Over the past three decades, research supported by this grant has had a major impact on our understanding of the how Sinorhizobium meliloti invades nodules and establishes the chronic intracellular infection that underlies the symbiosis with its legume host. Our work has also identified common bacterial functions that are important for both symbiotic and pathogenic bacteria to interact with their respective eukaryotic hosts, revealed the missing enzyme in vitamin B12 biosynthesis, and discovered a previously unrecognized, extremely highly conserved RNase. The proposed research addresses critical problems concerning how host antimicrobial peptides modulate S. meliloti's cell cycle and physiology during symbiosis, how the master regulator CtrA acts to control S. meliloti cell cycle progression and terminal differentiation during symbiosis, and how the RNase YbeY exerts its multiple biological roles. Plant-encoded NCR (Nodule Cysteine Rich) antimicrobial peptides play key roles in the striking process in which the bacteria undergo rounds of endoreduplication and terminally differentiate into bacteroids. We will extend our recent work that has offered new molecular insights into how these peptides exert their effects by identifying the biological activities of representative symbiotic NCR and glycine-rich host peptides, investigating the roles of ExoS-ChvI and FeuP-FeuQ signaling pathways in S. meliloti's response to NCR peptides and survival within host plant cells, developing a DNA-based strategy for making nodule NCR and glycine-rich peptides, and continuing to investigate how BacA and other S. meliloti functions provide resistance to the antimicrobial activity of NCR peptides. We have recently gained major insights into how S. meliloti, which has a tripartite genome, controls its cell cycle in the free-living state. A comparison with the well-studied Caulobacter crescentus cell cycle has not only revealed conserved regulatory features common to other ?-proteobacteria, but also many intriguing differences. We will gain insights into how regulation of the S. meliloti cell cycle has been adapted for symbiosis by elucidating the mechanism by which NCR247 alters cell cycle regulation and blocks cell division, defining the direct transcriptional targets of S. meliloti cel cycle regulator CtrA, and analyzing the role of CtrA in regulating physiological processes relevant to symbiosis. Our characterization of a symbiotically defective S. meliloti mutant led us to discover a previously unidentified RNase, YbeY, which is present in almost all bacteria and plays crucial roles in rRNA processing, 70S ribosome quality control, and small RNA regulation. We will follow up on our recent results by assessing the role of YbeY in B. abortus pathogenesis, completing our investigation of the role of YbeY in the maturation of the 3'terminus of 16S rRNA, gaining additional insights into the mechanism of 70S ribosome quality control mediated by YbeY and RNase R, identifying YbeY's cellular RNA targets, and identifying YbeY inhibitors that could be lead compounds for a potential new class of antibiotics.

Public Health Relevance

The proposed research will offer insights into fundamental processes that enable bacteria to establish chronic intracellular infections by controlling the manner in which they replicate and the patterns of genes they express. It will also offer new insights into how host factors can either kill bacteria or cause major physiological changes. Finally the research will offer insights into ribosomal RNA processing and ribosome quality control and could lead to the development of a new class of antibiotics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM031030-33
Application #
8757341
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Sledjeski, Darren D
Project Start
1982-07-01
Project End
2018-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
33
Fiscal Year
2014
Total Cost
$421,203
Indirect Cost
$151,201
Name
Massachusetts Institute of Technology
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02139
Ghosal, Anubrata; Babu, Vignesh M P; Walker, Graham C (2018) Elevated Levels of Era GTPase Improve Growth, 16S rRNA Processing, and 70S Ribosome Assembly of Escherichia coli Lacking Highly Conserved Multifunctional YbeY Endoribonuclease. J Bacteriol 200:
Budnick, James A; Sheehan, Lauren M; Colquhoun, Jennifer M et al. (2018) Endoribonuclease YbeY Is Linked to Proper Cellular Morphology and Virulence in Brucella abortus. J Bacteriol 200:
Arnold, Markus F F; Shabab, Mohammed; Penterman, Jon et al. (2017) Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides. MBio 8:
Ghosal, Anubrata; Köhrer, Caroline; Babu, Vignesh M P et al. (2017) C21orf57 is a human homologue of bacterial YbeY proteins. Biochem Biophys Res Commun 484:612-617
Shabab, Mohammed; Arnold, Markus F F; Penterman, Jon et al. (2016) Disulfide cross-linking influences symbiotic activities of nodule peptide NCR247. Proc Natl Acad Sci U S A 113:10157-62
Vercruysse, Maarten; Köhrer, Caroline; Shen, Yang et al. (2016) Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli. MBio 7:
Pini, Francesco; De Nisco, Nicole J; Ferri, Lorenzo et al. (2015) Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PLoS Genet 11:e1005232
Price, Paul A; Tanner, Houston R; Dillon, Brett A et al. (2015) Rhizobial peptidase HrrP cleaves host-encoded signaling peptides and mediates symbiotic compatibility. Proc Natl Acad Sci U S A 112:15244-9
Pandey, Shree P; Winkler, Jonathan A; Li, Hu et al. (2014) Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15:121
Penterman, Jon; Singh, Pradeep K; Walker, Graham C (2014) Biological cost of pyocin production during the SOS response in Pseudomonas aeruginosa. J Bacteriol 196:3351-9

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