Strand‐biased gene distribution, purine assymetry and environmental factors influence protein evolution in <i>Bacillus</i>

Goswami, Aranyak; Chowdhury, Anindya Roy; Sarkar, Manisha; Saha, Sanjoy Kumar; Paul, Sandip; Dutta, Chitra

doi:10.1016/j.febslet.2015.01.028

Cited by 3 publications

(3 citation statements)

References 46 publications

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“…Interestingly, genes encoding proteins acting on the lagging strand have evolved at a significantly higher rate than those dealing with the leading strand (13,14). All these features raise the question whether there is a division of labour between the two replicative DNA polymerases, each one being devoted to one strand (21), or if the B. subtilis replisome is more eukaryotic-like in that it relies on a two DNA polymerase system for chromosomal replication (5), using two polymerases at both strands.…”

Section: Introductionmentioning

confidence: 99%

Symmetric activity of DNA polymerases at and recruitment of exonuclease ExoR and of PolA to the Bacillus subtilis replication forks

Hernández-Tamayo

Oviedo-Bocanegra

Fritz

et al. 2019

Nucleic Acids Research

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DNA replication forks are intrinsically asymmetric and may arrest during the cell cycle upon encountering modifications in the DNA. We have studied real time dynamics of three DNA polymerases and an exonuclease at a single molecule level in the bacterium Bacillus subtilis. PolC and DnaE work in a symmetric manner and show similar dwell times. After addition of DNA damage, their static fractions and dwell times decreased, in agreement with increased re-establishment of replication forks. Only a minor fraction of replication forks showed a loss of active polymerases, indicating relatively robust activity during DNA repair. Conversely, PolA, homolog of polymerase I and exonuclease ExoR were rarely present at forks during unperturbed replication but were recruited to replications forks after induction of DNA damage. Protein dynamics of PolA or ExoR were altered in the absence of each other during exponential growth and during DNA repair, indicating overlapping functions. Purified ExoR displayed exonuclease activity and preferentially bound to DNA having 5′ overhangs in vitro. Our analyses support the idea that two replicative DNA polymerases work together at the lagging strand whilst only PolC acts at the leading strand, and that PolA and ExoR perform inducible functions at replication forks during DNA repair.

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Section: Introductionmentioning

confidence: 99%

Symmetric activity of DNA polymerases at and recruitment of exonuclease ExoR and of PolA to the Bacillus subtilis replication forks

Hernández-Tamayo

Oviedo-Bocanegra

Fritz

et al. 2019

Nucleic Acids Research

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“…Firmicutes possess three conspicuous genome features: purine asymmetry across the two strands of replication, a marked strand-biased gene distribution ( 5 – 8 ), and presence of two essential replicative C-family DNA polymerases, PolC and DnaE (also called DnaE3) ( 9 – 11 ). In contrast, E. coli codes for only one replicative C-family DNA polymerase, the Pol III-α subunit (also termed DnaE1, 11).…”

Section: Introductionmentioning

confidence: 99%

Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication

Seco

Ayora

2017

Nucleic Acids Research

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Firmicutes have two distinct replicative DNA polymerases, the PolC leading strand polymerase, and PolC and DnaE synthesizing the lagging strand. We have reconstituted in vitro Bacillus subtilis bacteriophage SPP1 θ-type DNA replication, which initiates unidirectionally at oriL. With this system we show that DnaE is not only restricted to lagging strand synthesis as previously suggested. DnaG primase and DnaE polymerase are required for initiation of DNA replication on both strands. DnaE and DnaG synthesize in concert a hybrid RNA/DNA ‘initiation primer’ on both leading and lagging strands at the SPP1 oriL region, as it does the eukaryotic Pol α complex. DnaE, as a RNA-primed DNA polymerase, extends this initial primer in a reaction modulated by DnaG and one single-strand binding protein (SSB, SsbA or G36P), and hands off the initiation primer to PolC, a DNA-primed DNA polymerase. Then, PolC, stimulated by DnaG and the SSBs, performs the bulk of DNA chain elongation at both leading and lagging strands. Overall, these modulations by the SSBs and DnaG may contribute to the mechanism of polymerase switch at Firmicutes replisomes.

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“…The amino acid composition was reported to be correlated with the protein structure classes (Bahar et al, 1997; Horner et al, 2008; Du et al, 2014), the metabolic efficiency (Akashi and Gojobori, 2002; Kaleta et al, 2013), and the translation efficiency (Du et al, 2017). Sueoka (1961, 1962) firstly reported that there is a correlation between GC contents and amino acid composition of proteins, and then the nucleotide bias causes the biased amino acid usage in bacterial and viral genomes was broadly reported (Rooney, 2003; Bohlin et al, 2013; Goswami et al, 2015). Cost-minimization could also shape the amino acid composition (Seligmann, 2003; Raiford et al, 2008; Bivort et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process

ChangJiang

Wang

et al. 2018

Front. Microbiol.

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Understanding how proteins evolve is important, and the order of amino acids being recruited into the genetic codons was found to be an important factor shaping the amino acid composition of proteins. The latest work about the last universal common ancestor (LUCA) makes it possible to determine the potential factors shaping amino acid compositions during evolution. Those LUCA genes/proteins from Methanococcus maripaludis S2, which is one of the possible LUCA, were investigated. The evolutionary rates of these genes positively correlate with GC contents with P-value significantly lower than 0.05 for 94% homologous genes. Linear regression results showed that compositions of amino acids coded by GC-rich codons positively contribute to the evolutionary rates, while these amino acids tend to be gained in GC-rich organisms according to our results. The first principal component correlates with the GC content very well. The ratios of amino acids of the LUCA proteins coded by GC rich codons positively correlate with the GC content of different bacteria genomes, while the ratios of amino acids coded by AT rich codons negatively correlate with the increase of GC content of genomes. Next, we found that the recruitment order does correlate with the amino acid compositions, but gain and loss in codons showed newly recruited amino acids are not significantly increased along with the evolution. Thus, we conclude that GC content is a primary factor shaping amino acid compositions. GC content shapes amino acid composition to trade off the cost of amino acids with bases, which could be caused by the energy efficiency.

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Strand‐biased gene distribution, purine assymetry and environmental factors influence protein evolution in Bacillus

Cited by 3 publications

References 46 publications

Symmetric activity of DNA polymerases at and recruitment of exonuclease ExoR and of PolA to the Bacillus subtilis replication forks

Symmetric activity of DNA polymerases at and recruitment of exonuclease ExoR and of PolA to the Bacillus subtilis replication forks

Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication

The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process

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