Thursday, November 21, 2024 11/21/2024

Investigating the Impact and Patterns of Homologous Recombination and Adaptive Evolution on Bacterial Genomes

Award Number: R01GM132137
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Project summary In contract to sexual organisms, the mechanisms of population genetics in bacteria are far less understood. Two fundamental aspects of bacterial population genetics remain sorely understudied: i) the impact of DNA exchange on the evolution of bacterial genomes and populations is largely unknown. ii) the prominence of adaptive evolution has not been comprehensively assessed in bacteria. Determining how recombination and adaptive evolution impact bacteria is key to understand the biology of these organisms and to develop relevant models of their evolution. Although bacteria reproduce clonally, there is increasing evidence that the vast majority of these organisms are capable of homologous recombination by exchanging pieces of DNA in a process similar to gene conversion in animals and plants. This process enhances microbial capacity to adapt to stresses or changing environments and the exchange of DNA between bacterial strains is a major concern for human health as exemplified by the transfer of virulence and antibiotic resistance genes. Despite the central role of this process, the rates and patterns of recombination remain unresolved in bacteria. The extent of recombination often varies greatly from one study to another and, as a result, the same bacterial species can be perceived as clonal in one study and highly recombining in another. In this project, we propose to re-evaluate the landscape of recombination rates and patterns along the genomes of hundreds of bacterial species. Using new methodological frameworks based on Approximate Bayesian Computation and Deep Learning, we will identify the factors shaping the variation in recombination rate across bacteria. We will also uncover recombination rate variation across bacterial chromosomes (i.e. hot spots and cold spots). Our rate estimates will also allow us to study how recombination drives the evolution of genomic architecture of bacteria, including turnover in gene content. Finally, we will quantify the impact of adaptive evolution in bacteria, which may be substantially larger than in other organisms due to large bacterial effective population sizes. We will also investigate the relationship between adaptation and recombination, and identify the genes/pathways responsible for adaptation. In summary, this study will evaluate the rates and patterns of recombination across hundreds of species, determine the factors driving the evolution of the recombination process, reveal the role of adaptive evolution in bacteria, and the interplay between recombination and adaptation.


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: 2024 ( Subtotal = $378,052 )
2024	2024	NORTH CAROLINA STATE UNIVERSITY	2601 WOLF VILLAGE WAY	RALEIGH	NC	27695	WAKE	USA	Biomedical Research and Research Training	006	6	6/25/2024	NON-COMPETING CONTINUATION	$33,332
2024	2024	NORTH CAROLINA STATE UNIVERSITY	2601 WOLF VILLAGE WAY	RALEIGH	NC	27695	WAKE	USA	Biomedical Research and Research Training	002	6	3/27/2024	NON-COMPETING CONTINUATION	$299,986
2024	2023	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN ST	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	004	4	5/6/2024	NON-COMPETING CONTINUATION	-$1
2024	2023	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN ST	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	000	4	2/26/2024	NON-COMPETING CONTINUATION	-$288,584
2024	2023	NORTH CAROLINA STATE UNIVERSITY	2601 WOLF VILLAGE WAY	RALEIGH	NC	27695	WAKE	USA	Biomedical Research and Research Training	005	5	5/6/2024	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$123,371
2024	2023	NORTH CAROLINA STATE UNIVERSITY	2601 WOLF VILLAGE WAY	RALEIGH	NC	27695	WAKE	USA	Biomedical Research and Research Training	001	5	2/27/2024	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$333,318
2024	2022	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN ST	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	003	3	5/6/2024	NON-COMPETING CONTINUATION	-$123,370
														Subtotal = $378,052

Issue Date FY: 2023 ( Subtotal = $288,585 )
2023	2023	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN STREET	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	000	4	3/23/2023	NON-COMPETING CONTINUATION	$288,585
														Subtotal = $288,585

Issue Date FY: 2022 ( Subtotal = $288,585 )
2022	2022	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN STREET	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	000	3	3/8/2022	NON-COMPETING CONTINUATION	$259,724
2022	2022	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN STREET	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	001	3	7/27/2022	NON-COMPETING CONTINUATION	$28,861
														Subtotal = $288,585

Issue Date FY: 2021 ( Subtotal = $289,206 )
2021	2021	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN STREET	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	000	2	2/26/2021	NON-COMPETING CONTINUATION	$289,206
														Subtotal = $289,206

Issue Date FY: 2020 ( Subtotal = $294,378 )
2020	2020	UNIVERSITY OF NORTH CAROLINA AT GREENSBORO	1000 SPRING GARDEN STREET	GREENSBORO	NC	27412	GUILFORD	USA	Biomedical Research and Research Training	000	1	3/30/2020	NEW	$294,378
														Subtotal = $294,378

Grand Total All Awards = $1,538,806

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Investigating the Impact and Patterns of Homologous Recombination and Adaptive Evolution on Bacterial Genomes

Award Number: R01GM132137

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

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