Close

Spontaneous isomerization of long-lived proteins provides a molecular mechanism for the lysosomal failure observed in Alzheimer’s disease

Tyler R. Lambeth, Dylan L. Riggs, Lance E. Talbert, Jin Tang, Emily Coburn, Amrik S. Kang, Jessica Noll, Catherine Augello, Byron D. Ford, Ryan R. Julian

Posted on: 15 May 2019

Preprint posted on 12 April 2019

Article now published in ACS Central Science at http://dx.doi.org/10.1021/acscentsci.9b00369

Do LSDs have the answer? Exploring a promising link between lysosomal storage disorders and Alzheimer’s disease.

Selected by Joanna Cross

Background

I was drawn to this preprint not by the topic of Alzheimer’s disease (AD), but by the word ‘lysosome’. This may surprise some people, but one of the disorders I studied during my PhD was Niemann-Pick type C disease, a lysosomal storage disorder (LSD) known colloquially as “childhood Alzheimer’s”.  The lysosomal system is the cell’s recycling facility; old proteins are deposited in the lysosomes, and amino acids are regurgitated out, ready to be made into something new and useful.  Within the lysosome, enzymes called endopeptidases cleave proteins at internal sites.  Exopeptidases finish the job by further digesting the resulting smaller peptides from both termini (at this point, I visualize Pac-man style objects consuming the little yellow dots before running head-long into each other).  LSDs arise when enzymes or proteins responsible for the efficient running of the ‘facility’ are faulty: imagine what would happen if the Pac-men lost their mouths.  There would be a lot of un-eaten yellow dots.  Many LSDs occur at a young age, but, like Alzheimer’s disease, are neurogenerative and often fatal.

The focus of this preprint is not on the machinery of the lysosomes, but on the substrates themselves.  In particular, two forms of chemical transformation known as isomerization and epimerization.  Isomerization primarily occurs at aspartic acid, when the side chain inserts into and elongates the peptide backbone (picture what happens when a couple of friends want to join a picture, not at the end, but right in the middle!).  Epimerization is when the side chain of an amino acid changes from the usual L-chirality to the D-chirality: L- and D- forms are mirror images of each other, just like your hands.  So, what is the importance of these two chemical transformations?  As with so many things, nature shows us the answer. Many venoms contain epimerized amino acids to help prevent degradation in the prey’s body, showing that these transformations cause resistance to protease degradation.

Amyloid-b(Ab) and tau are subjected to both chemical transformations and are major constituents of the senile plaques and tangles, respectively, present in AD.  Indeed, isomerized and epimerized Abhas been found in the brains of people with AD.   Therefore, if these chemical changes do indeed prevent lysosomal protein degradation, this could provide the link between LSDs and AD.

 

Key Findings

In order to demonstrate how iso/epi modifications can affect the lysosomal machinery, the authors first subjected synthetic peptides to endopeptidases (cathepsins D and L), and exopeptidases (cathepsins B and H).  The resulting peptide fragments were then measured using Liquid Chromatography Mass Spectrometry (LC-MS).

When a synthetic peptide, derived from aB-crystallin, was exposed to both cathepsins D and L, there was reduced digestion of the iso/epi form compared to the canonical peptide.  As exopeptidases function by breaking down peptides from each termini, a palindromic peptide was synthesized, “RLHTIDITHLR”. Intriguingly, changing the middle asparagine from L-asp to D-isoasp caused persistence of the “IDIT” peptide fragment, even after exposing the peptide to cathepsins B and H for 48 hours. Therefore, these experiments showed that iso/epi modifications can affect digestion by both endo- and exo-peptidases.

But how can iso/epi modifications contribute to the pathology of AD? Abis a peptide comprising 36-43 amino acids and these peptides are the main component of the amyloid plaques present in AD.  The authors used an Abpeptide fragment (Ab1-9) derived from the N-terminal end of this peptide, as this portion contains asparagine residues that are known to be highly isomerized in amyloid plaques.  Similar to the initial experiments, cathepsins B and L were able to significantly digest the canonical peptide but cannot alter the double isomer (L-isoAsp1, D-isoAsp7).   Interestingly, cathepsins D and H were unable to appreciably digest either form of the peptide, suggesting that the N-terminal portion of Abis generally hard to digest. Thus, addition of the iso/epi modifications can further complicate matters.

