Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

AbstractDPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 569 newly reconstructed genomes. Protein family content clearly separates DPANN from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.

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Folding of Bacterial Group I Ribozyme in Crowded Solutions

Biophysical Journal ◽

10.1016/j.bpj.2009.12.2570 ◽

2010 ◽

Vol 98 (3) ◽

pp. 472a

Author(s):

John D. Kilburn ◽

Joon Ho Roh ◽

Liang Guo ◽

Robert M. Briber ◽

Sarah A. Woodson

Keyword(s):

Bacterial Group ◽

Group I

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Identification of A-Minor Tertiary Interactions within a Bacterial Group I Intron Active Site by 3-Deazaadenosine Interference Mapping†

Biochemistry ◽

10.1021/bi020265l ◽

2002 ◽

Vol 41 (33) ◽

pp. 10426-10438 ◽

Cited By ~ 15

Author(s):

Juliane K. Soukup ◽

Noriaki Minakawa ◽

Akira Matsuda ◽

Scott A. Strobel

Keyword(s):

Active Site ◽

Group I Intron ◽

Bacterial Group ◽

Group I ◽

Interference Mapping ◽

Tertiary Interactions ◽

A Minor

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Unfolding Single RNA Molecules with Optical Tweezers

Microscopy and Microanalysis ◽

10.1017/s1431927600026209 ◽

2001 ◽

Vol 7 (S2) ◽

pp. 26-27

Author(s):

Carlos Bustamante ◽

Jan Liphardt ◽

Bibiana Onoa ◽

Steven B. Smith ◽

Delphine Collin ◽

...

Keyword(s):

Secondary Structure ◽

Optical Tweezers ◽

Single Molecule ◽

Structure Prediction ◽

Secondary Structure Prediction ◽

Structural Features ◽

Rna Molecules ◽

Group I ◽

Tertiary Folding ◽

Tertiary Interactions

RNA molecules must fold into specific three-dimensional shapes to perform their structural and catalytic functions. Unlike proteins, RNAs secondary structural features are usually stable enough to form by themselves in solution. The reason is that in RNA, the stabilization energy gained from the formation of secondary structure is substantially larger than the energies involved in tertiary interactions. As a result, the formation of tertiary interactions is expected to alter only slightly the pre-existing secondary structural contacts. Moreover, secondary structure prediction is robust and can be made without taking into consideration tertiary folding. However, bulk studies of the energetics and kinetics of their secondary and tertiary folding are often frustrated by the presence of multiple species and multiple folding pathways in solution. These problems are circumvented in single-molecule studies in which the folding/unfolding trajectories of the individual molecules can be followed. The T. thermophila group I intron ribozyme is organized into several domains whose mechanical unfolding can be investigated independently, and whose tertiary contacts are stabilized by numerous Mg++ ions.We have begun characterization of the ribozyme by analysis of the P5abc domain because:

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Time-Resolved Multiphase Folding of Bacterial Group I Ribozyme

Biophysical Journal ◽

10.1016/j.bpj.2009.12.2569 ◽

2010 ◽

Vol 98 (3) ◽

pp. 472a

Author(s):

Joon Ho Roh ◽

Liang Guo ◽

Duncan Kilburn ◽

Reza Behrouzi ◽

Robert M. Briber ◽

...

Keyword(s):

Bacterial Group ◽

Time Resolved ◽

Group I

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RNA Tertiary Interactions Mediate Native Collapse of a Bacterial Group I Ribozyme

Journal of Molecular Biology ◽

10.1016/j.jmb.2005.09.015 ◽

2005 ◽

Vol 353 (5) ◽

pp. 1199-1209 ◽

Cited By ~ 43

Author(s):

Seema Chauhan ◽

Gokhan Caliskan ◽

Robert M. Briber ◽

Ursula Perez-Salas ◽

Prashanth Rangan ◽

...

Keyword(s):

Bacterial Group ◽

Group I ◽

Tertiary Interactions

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Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea

Frontiers in Microbiology ◽

10.3389/fmicb.2021.660052 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cindy J. Castelle ◽

Raphaël Méheust ◽

Alexander L. Jaffe ◽

Kiley Seitz ◽

Xianzhe Gong ◽

...

Keyword(s):

Cell Walls ◽

Protein Family ◽

Hypothetical Proteins ◽

Bacterial Group ◽

Archaeal Protein ◽

Bacterial Proteins ◽

Lytic Transglycosylase ◽

Group I ◽

Genetic Overlap ◽

Candidate Phyla Radiation

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.

Download Full-text