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Methods in
Molecular Biology 2062
John LaCava
Štěpánka Vaňáčová
Editors
The Eukaryotic
RNA Exosome
Methods and Protocols
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, UK
Edited by
John LaCava
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen,
The Netherlands
Štěpánka Vaňáčová
Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
Editors
John LaCava Štěpánka Vaňáčová
Laboratory of Cellular Central European Institute
and Structural Biology of Technology (CEITEC)
The Rockefeller University Masaryk University
New York, NY, USA Brno, Czech Republic
European Research Institute
for the Biology of Ageing
University Medical Center Groningen
Groningen, The Netherlands
This Humana imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer
Nature.
The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A.
Preface
The RNA exosome complex was first described by Philip Mitchell, together with David
Tollervey and colleagues, in 1997 (Cell, Vol. 91, 457–466). In this seminal work, the exosome
was described as “a conserved eukaryotic RNA processing complex containing multiple 30 !50
exoribonucleases.” Since then, the field of exosome research has expanded steadily. The
proliferation of the field was fueled by the ever-growing list of roles played by the exosome
in (1) the precise processing of RNA precursors to mature forms and (2) the turnover of RNAs
in response to quality control surveillance and homeostatic RNA decay. The exosome was
found to be associated with a dizzying array of substrates and instance-specific modes of
enzymatic activity. The mechanisms regulating its biochemistry were thus swiftly brought to
the fore, inducing the search for adapter proteins and complexes that could impart functional
selectivity to the exosome. This, alongside abundant episodes of mystery and intrigue sur-
rounding the potential for exo- and endoribonucleolytic, as well as hydro- and phosphorolytic
exosome activities. Through the functions it serves, the exosome’s ubiquity extends to all the
domains of life. In bacteria and archaea, cognate proteins and complexes have been shown to
exhibit exosome-like activities, e.g., polynucleotide phosphorylase/the degradosome in bac-
teria and in archaea, a more orthologous complex, also called the exosome. Soon, it seemed
that the exosome was everywhere in RNA biology—and the situation remains much the same
today, 20 years on, with no sign that exosome research is yet petering out. Indeed, quite the
contrary, the exosome is understood to be a valuable biomedical target.
Thus, The Eukaryotic RNA Exosome: Methods and Protocols is intended to provide a
thorough basis in contemporary exosome research for the newcomer, this both in terms of
the techniques used and the general direction of the field. For those grizzled veterans of
exosome research who may have stuck mostly to their favorite model organism, we have
tried to provide a cross-section of protocols representing the diversity of model organisms
used for exosome research, hopefully empowering broader and more frequent cross-
organism comparisons within the same research team. This book begins with an introduc-
tion to RNA exosome biomedical relevance (Chapter 1) and then steps back to examine the
origins of exosome activity in bacteria (Chapters 2–3) and archaea (Chapter 4). From there,
methods of studying exosome RNA substrates are covered (Chapters 5–10), followed by the
study of exosome adapter complexes and the broader interaction networks that impart
selectivity to pathways the exosome participates in (Chapters 11–16). Finally, structural
and mechanistic biochemical studies are covered, with emphasis on methods that use
recombinant expression and exogenous reconstitution (Chapters 17–24).
Štěpánka and I would like to thank all the contributing authors for their enthusiasm,
professionalism, and scholarship. As our first experience editing a book of this nature, with
its associate learning curve and time commitment, we were lucky to have this group of
contributors to work with. Indeed, there was also a special “something” for us in being able
to edit this book together as a team. Additional thanks to Ms. Hua Jiang for proofreading
the chapters and to Dr. John Walker for the guidance on how to execute our tasks effectively
and the patience along the way to completion.
v
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
vii
viii Contents
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515
Contributors
xi
xii Contributors
Abstract
The evolutionarily conserved RNA exosome is a multisubunit ribonuclease complex that processes and/or
degrades numerous RNAs. Recently, mutations in genes encoding both structural and catalytic subunits of
the RNA exosome have been linked to human disease. Mutations in the structural exosome gene EXOSC2
cause a distinct syndrome that includes retinitis pigmentosa, hearing loss, and mild intellectual disability. In
contrast, mutations in the structural exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypo-
plasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are related autosomal recessive, neuro-
degenerative diseases. In addition, mutations in the structural exosome gene EXOSC9 cause a PCH-like
disease with cerebellar atrophy and spinal motor neuronopathy. Finally, mutations in the catalytic exosome
gene DIS3 have been linked to multiple myeloma, a neoplasm of plasma B cells. How mutations in these
RNA exosome genes lead to distinct, tissue-specific diseases is not currently well understood. In this
chapter, we examine the role of the RNA exosome complex in human disease and discuss the mechanisms
by which mutations in different exosome subunit genes could impair RNA exosome function and give rise
to diverse diseases.