Given that intracellular aggregates of tau are also a hallmark of AD, the authors also subjected a tau peptide fragment (Tau594IINKKLDL601) to cathepsins.  Tau contains two residues that can be subjected to iso/epi modifications: Asn596and Asp600.  The authors showed that while cathepsins B, L and H could fully digest the canonical sequence, this is prevented by the iso/epi modifications.

Although the four cathepsins used above are the most abundant, they are by no means the only lysosomal proteases present in cells. To explore additional enzymes, the authors exposed mouse microglial cells to a chimeric peptide derived from the N-terminus of Ab.  The peptide included a polyarginine sequence for lysosomal delivery, and a quencher peptide sequence that results in fluorescence when the peptide is cleaved. After 150 minutes, fluorescence was observed for the canonical chimeric peptide, whereas the double isomer produced a significantly lower intensity fluorescence.  This shows that there is not an unknown protease in the lysosomal system that is designed to digest iso/epi sites.  Additionally, these results were recapitulated by incubating the chimeric peptide with only cathepsin L, thereby confirming the validity of the LC-MS approach.

The next question is why these modifications affect their ability to be digested by cathepsins.  To answer this, the authors turned to X-ray crystallography.  By analyzing the crystal structure of a peptide bound to the active site of cathepsin L, it can be seen that several hydrogen bonds orientate the substrate backbone so the cleavage site is accessible. Iso/epi modifications would change the structure so that they cannot fit properly into the active site, thereby preventing cleavage.  This hampered ability of cathepsins to completely digest AD-associated peptides would produce peptide fragments that are too long to be recognized by the transporters responsible for releasing digested amino acids back to the cytosol. This indicates that accumulation of these byproducts in the lysosomes is possible.

 

What I like about this preprint

Since my PhD, I have been intrigued about the link between LSDs and AD, and this preprint puts forward an intriguing and believable option.  Although other proteolytic pathways exist that could also have difficulties dealing with these modifications, lysosomes may be especially vulnerable due to the inability to get rid of undigested byproducts, resulting in failure of the organelle.

Future questions could include:

  • What drives the epi/iso modifications in AD?
  • What mechanisms and pathways are affected by lysosomal failure and how this contributes to the disease pathology?
  • Do drug treatments known to have positive outcomes in LSDs also influence biomarkers of AD, such as the misfolding and aggregation of tau and Ab?

Ultimately, this study represents an intriguing connection between LSDs and AD and provides a novel avenue for study.  If those little Pac-Men could be given back their mouths so they can fully devour all the yellow dots, perhaps we will be a step closer to improving lives for so many people.

 

doi: https://doi.org/10.1242/prelights.10707

Read preprint (3 votes)

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

Also in the biochemistry category:

Triglyceride metabolism controls inflammation and APOE4-associated disease states in microglia

Roxan A. Stephenson, Kory R. Johnson, Linling Cheng, et al.

Selected by 22 August 2024

Gustavo Stelzer, Marcus Oliveira

Biochemistry

Impaired 26S proteasome causes learning and memory deficiency and induces neuroinflammation mediated by NF-κB in mice

Christa C. Huber, Eduardo Callegari, Maria Paez, et al.

Selected by 22 August 2024

Gustavo Stelzer, Marcus Oliveira

Biochemistry

Notch3 is a genetic modifier of NODAL signalling for patterning asymmetry during mouse heart looping

Tobias Holm Bønnelykke, Marie-Amandine Chabry, Emeline Perthame, et al.

Selected by 06 June 2024

Bhaval Parmar

Developmental Biology

Also in the cell biology category:

The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

Joelle Lo, Katherine F. Vaeth, Gurprit Bhardwaj, et al.

