Polyploidy in halophilic archaea: regulation, evolutionary advantages, and gene conversion

AbstractAll analyzed haloarachea are polyploid. In addition, haloarchaea contain more than one type of chromosome, and thus the gene dosage can be regulated independently on different replicons. Haloarchaea and several additional archaea have more than one replication origin on their major chromosome, in stark contrast with bacteria, which have a single replication origin. Two of these replication origins of Haloferax volcanii have been studied in detail and turned out to have very different properties. The chromosome copy number appears to be regulated in response to growth phases and environmental factors. Archaea typically contain about two Origin Recognition Complex (ORC) proteins, which are homologous to eukaryotic ORC proteins. However, haloarchaea are the only archaeal group that contains a multitude of ORC proteins. All 16 ORC protein paralogs from H. volcanii are involved in chromosome copy number regulation. Polyploidy has many evolutionary advantages for haloarchaea, e.g. a high resistance to desiccation, survival over geological times, and the relaxation of cell cycle-specific replication control. A further advantage is the ability to grow in the absence of external phosphate while using the many genome copies as internal phosphate storage polymers. Very efficient gene conversion operates in haloarchaea and results in the unification of genome copies. Taken together, haloarchaea are excellent models to study many aspects of genome biology in prokaryotes, exhibiting properties that have not been found in bacteria.

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Influence of Origin Recognition Complex Proteins on the Copy Numbers of Three Chromosomes in Haloferax volcanii

Journal of Bacteriology ◽

10.1128/jb.00161-18 ◽

2018 ◽

Vol 200 (17) ◽

Cited By ~ 4

Author(s):

Katharina Ludt ◽

Jörg Soppa

Keyword(s):

Copy Number ◽

Origin Recognition Complex ◽

Replication Initiation ◽

Haloferax Volcanii ◽

Deletion Mutants ◽

Replication Origins ◽

Content Type ◽

Chromosome Copy Number ◽

Copy Numbers ◽

Origin Recognition

ABSTRACT Replication initiation in archaea involves a protein named ORC, Cdc6, or ORC1/Cdc6, which is homologous to the eukaryotic origin recognition complex (ORC) proteins and to the eukaryotic Cdc6. Archaeal replication origins are comprised of origin repeat regions and adjacent orc genes. Some archaea contain a single replication origin and a single orc gene, while others have more than one of each. Haloferax volcanii is exceptional because it contains, in total, six replication origins on three chromosomes and 16 orc genes. Phylogenetic trees were constructed that showed that orc gene duplications occurred at very different times in evolution. To unravel the influence of the ORC proteins on chromosome copy number and cellular fitness, it was attempted to generate deletion mutants of all 16 genes. A total of 12 single-gene deletion mutants could be generated, and only three orc gene turned out to be essential. For one gene, the deletion analysis failed. Growth analyses revealed that no deletion mutant had a growth defect, but some had a slight growth advantage compared to the wild type. Quantification of the chromosome copy numbers in the deletion mutants showed that all 12 ORC proteins influenced the copy numbers of one, two, or all three chromosomes. The lack of an ORC led to an increase or decrease of chromosome copy number. Therefore, chromosome copy numbers in Hfx. volcanii are regulated by an intricate network of ORC proteins. This is in contrast to other archaea, in which ORC proteins typically bind specifically to the adjacent origin. IMPORTANCE The core origins of archaea are comprised of a repeat region and an adjacent gene for an origin recognition complex (ORC) protein, which is homologous to eukaryotic ORC proteins. Haloferax volcanii is exceptional because it contains six replication origins on three chromosomes and an additional 10 orc genes that are not adjacent to an origin. This unique ORC protein repertoire was used to unravel the importance of core origin orc genes and of origin-remote orc genes. Remarkably, all ORC proteins influenced the copy number of at least one chromosome. Some of them influenced those of all three chromosomes, showing that cross-regulation in trans exists in Hfx. volcanii. Furthermore, the evolution of the archaeal ORC protein family was analyzed.

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De Novo Chromosome Copy Number Variation in Fanconi Anemia-Associated Hematopoietic Defects

10.21236/ada586051 ◽

2013 ◽

Author(s):

Niall G. Howlett

Keyword(s):

Copy Number Variation ◽

Fanconi Anemia ◽

Copy Number ◽

De Novo ◽

Chromosome Copy Number ◽

Number Variation ◽

Chromosome Copy Number Variation

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Genetic interactions between CDC31 and KAR1, two genes required for duplication of the microtubule organizing center in Saccharomyces cerevisiae.