Key words Pontocerebellar hypoplasia, Retinitis pigmentosa, Spinal motor neuronopathy, Multiple
myeloma, RNA exosome, EXOSC2, EXOSC3, EXOSC8, EXOSC9, DIS3, Rrp4, Rrp40, Rrp43,
Rrp45, Rrp44
1 Introduction
John LaCava and Štěpánka Vaňáčová (eds.), The Eukaryotic RNA Exosome: Methods and Protocols, Methods in Molecular Biology,
vol. 2062, https://doi.org/10.1007/978-1-4939-9822-7_1, © Springer Science+Business Media, LLC, part of Springer Nature 2020
3
4 Milo B. Fasken et al.
A
Current Structure of
Human RNA Exosome
(11 Subunits) with Top View Side View Reverse Side View
MTREX & MPH6
Exosome Cofactors DNA/ MTREX
RNA (MTR4)
EXOSC1
1 MTREX EXOSC3
MPH6
MPH6 (MTR4) (MPP6) EXOSC10
(MPP6) EXOSC2
3 2 EXOSC6
10 6 EXOSC7
8 EXOSC4
5 7
9 4 EXOSC5
EXOSC9
DIS3 RNA
EXOSC8
DIS3
B 180°
Current Structure of 90°
Yeast RNA Exosome
(11 Subunits) with
Mtr4, Mpp6, & Rrp47
Exosome Cofactors Mtr4
RNA
Rrp47
Csl4
Mtr4 6 Csl4 Rrp6
Mpp6 Rrp40 Rrp4
47 Mpp6
40 4
Mtr3
43 Mtr3 Rrp42
Rrp41
46 42
45 41 Rrp46
Rrp45 Rrp43
Dis3/44
Dis3/Rrp44
Fig. 1 Structure of the RNA exosome, a multisubunit ribonuclease complex that processes/degrades multiple
classes of RNA. (a) To the left, a cartoon representation of one of the current structures of the 11-subunit
human RNA exosome in association with two exosome cofactors (MTREX (MTR4); MPH6 (MPP6)) is depicted
[7]. The 10-subunit core exosome is composed of a three-subunit cap (EXOSC1/2/3) at the top, a six-subunit
ring (EXOSC4-9) in the middle, and ribonuclease subunit, DIS3, at the bottom. Part of eleventh riboexonu-
clease subunit, EXOSC10, which could be resolved in the structure, associates with the EXOSC6 ring subunit.
The MTREX (MTR4) helicase cofactor associates with the EXOSC2 cap subunit and the MPH6 (MPP6) cofactor,
whereas the MPH6 (MPP6) cofactor associates with the EXOSC3 and EXOSC1 cap subunits. To the right of the
cartoon, surface representations of this 11-subunit human RNA exosome structure in complex with MTREX
(MTR4) and MPH6 (MPP6) cofactors (PDB# 6D6Q) [7] are shown, depicted in top, side, and reverse side views.
The structure of the 10-subunit human core exosome reveals a ring-like architecture composed of three cap
subunits—EXOSC1/Csl4 (gray), EXOSC2/Rrp4 (teal), and EXOSC3/Rrp40 (slate blue), six PH-like ring sub-
units—EXOSC4/Rrp41 (orange), EXOSC5/Rrp46 (yellow), EXOSC6/Mtr3 (marine blue), EXOSC7/Rrp42 (salmon
red), EXOSC8/Rrp43 (magenta), and EXOSC9/Rrp45 (firebrick red), and a catalytic base subunit, DIS3 (brown).