Selected by 24 September 2024

Felipe Del Valle Batalla

Neuroscience

Pharyngeal neuronal mechanisms governing sour taste perception in Drosophila melanogaster

Bhanu Shrestha, Jiun Sang, Suman Rimal, et al.

Selected by 23 September 2024

Matthew Davies

Cell Biology

Feedback regulation by the RhoA-specific GEF ARHGEF17 regulates actomyosin network disassembly

Vasundhara Rao, Benjamin Grädel, Lucien Hinderling, et al.

Selected by 18 September 2024

Vibha SINGH

Cell Biology

Also in the molecular biology category:

The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

Joelle Lo, Katherine F. Vaeth, Gurprit Bhardwaj, et al.

Selected by 24 September 2024

Felipe Del Valle Batalla

Neuroscience

The role of ER exit sites in maintaining P-body organization and transmitting ER stress response during Drosophila melanogaster oogenesis

Samantha N. Milano, Livia V. Bayer, Julie J. Ko, et al.

Selected by 04 September 2024

Jonathan Townson

Cell Biology

Adult caudal fin shape is imprinted in the embryonic fin fold

Eric Surette, Joan Donahue, Stephanie Robinson, et al.

Selected by 28 August 2024

Isabella Cisneros

Developmental Biology

Also in the neuroscience category:

The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

Joelle Lo, Katherine F. Vaeth, Gurprit Bhardwaj, et al.

Selected by 24 September 2024

Felipe Del Valle Batalla

Neuroscience

Pharyngeal neuronal mechanisms governing sour taste perception in Drosophila melanogaster

Bhanu Shrestha, Jiun Sang, Suman Rimal, et al.

Selected by 23 September 2024

Matthew Davies

Cell Biology

Triglyceride metabolism controls inflammation and APOE4-associated disease states in microglia

Roxan A. Stephenson, Kory R. Johnson, Linling Cheng, et al.

Selected by 22 August 2024

Gustavo Stelzer, Marcus Oliveira

Biochemistry

preLists in the biochemistry category:

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

Peer Review in Biomedical Sciences

Communication of scientific knowledge has changed dramatically in recent decades and the public perception of scientific discoveries depends on the peer review process of articles published in scientific journals. Preprints are key vehicles for the dissemination of scientific discoveries, but they are still not properly recognized by the scientific community since peer review is very limited. On the other hand, peer review is very heterogeneous and a fundamental aspect to improve it is to train young scientists on how to think critically and how to evaluate scientific knowledge in a professional way. Thus, this course aims to: i) train students on how to perform peer review of scientific manuscripts in a professional manner; ii) develop students' critical thinking; iii) contribute to the appreciation of preprints as important vehicles for the dissemination of scientific knowledge without restrictions; iv) contribute to the development of students' curricula, as their opinions will be published and indexed on the preLights platform. The evaluations will be based on qualitative analyses of the oral presentations of preprints in the field of biomedical sciences deposited in the bioRxiv server, of the critical reports written by the students, as well as of the participation of the students during the preprints discussions.

 



List by Marcus Oliveira et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

Cellular metabolism

A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.

 



List by Pablo Ranea Robles

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra

Also in the cell biology category:

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

The Society for Developmental Biology 82nd Annual Meeting

This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.

 



List by Joyce Yu, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

BioMalPar XVI: Biology and Pathology of the Malaria Parasite

[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria

 



List by Dey Lab, Samantha Seah

1

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Cellular metabolism

A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.

 



List by Pablo Ranea Robles

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

Biophysical Society Annual Meeting 2019

Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA

 



List by Joseph Jose Thottacherry

ASCB/EMBO Annual Meeting 2018

This list relates to preprints that were discussed at the recent ASCB conference.

 



List by Dey Lab, Amanda Haage

Also in the molecular biology category:

2024 Hypothalamus GRC

This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.

 



List by Nathalie Krauth

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra

Also in the neuroscience category:

2024 Hypothalamus GRC

This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.

 



List by Nathalie Krauth

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Young Embryologist Network Conference 2019

Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London

 



List by Alex Eve
Close