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Unraveling context specificity of translation by elucidating the mechanism of action of auxiliary translation factors

Award Number: R35GM127134
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 04/01/2018
PERIOD OF PERFORMANCE END DATE: 12/31/2028

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Unraveling context specificity of translation by elucidating the mechanism of action of auxiliary translation factors - The research in the laboratory focuses on understanding the fundamental mechanisms of translation and action of ribosome-targeting antibiotics. One of the underappreciated aspects of translation that has transpired from our studies is its context specific nature. We learned that the ability of the ribosome to decode genetic information rapidly and efficiently is significantly influenced by the nature of its tRNA and mRNA substrates and/or properties of the polypeptide being made. Specific sequences have been identified as difficult to polymerize but, more than likely, there are many other that also present an obstacle for the translating ribosome. Why some sequences are challenging for translation and what mechanisms exist in the cell to help the ribosome overcome such problems are questions that have remained unanswered. Several conserved auxiliary translation factors (auxTFs) encoded in the bacterial genomes are thought to assist the ribosome in synthesizing proteins during fast growth or under stress, likely facilitating translation of the problematic sequence motifs. However, our knowledge of the nature of the sequences whose translation is facilitated by the auxTFs, about the molecular mechanisms of their action and of their physiological significance is limited at best. Answering these vexing questions is the goal of the proposal. We will use crosslinking-based ribosome profiling (XLRibo-seq) to map the genomic sites where auxTFs are recruited to the ribosome. Guided by these genome-wide data, we will select the most revealing gene models to dissect in vitro the precise nature of the problematic sequence motifs and elucidate the molecular mechanisms of the auxTF action. The inferred mechanisms will be validated in vivo and the physiological role of the auxTFs will be deduced by following the expression of specifically designed reporters under suitable growth conditions or using the appropriate mutants. The overall experimental approach will be first optimized using, as a model system, translation termination factors RF1 and RF2, and then applied to four most intriguing auxTFs (LepA, EttA, BirA and HflX) whose specificity, activity and physiological role remain enigmatic despite being investigated previously by other techniques. The approach could be extended to several other known or suspected auxTFs and even to the main translation factors whose activity could be conceivably modulated by the context of the translated sequence. The innovation of the proposal stems from the development of new methodologies (XLRibo-seq) with a broad application to studies of basic mechanisms of translation, and from revealing the functions and molecular mechanisms of action of conserved proteins playing important roles in expression of genetic information. The experiments build upon the long-term interests, previous findings, and expertise of our research group. The project will provide new training and teaching opportunities and facilitate the outreach activities of the lab.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $395,753 )
2026	2026	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	8	12/17/2025	NON-COMPETING CONTINUATION	$395,753
														Subtotal = $395,753

Issue Date FY: 2025 ( Subtotal = $439,725 )
2025	2025	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	003	7	8/6/2025	NON-COMPETING CONTINUATION	$43,972
2025	2025	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	001	7	12/13/2024	NON-COMPETING CONTINUATION	$395,753
2025	2024	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	6	11/5/2024	COMPETING CONTINUATION	$0
2025	2022	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	002	5	1/15/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $439,725

Issue Date FY: 2024 ( Subtotal = $439,725 )
2024	2024	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	001	6	12/15/2023	COMPETING CONTINUATION	$439,725
2024	2022	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	5	12/7/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $439,725

Issue Date FY: 2023 ( Subtotal = $0 )
2023	2022	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD AVE M/C 551	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	5	4/19/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $363,556 )
2022	2022	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	5	3/14/2022	NON-COMPETING CONTINUATION	$327,197
2022	2022	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	001	5	6/28/2022	NON-COMPETING CONTINUATION	$36,359
														Subtotal = $363,556

Issue Date FY: 2021 ( Subtotal = $426,156 )
2021	2021	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	4	3/5/2021	NON-COMPETING CONTINUATION	$363,556
2021	2021	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	001	4	7/19/2021	SUPPLEMENT FOR EXPANSION	$62,600
														Subtotal = $426,156

Issue Date FY: 2020 ( Subtotal = $363,556 )
2020	2020	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	3	3/3/2020	NON-COMPETING CONTINUATION	$363,556
														Subtotal = $363,556

Issue Date FY: 2019 ( Subtotal = $363,556 )
2019	2019	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	2	3/20/2019	NON-COMPETING CONTINUATION	$363,556
														Subtotal = $363,556

Issue Date FY: 2018 ( Subtotal = $363,556 )
2018	2018	UNIVERSITY OF ILLINOIS	809 S MARSHFIELD RM 520	CHICAGO	IL	60612	COOK	USA	Biomedical Research and Research Training	000	1	3/13/2018	NEW	$363,556
														Subtotal = $363,556

Grand Total All Awards = $3,155,583

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Unraveling context specificity of translation by elucidating the mechanism of action of auxiliary translation factors

Award Number: R35GM127134

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 04/01/2018

PERIOD OF PERFORMANCE END DATE: 12/31/2028

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