Hydrogenase Gene Distribution and H2 Consumption Ability within the Thiomicrospira Lineage

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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Virulence Gene Distribution of Salmonella Pullorum Isolates Recovered from Chickens in China (1953–2015)

Avian Diseases ◽

10.1637/11927-071318-resnote.1 ◽

2018 ◽

Vol 62 (4) ◽

pp. 431 ◽

Cited By ~ 3

Author(s):

Di Zhang ◽

Linlin Zhuang ◽

Chengming Wang ◽

Ping Zhang ◽

Tengfei Zhang ◽

...

Keyword(s):

Virulence Gene ◽

Gene Distribution ◽

Salmonella Pullorum

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Correlation of microsynteny conservation and disease gene distribution in mammalian genomes

BMC Genomics ◽

10.1186/1471-2164-10-521 ◽

2009 ◽

Vol 10 (1) ◽

pp. 521 ◽

Cited By ~ 5

Author(s):

Simon C Lovell ◽

Xiting Li ◽

Nimmi R Weerasinghe ◽

Kathryn E Hentges

Keyword(s):

Disease Gene ◽

Gene Distribution ◽

Mammalian Genomes

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Mapping barley Ds insertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates

Genome ◽

10.1139/g09-029 ◽

2009 ◽

Vol 52 (6) ◽

pp. 566-575 ◽

Cited By ~ 4

Author(s):

Harpinder S. Randhawa ◽

Jaswinder Singh ◽

Peggy G. Lemaux ◽

Kulvinder S. Gill

Keyword(s):

Gene Cloning ◽

Single Copy ◽

Gene Density ◽

Targeted Mutagenesis ◽

Recombination Rates ◽

Transposition Frequency ◽

Deletion Lines ◽

Gene Distribution ◽

Flanking Sequences ◽

Large Genomes

Gene distribution is highly uneven in the large genomes of barley and wheat; however, location, order, and gene density of gene-containing regions are very similar between the two genomes. Flanking sequences from 35 unique, single-copy, barley Ds insertion events were physically mapped using wheat nullisomic-tetrasomic, ditelosomic, and deletion lines. Of the 35 sequences, 23 (66%) detected 34 loci mapping on all 7 homoeologous wheat groups. Seven sequences were not mapped owing to lack of polymorphism and the remaining 5 (14%) were barley-specific. All 34 loci physically mapped to the previously identified gene-rich regions (GRRs) of wheat, making the contained genes candidates for targeted mutagenesis by remobilization. Transpositions occurred preferentially into GRRs with higher recombination rates. The GRRs containing 17 of the 23 Ds insertions accounted for 60%–89% of the respective arm’s recombination. The remaining 6 (17%) insertions mapped to GRRs with <15% of the arm’s recombination. Overall, kb/cM estimates for the Ds-containing GRRs were twofold higher than those for regions without insertions. These results suggest that all genes may be targeted by transposon-based gene cloning, although the transposition frequency for genes present in recombination-poor regions is significantly less than that present in highly recombinogenic regions.

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Analysis of Extensive [FeFe] Hydrogenase Gene Diversity Within the Gut Microbiota of Insects Representing Five Families of Dictyoptera

Microbial Ecology ◽

10.1007/s00248-011-9941-5 ◽

2011 ◽

Vol 63 (3) ◽

pp. 586-595 ◽

Cited By ~ 11

Author(s):

Nicholas R. Ballor ◽

Jared R. Leadbetter

Keyword(s):

Gut Microbiota ◽

Gene Diversity ◽

Hydrogenase Gene

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Implication of gene distribution in the bacterial chromosome for the bacterial cell factory

Journal of Biotechnology ◽

10.1016/s0168-1656(00)00197-8 ◽

2000 ◽

Vol 78 (3) ◽

pp. 209-219 ◽

Cited By ~ 25

Author(s):

Eduardo P.C. Rocha ◽

Pascale Guerdoux-Jamet ◽

Ivan Moszer ◽

Alain Viari ◽

Antoine Danchin

Keyword(s):

Bacterial Cell ◽

Bacterial Chromosome ◽

Cell Factory ◽

Gene Distribution

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Overexpression of a hydrogenase gene inClostridium paraputrificumto enhance hydrogen gas production

FEMS Microbiology Letters ◽

10.1016/j.femsle.2005.04.014 ◽

2005 ◽

Vol 246 (2) ◽

pp. 229-234 ◽

Cited By ~ 78

Author(s):

Kenji Morimoto ◽

Tetsuya Kimura ◽

Kazuo Sakka ◽

Kunio Ohmiya

Keyword(s):

Gas Production ◽

Hydrogen Gas ◽

Hydrogenase Gene

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On the Order of Gene Distribution on Chromosomes Across the Animal Kingdom

10.1101/2019.12.15.877167 ◽

2019 ◽

Author(s):

Abdullah A. Toor ◽

Amir A. Toor

Keyword(s):

Gene Frequency ◽

Large Scale ◽

Animal Species ◽

Square Root ◽

Animal Kingdom ◽

Gene Distribution ◽

Complement Gene ◽

Gene Dispersion ◽

Average Gene ◽

Animal Genomes

SummaryBackgroundThe large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered manner across the animal kingdom.ResultsTwenty-one animal genomes reported in the NCBI database were examined. Numerically, there was a trend towards increasing overall gene content with increasing size of the genome as reflected by the chromosomal complement. Gene frequency on individual chromosomes in each animal genome was analyzed and demonstrated uniformity of proportions within each animal with respect to both average gene frequency on individual chromosomes and gene distribution across the unique genomes. Further, average gene distribution across animal species followed a relationship whereby it was, approximately, inversely proportional to the square root of the number of chromosomes in the unique animal genomes, consistent with the notion that there is an ordered increase in gene dispersion as the complexity of the genome increased. To further corroborate these findings a derived measure, termed gene spacing on chromosomes correlated with gene frequency and gene distribution.ConclusionAs animal species have evolved, the distribution of their genes on individual chromosomes and within their genomes, when viewed on a large scale is not random, but follows a mathematically ordered process, such that as the complexity of the organism increases, the genes become less densely distributed on the chromosomes and more dispersed across the genome.

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