Part of the eleventh catalytic subunit, EXOSC10/Rrp6 (forest green), associates with EXOSC6/Mtr3. At the top
of the complex, the cofactor, MTREX (MTR4) (deep olive green), associates with EXOSC2/Rrp4 and MPH6
(MPP6), whereas the cofactor, MPH6 (MPP6) (hot pink) associates with EXOSC3/Rrp40. The DNA/RNA chimera
(black) used to stall the MTREX (MTR4) helicase during unwinding is also shown in the structure. The EXOSC2/
The RNA Exosome and Human Disease 5
Fig. 1 (continued) Rrp4 (teal) and EXOSC3/Rrp40 (slate blue) cap subunits altered in novel syndrome and
pontocerebellar hypoplasia 1b (PCH1b), respectively [8, 9], EXOSC8/Rrp43 (magenta) ring subunit altered in
PCH1c [10], EXOSC9/Rrp45 (firebrick red) ring subunit altered in PCH-like disease [11], and DIS3 (brown)
catalytic subunit altered in multiple myeloma [12] are highlighted (b) To the left, a cartoon representation of
one of the current structures of the 11-subunit S. cerevisiae RNA exosome in association with three exosome
cofactors (Mtr4; Mpp6; Rrp47) is depicted [13]. The 11-subunit exosome is composed of a three subunit cap
(Csl4/Rrp4/Rrp40) at the top, a six-subunit ring (Rrp41/Rrp42/Rrp43/Rrp45/Rrp46/Mtr3), and two catalytic
subunits (Dis3/Rrp44 and Rrp6) [14]. The Mtr4 helicase cofactor associates with the Rrp4 cap subunit and the
Mpp6 cofactor, the Mpp6 cofactor associates with the Rrp40 and Csl4 cap subunits, and the Rrp47 cofactor
associates with Rrp6. To the right of the cartoon, surface representations of this 11-subunit yeast RNA
exosome structure in complex with Mtr4, Mpp6, and Rrp47 cofactors (PDB# 6FSZ) [13] are shown, depicted in
top, side, and reverse side views. The 11-subunit yeast RNA exosome structure shows a ring-like shape with
three cap subunits—Csl4 (gray), Rrp4 (teal), and Rrp40 (slate blue), six PH-like ring subunits—Rrp41 (orange),
Rrp46 (yellow), Mtr3 (marine blue), Rrp42 (salmon red), Rrp43 (magenta), and Rrp45 (firebrick red), and two
catalytic subunits, Dis3/Rrp44 (brown) and Rrp6 (forest green). The cofactor, Mtr4 (deep olive green),
associates with Rrp4 and Mpp6, the cofactor, Mpp6 (hot pink), associates with Rrp40, and the cofactor,
Rrp47 (pink), associates with Rrp6. The RNA (black) is also shown in the structure. The DIS3/Dis3/Rrp44
ribonuclease subunit contains both a riboexonuclease (large oval) and riboendonuclease (small oval) catalytic
site. The RNA exosome structures illustrate how the catalytic subunits, DIS3/Dis3/Rrp44 and EXOSC10/Rrp6,
and the exosome cofactors, MTREX/Mtr4, MPH6/Mpp6, and Rrp47, interface with the ring-like core of the RNA
exosome. The ring-like RNA exosome structures forms a central channel through which RNA is directed to the
catalytic subunit, DIS3/Dis3/Rrp44, for processing/degradation. In the yeast RNA exosome, RNA can also gain
access to Dis3/Rrp44 in a channel-independent or direct access manner [15–17]. The color scheme of the
human and yeast RNA exosome subunits is identical. Comparison of the human and yeast RNA exosome
structures reveals that the RNA exosome structure is highly evolutionarily conserved in eukaryotes
(Figure adapted from Morton et al. [18])
