Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

Abstract Background The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories. Results We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression. Conclusion The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.

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Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

10.21203/rs.3.rs-34687/v2 ◽

2020 ◽

Author(s):

Cecilie Bækkedal Sonnenberg ◽

Tim Kahlke ◽

Peik Haugen

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Fast Growth ◽

Gene Copy ◽

Distribution Data ◽

Optimization Strategy ◽

Gene Distribution ◽

Fast Growing ◽

Genomic Location ◽

Growing Conditions

Abstract Background: The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.Results: We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.Conclusion: The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.

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Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

10.21203/rs.3.rs-34687/v3 ◽

2020 ◽

Author(s):

Cecilie Bækkedal Sonnenberg ◽

Tim Kahlke ◽

Peik Haugen

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Fast Growth ◽

Gene Copy ◽

Distribution Data ◽

Optimization Strategy ◽

Gene Distribution ◽

Fast Growing ◽

Genomic Location ◽

Growing Conditions

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Vibrionaceae core and shell genes are non-randomly distributed into spatially distinct intracellular domains

10.21203/rs.3.rs-34687/v1 ◽

2020 ◽

Author(s):

Cecilie Sonnenberg Bækkedal ◽

Tim Kahlke ◽

Peik Haugen

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Global Gene Expression ◽

Fast Growth ◽

Gene Copy ◽

Distribution Data ◽

Optimization Strategy ◽

Gene Distribution ◽

Fast Growing ◽

Growing Conditions

Abstract Background: The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1 ). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1 -proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1 -proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories. Results: We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1 , while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1 ). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1 . Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression. Conclusion: The pangene categories were non-randomly organized on the two chromosomes, with an overrepresentation of core and softcore genes around ori1 . We mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae , and suggested that core/softcore and shell/cloud genes were enriched at two spatially separated intracellular regions in the cell. The concurrence of the spatial distribution of core and the level of gene expression in one intracellular region, implied that there is a link between the structural organization of core genes and their cellular function in the cell.

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CG gene body DNA methylation changes and evolution of duplicated genes in cassava

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1519067112 ◽

2015 ◽

Vol 112 (44) ◽

pp. 13729-13734 ◽

Cited By ~ 65

Author(s):

Haifeng Wang ◽

Getu Beyene ◽

Jixian Zhai ◽

Suhua Feng ◽

Noah Fahlgren ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Expression Patterns ◽

Regulation Of Gene Expression ◽

Gene Copy ◽

Gene Body ◽

Duplicated Genes ◽

Gene Body Methylation ◽

Substantial Impact ◽

Tropical Regions

DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.

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Tissue-specificity of gene expression diverges slowly between orthologs, and rapidly between paralogs

10.1101/065086 ◽

2016 ◽

Cited By ~ 1

Author(s):

Nadezda Kryuchkova-Mostacci ◽

Marc Robinson-Rechavi

Keyword(s):

Gene Expression ◽

Tissue Specificity ◽

Pearson Correlation ◽

Expression Patterns ◽

Divergence Time ◽

Gene Copy ◽

Strong Increase ◽

Small Scale ◽

Ontology Term ◽

Tissue Specific

AbstractThe ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.Author summaryFrom specific examples, it has been assumed by comparative biologists that the same gene in different species has the same function, whereas duplication of a gene inside one species to create several copies allows them to acquire different functions. Yet this model was little tested until recently, and then has proven harder than expected to confirm. One of the problems is defining “function” in a way which can be easily studied. We introduce a new way of considering function: how specific is the activity (“expression”) of a gene? Genes which are specific to certain tissues have functions related to these tissues, whereas genes which are broadly active over many or all tissues have more general functions for the organism. We find that this “tissue-specificity” evolves very slowly in the absence of duplication, while immediately after duplication the new gene copy differs. This shows that indeed duplication leads to a strong increase in the evolution of new functions.

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Gene Expression Patterns and Gene Copy Number Changes in Dermatofibrosarcoma Protuberans

American Journal Of Pathology ◽

10.1016/s0002-9440(10)63593-6 ◽

2003 ◽

Vol 163 (6) ◽

pp. 2383-2395 ◽

Cited By ~ 101

Author(s):

Sabine C. Linn ◽

Rob B. West ◽

Jonathan R. Pollack ◽

Shirley Zhu ◽

Tina Hernandez-Boussard ◽

...

Keyword(s):

Gene Expression ◽

Copy Number ◽

Expression Patterns ◽

Gene Copy Number ◽

Dermatofibrosarcoma Protuberans ◽

Gene Copy ◽

Gene Expression Patterns ◽

Copy Number Changes

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The Proximity of Ribosomal Protein Genes tooriCEnhancesVibrio choleraeFitness in the Absence of Multifork Replication

mBio ◽

10.1128/mbio.00097-17 ◽

2017 ◽

Vol 8 (1) ◽

Cited By ~ 7

Author(s):

Alfonso Soler-Bistué ◽

Michaël Timmermans ◽

Didier Mazel

Keyword(s):

