Gene transferability and sociality do not correlate with gene connectivity

Hao, Chunhui; Dewar, Anna E; West, Stuart A.; Ghoul, Melanie

doi:10.1098/rspb.2022.1819

Cited by 5 publications

(9 citation statements)

References 93 publications

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“…For instance, we can use simple BLAST searches to identify extracellular proteins based on similarity to proteins known from lab assays to be secreted, or more sophisticated tools like PSORTb, which also looks at the presence of known sequence motifs (28). This method is the most established for finding cooperative genes, having been used in a number of studies (20)(21)(22)(23)(24)(25)49). One recent study of 51 diverse bacterial species found that on average ~2% of genes code for extracellular proteins (25).…”

Section: Extracellular Proteinsmentioning

confidence: 99%

“…An alternative approach is to use bioinformatic tools to identify genes for cooperative behaviours (28)(29)(30)(31)(32)(33). Comparisons can then be made across species in order to examine how the number or proportion of cooperative genes varies, and if this can be explained by evolutionary theory (20)(21)(22)(23)(24)(25). For example, do species where interacting individuals are more likely to be clonally related have more cooperative genes (20)?…”

Section: Introductionmentioning

confidence: 99%

“…These genes are likely to be cooperative because the proteins can diffuse away from the cell. Any effect of the protein, such as breaking down food or neutralising antibiotics, can therefore provide benefits to the whole group of cells (21)(22)(23)(24)(25). Another tool is PANNZER, which predicts the function of any gene based on sequence similarity to known proteins (a process known as 'functional annotation') (29).…”

Section: Introductionmentioning

confidence: 99%

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SOCfinder: a genomic tool for identifying cooperative genes in bacteria

Belcher,

Dewar,

Hao

et al. 2023

Preprint

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Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial cooperation, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify cooperative traits and their underlying genes across diverse species. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. Here, we introduce SOCfinder as a new tool to find cooperative genes in bacterial genomes. SOCfinder combines information from several methods, considering if a gene is likely to (1) code for an extracellular protein, (2) have a cooperative functional annotation, or (3) be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (P. aeruginosa & B. subtilis) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder.

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Section: Extracellular Proteinsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

SOCfinder: a genomic tool for identifying cooperative genes in bacteria

Belcher,

Dewar,

Hao

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…An alternative approach is to use bioinformatic tools to identify genes for cooperative behaviours [20][21][22][23][24][25]. Comparisons can then be made across species in order to examine how the number or proportion of cooperative genes varies, and if this can be explained by evolutionary theory [26][27][28][29][30][31]. For example, do species where interacting individuals are more likely to be clonally related have more cooperative genes [26]?…”

Section: Introductionmentioning

confidence: 99%

“…These genes are likely to be for cooperative traits because the proteins can diffuse away from the cell. Any effect of the protein, such as breaking down food or neutralising antibiotics, can therefore provide benefits to the whole group of cells [27][28][29][30][31]. Another tool is PANNZER, which predicts the function of any gene based on sequence similarity to known proteins (a process known as 'functional annotation') [21].…”

Section: Introductionmentioning

confidence: 99%

SOCfinder: a genomic tool for identifying social genes in bacteria

Belcher,

Dewar,

Hao

et al. 2023

Microbial Genomics

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Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify genes that control cooperative or otherwise social traits. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. We introduce SOCfinder as a new tool to find bacterial genes that control cooperative or otherwise social traits. SOCfinder combines information from several methods, considering if a gene is likely to [] code for an extracellular protein [], have a cooperative functional annotation, or [] be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species ( P. aeruginosa and B. subtilis ) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder.

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Gene transferability and sociality do not correlate with gene connectivity

et al. 2022

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The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.

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Gene transferability and sociality do not correlate with gene connectivity

Cited by 5 publications

References 93 publications

SOCfinder: a genomic tool for identifying cooperative genes in bacteria

SOCfinder: a genomic tool for identifying cooperative genes in bacteria

SOCfinder: a genomic tool for identifying social genes in bacteria

Gene transferability and sociality do not correlate with gene connectivity

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