6 Milo B. Fasken et al.
G30V G198D
Hs EXOSC2 N S1 KH
1 74 80 159 168 293
G30 G198 GxNG
Hs EXOSC2 27 VVPGDTI 195 VILGNNGFIWIYP
Mm EXOSC2 26 LVVGDTI 195 VILGNNGFIWIYP
Dm Rrp4 30 YTPGEVL 198 VILGNNGYIWISP
Sc Rrp4 55 VTPGELV 223 VVLGVNGYIWLRK
V80F Y109N G135E A139P G191C
G31A D132A W238R
Hs EXOSC3 N S1 KH
1 107 113 181 196 275
G31 D132 GxNGW238
Hs EXOSC3 28 VLPGEEL 129 FKVDVGG 229 IVFGMNGRIWVKA
Mm EXOSC3 28 VLPGEEL 128 FKVDVGG 228 IVFGMNGRIWVKA
Dm Rrp40 8 VMPGERI 84 YRVDIGA 183 IAVGVNGRIWLKA
Sc Rrp40 5 IFPGDSF 84 YKVSLQN 186 VAIGLNGKIWVKC
A2V S272T
Hs EXOSC8 PH
1 276
A2 S272
Hs EXOSC8 1 MAAGFKT 272 IKSMKPK
Mm EXOSC8 1 MAAGFKT 272 IQSMRHK
Sc Rrp43 1 MAESTLL` 387 DLSTRFNI
L14P
Hs EXOSC9 PH
1 439
L14
Hs EXOSC9 11 RRFLLRA
Mm EXOSC9 11 RRFLLRA
Dm Rrp45 17 RSFVQLA
Sc Rrp45 12 SKFILEA
Fig. 2 Amino acid substitutions identified in the EXOSC2, EXOSC3, EXOSC8, and EXOSC9 subunits of the RNA
exosome in individuals with a novel syndrome, pontocerebellar hypoplasia (PCH), and PCH-like disease.
Domain structures of human EXOSC2, EXOSC3, EXOSC8, EXOSC9 proteins highlighting the amino acid
changes identified in affected individuals [8–11, 73, 74, 79, 80]. Amino acid changes in the EXOSC2 and
EXOSC3 cap subunits (shown in red), linked to a novel syndrome and pontocerebellar hypoplasia type 1b
(PCH1b), respectively, are located in the N-terminal domain (green), the central putative RNA-binding S1
domain (blue), or the C-terminal putative RNA-binding K homology (KH) domain (yellow). Amino acid changes
in the EXOSC8 and EXOSC9 ring subunits (shown in red), linked to pontocerebellar hypoplasia type 1c (PCH1c)
and PCH-like disease (cerebellar atrophy with spinal motor neuronopathy), respectively, are located in the
PH-like domain (orange). Below the domain structures, alignments of EXOSC2/3/8/9 ortholog sequences from
human (Hs), mouse (Mm), Drosophila melanogaster (Dm), and S. cerevisiae (Sc) that surround the evolution-
arily conserved residues altered in disease (highlighted in red, labeled in black above) are shown. The GxNG
motif (boxed in green) present in the EXOSC2/Rrp4 and EXOSC3/Rrp40 KH domains may play a structural role,
as the GXNG motif in ScRrp40 is buried at the interface between the S1 and KH domains [81]. Amino acid
positions are shown below the domain structures (Figure adapted from Morton et al. [18])
3 EXOSC2 Mutations
Anna Margarethe harjasi kynsiä, niin että nahka oli vähällä lähteä
sormenpäistä.
— Antakaa tänne.
Punaisia ne olivatkin.
— No.
— Voihan kieli tosin olla kaunista, sanoi Thilda täti; mutta sisällys,
ystäväiseni, aina vain sitä alituista rakkautta.
— Ja senhän asteen, Jumalan kiitos, pian sivuuttaa. Sitäpaitsi on
elämässä rakkautta kylliksi.
*****
Lady vastasi.
Lady nauroi.
— Niin, viimeisen.
Ja äärettömän hellästi, melkein kuulumattomasti, lausui hän
uudelleen vieraat sanat. Kädet olivat yhä ristissä polvilla:
Oli äänetöntä.
*****
Pitkään aikaan ei kukaan puhunut. Sitten sanoi äiti, joka näytti niin
pitkältä pimeässä:
*****
*****
‒ Niin,
— Olen, rouva.
— Ei, Tine, minä olen sanonut sen Teille ennen: on vain yksi onni
ja se lienee onnellisin, joka ei sitä milloinkaan ole tuntenut.
Laulu lakkasi.
Äiti nousi.
Updated editions will replace the previous one—the old editions will
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