Habitat variability does not generally promote metabolic network modularity in flies and mammals

Takemoto, Kazuhiro

doi:10.1016/j.biosystems.2015.12.004

Cited by 3 publications

(3 citation statements)

References 75 publications

(48 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, this may not be a general case. The metabolic networks in diverse fly or mammal species do not follow the same pattern [ 77 ]. Moreover, this scenario demands specifically ‘modular’ fluctuations, since fluctuations between random phenotypic optima do not promote modularity [ 38 ].…”

Section: Discussionmentioning

confidence: 99%

On the role of sparseness in the evolution of modularity in gene regulatory networks

Espinosa‐Soto

2018

PLoS Comput Biol

View full text Add to dashboard Cite

Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases.

show abstract

Section: Discussionmentioning

confidence: 99%

On the role of sparseness in the evolution of modularity in gene regulatory networks

Espinosa‐Soto

2018

PLoS Comput Biol

View full text Add to dashboard Cite

show abstract

“…To remove any phylogenetic effects from the association between biological variables, phylogenetically independent contrasts (PICs) of the variables were computed from phylogenetic trees using the pic function in the R-package ape (v. 3.5). According to previous studies [8,16,29] (and also for comparison with the previous study [8]), the mammalian phylogenetic tree (electronic supplementary material, figure S1) used in the analyses was constructed using the matrix extracellular phosphoglycoprotein precursor gene, downloaded from the KEGG database on 29 August 2016. We performed the parameter selection using the LASSO method using the cv.glmnet and glmnet functions in the R-package glmnet (v. 2.0.5).…”

Section: Discussionmentioning

confidence: 99%

Exosomes in mammals with greater habitat variability contain more proteins and RNAs

Takemoto

Miku

2017

R. Soc. open sci.

Self Cite

View full text Add to dashboard Cite

Factors determining habitat variability are poorly understood despite possible explanations based on genome and physiology. This is because previous studies only focused on primary measures such as genome size and body size. In this study, we hypothesize that specific gene functions determine habitat variability in order to explore new factors beyond primary measures. We comprehensively evaluate the relationship between gene functions and the climate envelope while statistically controlling for potentially confounding effects by using data on the habitat range, genome, body size and metabolism of various mammals. Our analyses show that the number of proteins and RNAs contained in exosomes is predominantly associated with the climate envelope. This finding indicates the importance of exosomes to habitat range expansion of mammals and provides a new hypothesis for the relationship between the genome and habitat variability.

show abstract

“…Phylogenetically independent contrasts (PICs) [ 35 ] of the variables were evaluated in order to remove any possible phylogenetic effect on the association between biological variables in the context of the phylogenetic comparative analysis [ 36 , 37 ]. This method is similar to that used in our previous study [ 38 ]. In particular, the mammalian phylogenetic tree was constructed using the matrix extracellular phosphoglycoprotein precursor (MEPE) gene (electronic supplementary material, figure S1), downloaded from the KEGG database on 20 August 2015.…”

Section: Methodsmentioning

confidence: 99%

Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer

2016

Self Cite

View full text Add to dashboard Cite

Elucidation of tumour suppression mechanisms is a major challenge in cancer biology. Therefore, Peto's paradox, or low cancer incidence in large animals, has attracted focus. According to the gene-abundance hypothesis, which considers the increase/decrease in cancer-related genes with body size, researchers evaluated the associations between gene abundance and body size. However, previous studies only focused on a few specific gene functions and have ignored the alternative hypothesis (metabolic rate hypothesis): in this hypothesis, the cellular metabolic rate and subsequent oxidative stress decreases with increasing body size. In this study, we have elected to explore the gene-abundance hypothesis taking into account the metabolic rate hypothesis. Thus, we comprehensively investigated the correlation between the number of genes in various functional categories and body size while at the same time correcting for the mass-specific metabolic rate (Bc). A number of gene functions that correlated with body size were initially identified, but they were found to be artefactual due to the decrease in Bc with increasing body size. By contrast, immune system-related genes were found to increase with increasing body size when the correlation included this correction for Bc. These findings support the gene-abundance hypothesis and emphasize the importance of also taking into account the metabolic rate when evaluating gene abundance–body size relationships. This finding may be useful for understanding cancer evolution and tumour suppression mechanisms as well as for determining cancer-related genes and functions.

show abstract

Habitat variability does not generally promote metabolic network modularity in flies and mammals

Cited by 3 publications

References 75 publications

On the role of sparseness in the evolution of modularity in gene regulatory networks

On the role of sparseness in the evolution of modularity in gene regulatory networks

Exosomes in mammals with greater habitat variability contain more proteins and RNAs

Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer

Contact Info

Product

Resources

About