Simplification of Ribosomes in Bacteria with Tiny Genomes.

Molecular Biology and Evolution
Daria D NikolaevaSofya K Garushyants

Abstract

The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.

References

Jan 1, 1972·Annual Review of Biochemistry·C G Kurland
Sep 1, 1981·European Journal of Biochemistry·J Van Duin, R Wijnands
Apr 9, 1981·Nature·S AndersonI G Young
Jan 1, 1997·Annual Review of Biochemistry·R Green, H F Noller
Jan 6, 1999·Proceedings of the National Academy of Sciences of the United States of America·P KhaitovichH F Noller
Oct 3, 2000·Nature·B T WimberlyV Ramakrishnan
Mar 23, 2002·Cell·V Ramakrishnan
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 12, 2005·Nature Structural & Molecular Biology·Laurent ChavatteDonna M Driscoll
Nov 8, 2005·Science·Barbara S SchuwirthJamie H Doudna Cate
Jan 3, 2007·Journal of Molecular Biology·Alexey P KorepanovMikhail G Bubunenko
Sep 7, 2007·Microbiology and Molecular Biology Reviews : MMBR·Magdalena Kaczanowska, Monica Rydén-Aulin
Apr 24, 2008·Biology Direct·Temple F SmithHyman Hartman
Sep 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Elijah RobertsZaida Luthey-Schulten
Jul 25, 2009·Molecular Biology and Evolution·Chiaolong HsiaoLoren Dean Williams
Feb 6, 2010·Biochimica Et Biophysica Acta·Anja HoffmannGünter Kramer
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jack A DunkleJamie H D Cate
Feb 22, 2011·Bioinformatics·Diego DarribaDavid Posada
Mar 16, 2011·Proceedings of the National Academy of Sciences of the United States of America·Justin J LemkeRichard L Gourse
Apr 8, 2011·Nucleic Acids Research·Ivica Letunic, Peer Bork
Sep 29, 2011·Journal of Molecular Biology·Shinichiro ShojiPeter G Schultz
Nov 9, 2011·Nature Reviews. Microbiology·John P McCutcheon, Nancy A Moran
Mar 27, 2012·Molecular Biology and Evolution·Kyungtaek LimIchizo Kobayashi
May 5, 2012·Bioinformatics·Elmar PruesseFrank Oliver Glöckner
May 23, 2012·PloS One·Natalya YutinYuri I Wolf
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui QuIgnacio Tinoco
Feb 19, 2013·Current Opinion in Microbiology·Konstantin ByrgazovIsabella Moll
Apr 20, 2013·Nucleic Acids Research·Jaina MistryMarco Punta
Feb 15, 2014·Current Opinion in Structural Biology·Nenad BanMarat Yusupov
Dec 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Anton S PetrovLoren Dean Williams
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Oct 16, 2016·Nucleic Acids Research·I-Min A ChenNikos C Kyrpides
Oct 14, 2017·ELife·Gabriel DemoAndrei A Korostelev

❮ Previous
Next ❯

Citations

Sep 23, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Frédéric PoitevinKhanh Dao Duc
Nov 10, 2020·Nucleic Acids Research·Michael Y GalperinEugene V Koonin
Mar 24, 2021·Journal of Bacteriology·Michael Y GalperinEugene V Koonin
Nov 11, 2021·Microbiology and Molecular Biology Reviews : MMBR·Madhan R TirumalaiGeorge E Fox

❮ Previous
Next ❯

Methods Mentioned

BETA
protein folding

Software Mentioned

iTOL
PyMOL
PhyML
SINA Alignment Service
HMMer
package phytools
ggplot2
R
exactRankTests
Muscle

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
Daria D NikolaevaMikhail S Gelfand
Biotechnology Progress
R J Leipold, P Dhurjati
Nucleic Acids Research
Gustavo Caetano-Anollés
© 2021 Meta ULC. All rights reserved