Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages

McCarthy, Charley G. P.; Fitzpatrick, David A.

doi:10.1128/msphere.00195-16

Cited by 23 publications

(18 citation statements)

References 85 publications

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“…BLASTp searches of the 25 type 2 NLPs against the NCBI databases revealed top hits with proteobacterial species. To reconstruct the evolutionary history of these proteins, we used the 25 type 2 NLPs as bait sequences in a BLASTp homology search ( E value cutoff of 10 −20 ) against a local database of 8,805,033 proteins, with broad taxon sampling across prokaryotes and eukaryotes ( 53 ). This search identified 87 homologous proteins, including 25 oomycete proteins (included in our data set), 33 fungal proteins, and 29 bacterial proteins.…”

Section: Resultsmentioning

confidence: 99%

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Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal

McGowan

Fitzpatrick

2017

mSphere

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The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.

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Section: Resultsmentioning

confidence: 99%

“…For the NLP phylogeny, the 25 type 2 NLPs were used as bait sequences in a BLASTp ( 89 ) homology search ( E value cutoff of 10 −20 ) against a local database of 8,805,033 proteins ( 53 ). All homologs were aligned using MUSCLE ( 87 ) and manually edited, giving a final alignment of 460 amino acids.…”

Section: Methodsmentioning

confidence: 99%

Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal

McGowan

Fitzpatrick

2017

mSphere

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“…Several authors suggested that the interdomain gene transfer from bacteria and archaea into eukaryotes is more common than could be expected in the eukaryote and human genomes ( 137 , 138 ). Acquisition of foreign genes via the mitochondrial or plastid or other organelle progenitors is not sufficient to explain this frequency and the weak-link model was proposed suggesting that the genetic transfer into multicellular eukaryotes happens during the unicellular or early developmental stages ( 139 ).…”

Section: Hgt In Eukaryotesmentioning

confidence: 99%

Potential Effects of Horizontal Gene Exchange in the Human Gut

Tenbusch²,

2017

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Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host–microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange. Thus, the gut microbial system genetically is very dynamic and capable of rapid response, at the genetic level, to selection, for example, by antibiotics. There are many other factors to which the microbiota may dynamically respond including lifestyle, therapy, diet, refined food, food additives, consumption of pre- and probiotics, and many others. The impact of the changing selective pressures on gut microbiota, however, is poorly understood. Presumably, the gut microbiome responds to these changes by genetic restructuring of gut populations, driven mainly via horizontal gene exchange. Thus, our main goal is to reveal the role played by horizontal gene exchange in the changing landscape of the gastrointestinal microbiome and potential effect of these changes on human health in general and autoimmune diseases in particular.

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“…We found bactofilins in eukaryotes, although, as far as we could tell, restricted to Stramenopiles and Ascomycete fungi. Although more analysis will be needed, we believe that this is the result of horizontal gene transfer from prokaryotes into these organisms (McCarthy and Fitzpatrick, 2016;Richards et al, 2006). It will be interesting to determine the function of bactofilins in eukaryotes as well as in archaea where they appear to be more widespread.…”

Section: Discussionmentioning

confidence: 99%

Bactofilins form non-polar filaments that bind to membranes directly

Deng

Llamazares

Wagstaff

et al. 2019

Preprint

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Bactofilins are small beta-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions: filaments in Caulobacter crescentus are involved in cell stalk formation whereas Myxococcus xanthus filaments aid chromosome segregation and motility. The precise molecular architecture of bactofilin filaments has remained unclear. Here we revealed by sequence analyses and electron microscopy that in addition to wide distribution across bacteria and archaea, bactofilins are also present in a few eukaryotic cells such as oomycetes. The sole bactofilin from Thermus thermophilus was demonstrated to form constitutive filaments and cryo-EM analysis revealed that protofilaments formed through end-to-end association of the beta-helical domains. Using a nanobody against Thermus bactofilin we determined the nearatomic filament structure, showing that the filaments are non-polar, with subunits arranged head-to-head and tail-to-tail. A polymerisation-impaired mutant F105R, that disrupts one of the two protofilament interfaces, enabled crystallisation. The crystal structure also revealed non-polar protofilaments, and the dominance of the beta-stacking interface that formed despite the inhibiting mutation. To confirm the generality of the lack of polarity, we performed coevolutionary analysis of a large set of sequences. Finally, using Thermus bactofilin, we determined that the N-terminal disordered tail of the protein is responsible for direct binding to lipid membranes both on liposomes and by electron cryotomography in E. coli cells. The tail is conserved, suggesting that membrane binding is likely a general feature of these very common but only recently discovered filaments of the prokaryotic cytoskeleton.Bactofilin filament structure Deng 2019

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Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages

Cited by 23 publications

References 85 publications

Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal

Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal

Potential Effects of Horizontal Gene Exchange in the Human Gut

Bactofilins form non-polar filaments that bind to membranes directly

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