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Correlation between genome reduction and bacterial growth.

ABSTRACT: Genome reduction by removing dispensable genomic sequences in bacteria is commonly used in both fundamental and applied studies to determine the minimal genetic requirements for a living system or to develop highly efficient bioreactors. Nevertheless, whether and how the accumulative loss of dispensable genomic sequences disturbs bacterial growth remains unclear. To investigate the relationship between genome reduction and growth, a series of Escherichia coli strains carrying genomes reduced in a stepwise manner were used. Intensive growth analyses revealed that the accumulation of multiple genomic deletions caused decreases in the exponential growth rate and the saturated cell density in a deletion-length-dependent manner as well as gradual changes in the patterns of growth dynamics, regardless of the growth media. Accordingly, a perspective growth model linking genome evolution to genome engineering was proposed. This study provides the first demonstration of a quantitative connection between genomic sequence and bacterial growth, indicating that growth rate is potentially associated with dispensable genomic sequences.

SUBMITTER: Kurokawa M

PROVIDER: S-EPMC5144675 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Correlation between genome reduction and bacterial growth.

Kurokawa Masaomi M Seno Shigeto S Matsuda Hideo H Ying Bei-Wen BW

DNA research : an international journal for rapid publication of reports on genes and genomes 20160703 6

Genome reduction by removing dispensable genomic sequences in bacteria is commonly used in both fundamental and applied studies to determine the minimal genetic requirements for a living system or to develop highly efficient bioreactors. Nevertheless, whether and how the accumulative loss of dispensable genomic sequences disturbs bacterial growth remains unclear. To investigate the relationship between genome reduction and growth, a series of Escherichia coli strains carrying genomes reduced in ...[more]

PMID: 27374613

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Project description:Genome reduction in obligately intracellular bacteria is one of the most well-established patterns in the field of molecular evolution. In the extreme, many sap-feeding insects harbor nutritional symbionts with genomes that are so reduced that it is not clear how they perform basic cellular functions. For example, the primary symbiont of psyllids (Carsonella) maintains one of the smallest and most AT-rich bacterial genomes ever identified and has surprisingly lost many genes that are thought to be essential for its role in provisioning its host with amino acids. However, our understanding of this extreme case of genome reduction is limited, as genomic data for Carsonella are available from only a single host species, and little is known about the functional role of "secondary" bacterial symbionts in psyllids. To address these limitations, we analyzed complete Carsonella genomes from pairs of congeneric hosts in three divergent genera within the Psyllidae (Ctenarytaina, Heteropsylla, and Pachypsylla) as well as complete secondary symbiont genomes from two of these host species (Ctenarytaina eucalypti and Heteropsylla cubana). Although the Carsonella genomes are generally conserved in size, structure, and GC content and exhibit genome-wide signatures of purifying selection, we found that gene loss has remained active since the divergence of the host species and had a particularly large impact on the amino acid biosynthesis pathways that define the symbiotic role of Carsonella. In some cases, the presence of additional bacterial symbionts may compensate for gene loss in Carsonella, as functional gene content indicates a high degree of metabolic complementarity between co-occurring symbionts. The genomes of the secondary symbionts also show signatures of long-term evolution as vertically transmitted, intracellular bacteria, including more extensive genome reduction than typically observed in facultative symbionts. Therefore, a history of co-evolution with secondary bacterial symbionts can partially explain the ongoing genome reduction in Carsonella. However, the absence of these secondary symbionts in other host lineages indicates that the relationships are dynamic and that other mechanisms, such as changes in host diet or functional coordination with the host genome, must also be at play.

Project description:The relationship between growth and immune phenotypes has been presented in the context of physiology and energy allocation theory, but has rarely been explained genetically in humans. As more summary statistics of genome-wide association studies (GWAS) become available, it is increasingly possible to explore the genetic relationship between traits at the level of genome-wide summary statistics. In this study, publicly available summary statistics of growth and immune related traits were used to evaluate the genetic correlation coefficients between immune and growth traits, as well as the cause and effect relationship between them. In addition, pleiotropic variants and KEGG pathways were identified. As a result, we found negative correlations between birthweight and immune cell count phenotypes, a positive correlation between childhood head circumference and eosinophil counts (EO), and positive or negative correlations between childhood body mass index and immune phenotypes. Statistically significant negative effects of immune cell count phenotypes on human height, and a slight but significant negative influence of human height on allergic disease were also observed. A total of 98 genomic regions were identified as containing variants potentially related to both immunity and growth. Some variants, such as rs3184504 located in SH2B3, rs13107325 in SLC39A8, and rs1260326 located in GCKR, which have been identified to be pleiotropic SNPs among other traits, were found to also be related to growth and immune traits in this study. Meanwhile, the most frequent overlapping KEGG pathways between growth and immune phenotypes were autoimmune related pathways. Pleiotropic pathways such as the adipocytokine signaling pathway and JAK-STAT signaling pathway were also identified to be significant. The results of this study indicate the complex genetic relationship between growth and immune phenotypes, and reveal the genetic background of their correlation in the context of pleiotropy.

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Correlation between genome reduction and bacterial growth.

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Correlation between genome reduction and bacterial growth.

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