Genetics ◽

10.1093/genetics/137.2.407 ◽

1994 ◽

Vol 137 (2) ◽

pp. 407-422 ◽

Cited By ~ 8

Author(s):

E A Vallen ◽

W Ho ◽

M Winey ◽

M D Rose

Keyword(s):

Copy Number ◽

Gene Dosage ◽

Spindle Pole Body ◽

Direct Interaction ◽

Spindle Pole ◽

High Copy Number ◽

Temperature Sensitive ◽

Microtubule Organizing Center ◽

Recessive Mutations ◽

Organizing Center

Abstract KAR1 encodes an essential component of the yeast spindle pole body (SPB) that is required for karyogamy and SPB duplication. A temperature-sensitive mutation, kar1-delta 17, mapped to a region required for SPB duplication and for localization to the SPB. To identify interacting SPB proteins, we isolated 13 dominant mutations and 3 high copy number plasmids that suppressed the temperature sensitivity of kar1-delta 17. Eleven extragenic suppressor mutations mapped to two linkage groups, DSK1 and DSK2. The extragenic suppressors were specific for SPB duplication and did not suppress karyogamy-defective alleles. The major class, DSK1, consisted of mutations in CDC31. CDC31 is required for SPB duplication and encodes a calmodulin-like protein that is most closely related to caltractin/centrin, a protein associated with the Chlamydomonas basal body. The high copy number suppressor plasmids contained the wild-type CDC31 gene. One CDC31 suppressor allele conferred a temperature-sensitive defect in SPB duplication, which was counter-suppressed by recessive mutations in KAR1. In spite of the evidence for a direct interaction, the strongest CDC31 alleles, as well as both DSK2 alleles, suppressed a complete deletion of KAR1. However, the CDC31 alleles also made the cell supersensitive to KAR1 gene dosage, arguing against a simple bypass mechanism of suppression. We propose a model in which Kar1p helps localize Cdc31p to the SPB and that Cdc31p then initiates SPB duplication via interaction with a downstream effector.

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Sex differences in circadian food anticipatory activity are not altered by individual manipulations of sex hormones or sex chromosome copy number in mice

PLoS ONE ◽

10.1371/journal.pone.0191373 ◽

2018 ◽

Vol 13 (1) ◽

pp. e0191373 ◽

Cited By ~ 3

Author(s):

Antonio Aguayo ◽

Camille S. Martin ◽

Timothy F. Huddy ◽

Maya Ogawa-Okada ◽

Jamie L. Adkins ◽

...

Keyword(s):

Sex Differences ◽

Sex Hormones ◽

Copy Number ◽

Sex Chromosome ◽

Chromosome Copy Number ◽

Food Anticipatory Activity ◽

Anticipatory Activity

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Investigation of the Interaction of Human Origin Recognition Complex Subunit 1 with G-Quadruplex DNAs of Human c-myc Promoter and Telomere Regions

International Journal of Molecular Sciences ◽

10.3390/ijms22073481 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3481

Author(s):

Afaf Eladl ◽

Yudai Yamaoki ◽

Shoko Hoshina ◽

Haruka Horinouchi ◽

Keiko Kondo ◽

...

Keyword(s):

Fluorescence Anisotropy ◽

Binding Sites ◽

Replication Origin ◽

Origin Recognition Complex ◽

Chemical Shift Perturbation ◽

Human Origin ◽

Replication Origins ◽

Genome Wide ◽

G Quadruplex ◽

Origin Recognition

Origin recognition complex (ORC) binds to replication origins in eukaryotic DNAs and plays an important role in replication. Although yeast ORC is known to sequence-specifically bind to a replication origin, how human ORC recognizes a replication origin remains unknown. Previous genome-wide studies revealed that guanine (G)-rich sequences, potentially forming G-quadruplex (G4) structures, are present in most replication origins in human cells. We previously suggested that the region comprising residues 413–511 of human ORC subunit 1, hORC1413–511, binds preferentially to G-rich DNAs, which form a G4 structure in the absence of hORC1413–511. Here, we investigated the interaction of hORC1413-511 with various G-rich DNAs derived from human c-myc promoter and telomere regions. Fluorescence anisotropy revealed that hORC1413–511 binds preferentially to DNAs that have G4 structures over ones having double-stranded structures. Importantly, circular dichroism (CD) and nuclear magnetic resonance (NMR) showed that those G-rich DNAs retain the G4 structures even after binding with hORC1413–511. NMR chemical shift perturbation analyses revealed that the external G-tetrad planes of the G4 structures are the primary binding sites for hORC1413–511. The present study suggests that human ORC1 may recognize replication origins through the G4 structure.

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Studies on the alteration of chromosome copy number and cell division potential in a dnaA mutant of Escherichia coli

MGG Molecular & General Genetics ◽

10.1007/bf00272153 ◽

1991 ◽

Vol 229 (2) ◽

pp. 175-180 ◽

Cited By ~ 1

Author(s):

Joe A. Fralick

Keyword(s):

Escherichia Coli ◽

Cell Division ◽

Copy Number ◽

Dnaa Mutant ◽

Chromosome Copy Number

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Extensive protein dosage compensation in aneuploid human cancers

10.1101/2021.06.18.449005 ◽

2021 ◽

Author(s):

Klaske Marijke Schukken ◽

Jason Meyer Sheltzer

Keyword(s):

Protein Expression ◽

Dosage Compensation ◽

Copy Number ◽

Human Cancer ◽

Tumor Development ◽

Driver Genes ◽

Human Cancer Cell Lines ◽

Chromosome Copy Number ◽

Human Cancers ◽

Copy Number Changes

Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we have conducted an analysis of hundreds of human cancer cell lines with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins exhibit dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has an unexpectedly moderate effect on the expression of oncogenes and tumor suppressors, demonstrating that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.

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