TY - JOUR
T1 - Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment
AU - Chewapreecha, Claire
AU - Pensar, Johan
AU - Chattagul, Supaksorn
AU - Pesonen, Maiju
AU - Sangphukieo, Apiwat
AU - Boonklang, Phumrapee
AU - Potisap, Chotima
AU - Koosakulnirand, Sirikamon
AU - Feil, Edward J.
AU - Dunachie, Susanna
AU - Chantratita, Narisara
AU - Limmathurotsakul, Direk
AU - Peacock, Sharon J.
AU - Day, Nick P.J.
AU - Parkhill, Julian
AU - Thomson, Nicholas R.
AU - Sermswan, Rasana W.
AU - Corander, Jukka
N1 - Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2022/1/1
Y1 - 2022/1/1
N2 - The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of "co-selection"- that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.
AB - The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of "co-selection"- that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.
KW - Burkholderia pseudomallei
KW - co-selection study
KW - nutrient depletion
UR - http://www.scopus.com/inward/record.url?scp=85123812922&partnerID=8YFLogxK
U2 - 10.1093/molbev/msab306
DO - 10.1093/molbev/msab306
M3 - Article
C2 - 34662416
AN - SCOPUS:85123812922
SN - 0737-4038
VL - 39
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 1
M1 - msab306
ER -