10,024 research outputs found
Molecular Simulations of the Ribosome and Associated Translation Factors
The ribosome is a macromolecular complex which is responsible for protein
synthesis in all living cells according to their transcribed genetic
information. Using X-ray crystallography and, more recently, cryo-electron
microscopy (cryo-EM), the structure of the ribosome was resolved at atomic
resolution in many functional and conformational states. Molecular dynamics
simulations have added information on dynamics and energetics to the available
structural information, thereby have bridged the gap to the kinetics obtained
from single-molecule and bulk experiments. Here, we review recent computational
studies that brought notable insights into ribosomal structure and function.Comment: 11 pages, 3 figures, to be published in Current Opinion in Structural
Biolog
Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups
With the astonishing rate that the genomic and metagenomic sequence data sets
are accumulating, there are many reasons to constrain the data analyses. One
approach to such constrained analyses is to focus on select subsets of gene
families that are particularly well suited for the tasks at hand. Such gene
families have generally been referred to as marker genes. We are particularly
interested in identifying and using such marker genes for phylogenetic and
phylogeny-driven ecological studies of microbes and their communities. We
therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology)
markers. The dual use of these PhyEco markers means that we needed to develop
and apply a set of somewhat novel criteria for identification of the best
candidates for such markers. The criteria we focused on included universality
across the taxa of interest, ability to be used to produce robust phylogenetic
trees that reflect as much as possible the evolution of the species from which
the genes come, and low variation in copy number across taxa. We describe here
an automated protocol for identifying potential PhyEco markers from a set of
complete genome sequences. The protocol combines rapid searching, clustering
and phylogenetic tree building algorithms to generate protein families that
meet the criteria listed above. We report here the identification of PhyEco
markers for different taxonomic levels including 40 for all bacteria and
archaea, 114 for all bacteria, and much more for some of the individual phyla
of bacteria. This new list of PhyEco markers should allow much more detailed
automated phylogenetic and phylogenetic ecology analyses of these groups than
possible previously.Comment: 24 pages, 3 figure
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation
Determining the mechanism by which transfer RNAs (tRNAs) rapidly and
precisely transit through the ribosomal A, P and E sites during translation
remains a major goal in the study of protein synthesis. Here, we report the
real-time dynamics of the L1 stalk, a structural element of the large ribosomal
subunit that is implicated in directing tRNA movements during translation.
Within pre-translocation ribosomal complexes, the L1 stalk exists in a dynamic
equilibrium between open and closed conformations. Binding of elongation factor
G (EF-G) shifts this equilibrium towards the closed conformation through one of
at least two distinct kinetic mechanisms, where the identity of the P-site tRNA
dictates the kinetic route that is taken. Within post-translocation complexes,
L1 stalk dynamics are dependent on the presence and identity of the E-site
tRNA. Collectively, our data demonstrate that EF-G and the L1 stalk
allosterically collaborate to direct tRNA translocation from the P to the E
sites, and suggest a model for the release of E-site tRNA
Trends of the major porin gene (ompF) evolution
OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species
Fundamental Principles in Bacterial Physiology - History, Recent progress, and the Future with Focus on Cell Size Control: A Review
Bacterial physiology is a branch of biology that aims to understand
overarching principles of cellular reproduction. Many important issues in
bacterial physiology are inherently quantitative, and major contributors to the
field have often brought together tools and ways of thinking from multiple
disciplines. This article presents a comprehensive overview of major ideas and
approaches developed since the early 20th century for anyone who is interested
in the fundamental problems in bacterial physiology. This article is divided
into two parts. In the first part (Sections 1 to 3), we review the first
`golden era' of bacterial physiology from the 1940s to early 1970s and provide
a complete list of major references from that period. In the second part
(Sections 4 to 7), we explain how the pioneering work from the first golden era
has influenced various rediscoveries of general quantitative principles and
significant further development in modern bacterial physiology. Specifically,
Section 4 presents the history and current progress of the `adder' principle of
cell size homeostasis. Section 5 discusses the implications of coarse-graining
the cellular protein composition, and how the coarse-grained proteome `sectors'
re-balance under different growth conditions. Section 6 focuses on
physiological invariants, and explains how they are the key to understanding
the coordination between growth and the cell cycle underlying cell size control
in steady-state growth. Section 7 overviews how the temporal organization of
all the internal processes enables balanced growth. In the final Section 8, we
conclude by discussing the remaining challenges for the future in the field.Comment: Published in Reports on Progress in Physics.
(https://doi.org/10.1088/1361-6633/aaa628) 96 pages, 48 figures, 7 boxes, 715
reference
A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome
This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions
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Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.
Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Ã… as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible
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