different E3 ubiquitin-ligases (e.g., Mule, SCFβ-TrCP, SCFFbw7 and Trim17) and one deubiquitinase (e.g., USP9X), that respectively mediate and oppose Mcl-1 ubiquitination, have been formerly identified. The interaction between Mule and Mcl-1 can be modulated by other Bcl-2 family proteins, while recognition of Mcl-1 by the other E3 ubiquitin-ligases and deubiquitinase is influenced by phosphorylation of specific residues in Mcl-1. The protein kinases and E3 ubiquitin-ligases that are involved in the regulation of Mcl-1 stability vary depending on the cellular context, highlighting the complexity and pivotal role of Mcl-1 regulation. In this review, we attempt to recapitulate progress in understanding Mcl-1 regulation by the ubiquitin-proteasome system. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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631 KiB  
Review
The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection
by Arianna Calistri, Denis Munegato, Ilaria Carli, Cristina Parolin and Giorgio Palù
Cells 2014, 3(2), 386-417; https://doi.org/10.3390/cells3020386 - 06 May 2014
Cited by 70 | Viewed by 11493
Abstract
Through the combined action of ubiquitinating and deubiquitinating enzymes, conjugation of ubiquitin to a target protein acts as a reversible post-translational modification functionally similar to phosphorylation. Indeed, ubiquitination is more and more recognized as a central process for the fine regulation of many [...] Read more.
Through the combined action of ubiquitinating and deubiquitinating enzymes, conjugation of ubiquitin to a target protein acts as a reversible post-translational modification functionally similar to phosphorylation. Indeed, ubiquitination is more and more recognized as a central process for the fine regulation of many cellular pathways. Due to their nature as obligate intracellular parasites, viruses rely on the most conserved host cell machineries for their own replication. Thus, it is not surprising that members from almost every viral family are challenged by ubiquitin mediated mechanisms in different steps of their life cycle and have evolved in order to by-pass or exploit the cellular ubiquitin conjugating system to maximize their chance to establish a successful infection. In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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506 KiB  
Review
Ubiquitination Regulates the Morphogenesis and Function of Sperm Organelles
by Nobuhiro Nakamura
Cells 2013, 2(4), 732-750; https://doi.org/10.3390/cells2040732 - 05 Dec 2013
Cited by 33 | Viewed by 18489
Abstract
It is now understood that protein ubiquitination has diverse cellular functions in eukaryotes. The molecular mechanism and physiological significance of ubiquitin-mediated processes have been extensively studied in yeast, Drosophila and mammalian somatic cells. Moreover, an increasing number of studies have emphasized the importance [...] Read more.
It is now understood that protein ubiquitination has diverse cellular functions in eukaryotes. The molecular mechanism and physiological significance of ubiquitin-mediated processes have been extensively studied in yeast, Drosophila and mammalian somatic cells. Moreover, an increasing number of studies have emphasized the importance of ubiquitination in spermatogenesis and fertilization. The dysfunction of various ubiquitin systems results in impaired sperm development with abnormal organelle morphology and function, which in turn is highly associated with male infertility. This review will focus on the emerging roles of ubiquitination in biogenesis, function and stability of sperm organelles in mammals. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
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