100S formation in the stationary phase of
Escherichia
coli.
Genes
Cells
10
(12):1103–1112. https://doi.org/10.1111/j.
1365-2443.2005.00903.x
7. Agafonov DE, Kolb VA, Nazimov IV, Spirin
AS (1999) A protein residing at the subunit
interface of the bacterial ribosome. Proc Natl
Acad Sci U S A 96(22):12345–12349. https://
doi.org/10.1073/pnas.96.22.12345
8. Polikanov YS, Blaha GM, Steitz TA (2012)
How hibernation factors RMF, HPF, and
YfiA turn off protein synthesis. Science 336
(6083):915–918. https://doi.org/10.1126/
science.1218538
9. Franken LE, Oostergetel GT, Pijning T, Puri P,
Arkhipova V, Boekema EJ, Poolman B, Guskov
A (2017) A general mechanism of ribosome
dimerization revealed by single-particle cryoelectron microscopy. Nat Commun 8(1):722.
https://doi.org/10.1038/s41467-01700718-x
10. Beckert B, Abdelshahid M, Schafer H,
Steinchen W, Arenz S, Berninghausen O,
Beckmann R, Bange G, Turgay K, Wilson DN
(2017) Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S
dimerization. EMBO J 36(14):2061–2072.
https://doi.org/10.15252/embj.201696189
11. Khusainov I, Vicens Q, Ayupov R, Usachev K,
Myasnikov A, Simonetti A, Validov S, Kieffer B,
Yusupova G, Yusupov M, Hashem Y (2017)
Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated
by intermolecular interactions of HPF.
EMBO J 36(14):2073–2087. https://doi.
org/10.15252/embj.201696105
12. Li Y, Sharma MR, Koripella RK, Yang Y,
Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK (2018) Zinc
depletion induces ribosome hibernation in
mycobacteria. Proc Natl Acad Sci U S A 115
(32):8191–8196. https://doi.org/10.1073/
pnas.1804555115
13. Matzov D, Aibara S, Basu A, Zimmerman E,
Bashan A, Yap MF, Amunts A, Yonath AE
(2017) The cryo-EM structure of hibernating
100S ribosome dimer from pathogenic Staphylococcus aureus. Nat Commun 8(1):723.
https://doi.org/10.1038/s41467-01700753-8
14. Flygaard RK, Boegholm N, Yusupov M, Jenner
LB (2018) Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome
reveals a protein-mediated dimerization mechanism. Nat Commun 9(1):4179. https://doi.
org/10.1038/s41467-018-06724-x
15. Yusupova GZ, Yusupov MM, Cate JH, Noller
HF (2001) The path of messenger RNA
through the ribosome. Cell 106(2):233–241.
https://doi.org/10.1016/s0092-8674(01)
00435-4
16. Agrawal RK, Spahn CM, Penczek P, Grassucci
RA, Nierhaus KH, Frank J (2000) Visualization of tRNA movements on the Escherichia
coli 70S ribosome during the elongation cycle.
J Cell Biol 150(3):447–460. https://doi.org/
10.1083/jcb.150.3.447
17. Carter AP, Clemons WM Jr, Brodersen DE,
Morgan-Warren RJ, Hartsch T, Wimberly BT,
Ramakrishnan V (2001) Crystal structure of an
initiation factor bound to the 30S ribosomal
subunit. Science 291(5503):498–501. https://
doi.org/10.1126/science.1057766
18. Hussain T, Lla ´cer JL, Wimberly BT, Kieft JS,
Ramakrishnan V (2016) Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 167(1):133–144.e13.
https://doi.org/10.1016/j.cell.2016.08.074
19. Agrawal RK, Penczek P, Grassucci RA, Frank J
(1998) Visualization of elongation factor G on
the Escherichia coli 70S ribosome: the mechanism of translocation. Proc Natl Acad Sci U S A
95(11):6134–6138.
https://doi.org/10.
1073/pnas.95.11.6134
20. Prisic S, Hwang H, Dow A, Barnaby O, Pan
TS, Lonzanida JA, Chazin WJ, Steen H, Husson RN (2015) Zinc regulates a switch
between primary and alternative S18 ribosomal
proteins in Mycobacterium tuberculosis. Mol
Microbiol 97(2):263–280. https://doi.org/
10.1111/mmi.13022
21. Li Y, Corro J, Palmer C, Ojha AK (2020)
Progression from remodelling to hibernation
of ribosomes in zinc starved mycobacteria.
Proc Natl Acad Sci U S A 117
(32):19528–19537
22. Snapper SB, Melton RE, Mustafa S, Kieser T,
Jacobs WR Jr (1990) Isolation and characterization of efficient plasmid transformation
mutants of Mycobacterium smegmatis. Mol
Microbiol 4(11):1911–1919. https://doi.
org/10.1111/j.1365-2958.1990.tb02040.x
23. Ojha AK, Baughn AD, Sambandan D, Hsu T,
Trivelli X, Guerardel Y, Alahari A, Kremer L,
Jacobs WR Jr, Hatfull GF (2008) Growth of
Mycobacterium tuberculosis biofilms containing free mycolic acids and harbouring drugtolerant bacteria. Mol Microbiol 69
(1):164–174.
https://doi.org/10.1111/j.
1365-2958.2008.06274.x
24. Vilcheze C, Copeland J, Keiser TL,
Weisbrod T, Washington J, Jain P, Malek A,
Purification of Three Types of Ribosomes from Mycobacteria
165
Escherichia
coli.