Life Cycle ◽

Ribosomal Protein ◽

Gene Order ◽

Growth Conditions ◽

Fast Growth ◽

Optimization Strategy ◽

Ribosomal Protein Genes ◽

Fast Growing ◽

Growth Optimization ◽

Whole Life Cycle

ABSTRACTRecent works suggest that bacterial gene order links chromosome structure to cell homeostasis. Comparative genomics showed that, in fast-growing bacteria, ribosomal protein genes (RP) locate near the replication origin (oriC). We recently showed thatVibrio choleraeemploys this positional bias as a growth optimization strategy: under fast-growth conditions, multifork replication increases RP dosage and expression. However, RP location may provide advantages in a dosage-independent manner: for example, the physical proximity of the many ribosomal components, in the context of a crowded cytoplasm, may favor ribosome biogenesis. To uncover putative dosage-independent effects, we studied isogenicV. choleraederivatives in which the major RP locus,S10-spc-α(S10), was relocated to alternative genomic positions. When bacteria grew fast, bacterial fitness was reduced according to the S10 relative distance tooriC. The growth of wild-typeV. choleraecould not be improved by additional copies of the locus, suggesting a physiologically optimized genomic location. Slow growth is expected to uncouple RP position from dosage, since multifork replication does not occur. Under these conditions, we detected a fitness impairment when S10 was far fromoriC. Deep sequencing followed by marker frequency analysis in the absence of multifork replication revealed an up to 30% S10 dosage reduction associated with its relocation that closely correlated with fitness alterations. Hence, the impact of S10 location goes beyond a growth optimization strategy during feast periods. RP location may be important during the whole life cycle of this pathogen.IMPORTANCEThe role of gene order within the bacterial chromosome is poorly understood. In fast growers, the location of genes linked with the expression of genetic information (i.e., transcription and translation) is biased towardoriC. It was proposed that the location of these genes helps to maximize their expression by recruiting multifork replication during fast growth. Our results show that such genomic positioning impacts cell fitness beyond fast-growth conditions, probably across the whole life cycle of fast growers. Thus, the genomic position of key highly expressed genes, such as RP, was finely tuned during the evolution of fast-growing bacteria and may also be important in slow growers. In the near future, many more genes whose genomic position impacts bacterial phenotype will be described. These studies will contribute to discovery the rules of genome organization and application of them for the design of synthetic chromosomes and the creation of artificial life forms.

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Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation.

10.1101/2021.12.09.471776 ◽

2021 ◽

Author(s):

Roberto de la Cerda ◽

Karsten Hookamp ◽

Fiona Roche ◽

Georgia Thompson ◽

Soukaina Timouma ◽

...

Keyword(s):

Gene Expression ◽

Copy Number ◽

Gene Dosage ◽

Expression Patterns ◽

Gene Copy Number ◽

Gene Copy ◽

Gene Expression Patterns ◽

Group I ◽

Saccharomyces Pastorianus ◽

Group Ii

The lager yeasts, Saccharomyces pastorianus, are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus and are divided into two broad groups, Group I and II. The two groups evolved from at least one common hybridisation event but have subsequently diverged with Group I strains losing many S. cerevisiae chromosomes while the Group II strains retain both sub-genomes. The complex genomes, containing orthologous alleles from the parental chromosomes, pose interesting questions regarding gene regulation and its impact on the fermentation properties of the strains. Superimposed on the presence of orthologous alleles are complexities of gene dosage due to the aneuploid nature of the genomes. We examined the contribution of the S. cerevisiae and S. eubayanus alleles to the gene expression patterns of Group I and II strains during fermentation. We show that the relative expression of S. cerevisiae and S. eubayanus orthologues is positively correlated with gene copy number. Despite the reduced S. cerevisiae content in the Group I strain, S. cerevisiae orthologues contribute to biochemical pathways upregulated during fermentation which may explain the retention of specific chromosomes in the strain. Conversely, S. eubayanus genes are significantly overrepresented in the upregulated gene pool in the Group II strain. Comparison of the transcription profiles of Group I and II strains during fermentation identified both common and unique gene expression patterns, with gene copy number being a dominant contributory factor. Thus, the aneuploid genomes create complex patterns of gene expression during fermentation with gene dosage playing a crucial role both within and between strains.

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Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.1071 ◽

2010 ◽

Vol 277 (1699) ◽

pp. 3519-3525 ◽

Cited By ~ 8

Author(s):

Irene Pala ◽

Manfred Schartl ◽

Miguel Brito ◽

Joana Malta Vacas ◽

Maria Manuela Coelho

Keyword(s):

Gene Expression ◽

Regulatory Networks ◽

Gene Expression Regulation ◽

Expression Patterns ◽

Gene Copy ◽

Polyploid Evolution ◽

Variable Expression ◽

The North ◽

Specific Allele ◽

The Impact

The evolution of hybrid polyploid vertebrates, their viability and their perpetuation over evolutionary time have always been questions of great interest. However, little is known about the impact of hybridization and polyploidization on the regulatory networks that guarantee the appropriate quantitative and qualitative gene expression programme. The Squalius alburnoides complex of hybrid fish is an attractive system to address these questions, as it includes a wide variety of diploid and polyploid forms, and intricate systems of genetic exchange. Through the study of genome-specific allele expression of seven housekeeping and tissue-specific genes, we found that a gene copy silencing mechanism of dosage compensation exists throughout the distribution range of the complex. Here we show that the allele-specific patterns of silencing vary within the complex, according to the geographical origin and the type of genome involved in the hybridization process. In southern populations, triploids of S. alburnoides show an overall tendency for silencing the allele from the minority genome, while northern population polyploids exhibit preferential biallelic gene expression patterns, irrespective of genomic composition. The present findings further suggest that gene copy silencing and variable expression of specific allele combinations may be important processes in vertebrate polyploid evolution.

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