Genes
Cells
10
(12):1103–1112. https://doi.org/10.1111/j.
1365-2443.2005.00903.x
7. Agafonov DE, Kolb VA, Nazimov IV, Spirin
AS (1999) A protein residing at the subunit
interface of the bacterial ribosome. Proc Natl
Acad Sci U S A 96(22):12345–12349. https://
doi.org/10.1073/pnas.96.22.12345
8. Polikanov YS, Blaha GM, Steitz TA (2012)
How hibernation factors RMF, HPF, and
YfiA turn off protein synthesis. Science 336
(6083):915–918. https://doi.org/10.1126/
science.1218538
9. Franken LE, Oostergetel GT, Pijning T, Puri P,
Arkhipova V, Boekema EJ, Poolman B, Guskov
A (2017) A general mechanism of ribosome
dimerization revealed by single-particle cryoelectron microscopy. Nat Commun 8(1):722.
https://doi.org/10.1038/s41467-01700718-x
10. Beckert B, Abdelshahid M, Schafer H,
Steinchen W, Arenz S, Berninghausen O,
Beckmann R, Bange G, Turgay K, Wilson DN
(2017) Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S
dimerization. EMBO J 36(14):2061–2072.
https://doi.org/10.15252/embj.201696189
11. Khusainov I, Vicens Q, Ayupov R, Usachev K,
Myasnikov A, Simonetti A, Validov S, Kieffer B,
Yusupova G, Yusupov M, Hashem Y (2017)
Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated
by intermolecular interactions of HPF.
EMBO J 36(14):2073–2087. https://doi.
org/10.15252/embj.201696105
12. Li Y, Sharma MR, Koripella RK, Yang Y,
Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK (2018) Zinc
depletion induces ribosome hibernation in
mycobacteria. Proc Natl Acad Sci U S A 115
(32):8191–8196. https://doi.org/10.1073/
pnas.1804555115
13. Matzov D, Aibara S, Basu A, Zimmerman E,
Bashan A, Yap MF, Amunts A, Yonath AE
(2017) The cryo-EM structure of hibernating
100S ribosome dimer from pathogenic Staphylococcus aureus. Nat Commun 8(1):723.
https://doi.org/10.1038/s41467-01700753-8
14. Flygaard RK, Boegholm N, Yusupov M, Jenner
LB (2018) Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome
reveals a protein-mediated dimerization mechanism. Nat Commun 9(1):4179. https://doi.
org/10.1038/s41467-018-06724-x
15. Yusupova GZ, Yusupov MM, Cate JH, Noller
HF (2001) The path of messenger RNA
through the ribosome. Cell 106(2):233–241.
https://doi.org/10.1016/s0092-8674(01)
00435-4
16. Agrawal RK, Spahn CM, Penczek P, Grassucci
RA, Nierhaus KH, Frank J (2000) Visualization of tRNA movements on the Escherichia
coli 70S ribosome during the elongation cycle.
J Cell Biol 150(3):447–460. https://doi.org/
10.1083/jcb.150.3.447
17. Carter AP, Clemons WM Jr, Brodersen DE,
Morgan-Warren RJ, Hartsch T, Wimberly BT,
Ramakrishnan V (2001) Crystal structure of an
initiation factor bound to the 30S ribosomal
subunit. Science 291(5503):498–501. https://
doi.org/10.1126/science.1057766
18. Hussain T, Lla ´cer JL, Wimberly BT, Kieft JS,
Ramakrishnan V (2016) Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 167(1):133–144.e13.
https://doi.org/10.1016/j.cell.2016.08.074
19. Agrawal RK, Penczek P, Grassucci RA, Frank J
(1998) Visualization of elongation factor G on
the Escherichia coli 70S ribosome: the mechanism of translocation. Proc Natl Acad Sci U S A
95(11):6134–6138.
https://doi.org/10.
1073/pnas.95.11.6134
20. Prisic S, Hwang H, Dow A, Barnaby O, Pan
TS, Lonzanida JA, Chazin WJ, Steen H, Husson RN (2015) Zinc regulates a switch
between primary and alternative S18 ribosomal
proteins in Mycobacterium tuberculosis. Mol
Microbiol 97(2):263–280. https://doi.org/
10.1111/mmi.13022
21. Li Y, Corro J, Palmer C, Ojha AK (2020)
Progression from remodelling to hibernation
of ribosomes in zinc starved mycobacteria.
Proc Natl Acad Sci U S A 117
(32):19528–19537
22. Snapper SB, Melton RE, Mustafa S, Kieser T,
Jacobs WR Jr (1990) Isolation and characterization of efficient plasmid transformation
mutants of Mycobacterium smegmatis. Mol
Microbiol 4(11):1911–1919. https://doi.
org/10.1111/j.1365-2958.1990.tb02040.x
23. Ojha AK, Baughn AD, Sambandan D, Hsu T,
Trivelli X, Guerardel Y, Alahari A, Kremer L,
Jacobs WR Jr, Hatfull GF (2008) Growth of
Mycobacterium tuberculosis biofilms containing free mycolic acids and harbouring drugtolerant bacteria. Mol Microbiol 69
(1):164–174.
https://doi.org/10.1111/j.
1365-2958.2008.06274.x
24. Vilcheze C, Copeland J, Keiser TL,
Weisbrod T, Washington J, Jain P, Malek A,
Purification of Three Types of Ribosomes from Mycobacteria
165