Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes

Kochiwa, Hiromi; Tomita, Masaru; Kanai, Akio

doi:10.1186/1471-2148-7-128

Cited by 43 publications

(74 citation statements)

References 60 publications

(71 reference statements)

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“…Phylogenetic reconstruction of bacterial evolution can be more straightforward than searches for protein orthologs, and this has been done for Firmicutes species in the past (15). We have reconstructed a Firmicutes phylogenetic tree that includes all known sspE-containing species, along with a number of other Firmicutes, including those of Bacillales species that lack an sspE gene.…”

Section: Discussionmentioning

confidence: 99%

Extremely Variable Conservation of -Type Small, Acid-Soluble Proteins from Spores of Some Species in the Bacterial Order Bacillales

Vyas¹,

Cox²,

Setlow³

et al. 2011

Journal of Bacteriology

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␥-Type small, acid-soluble spore proteins (SASP) are the most abundant proteins in spores of at least some members of the bacterial order Bacillales, yet they remain an enigma from both functional and phylogenetic perspectives. Current work has shown that the ␥-type SASP or their coding genes (sspE genes) are present in most spore-forming members of Bacillales, including at least some members of the Paenibacillus genus, although they are apparently absent from Clostridiales species. We have applied a new method of searching for sspE genes, which now appear to also be absent from a clade of Bacillales species that includes Alicyclobacillus acidocaldarius and Bacillus tusciae. In addition, no ␥-type SASP were found in A. acidocaldarius spores, although several of the DNA-binding ␣/␤-type SASP were present. These findings have elucidated the phylogenetic origin of the sspE gene, and this may help in determining the precise function of ␥-type SASP.Bacterial spores of species of the Firmicutes phylum contain a number of small, acid-soluble proteins (SASP) that comprise 10 to 15% of the protein in the spore's central region or core (30, 32). The following two types of major SASP have been identified in spores: (i) ␣/␤-type SASP that are products of a multi-ssp gene family and have extremely similar sequences both within and across species and (ii) ␥-type SASP that are almost always encoded by a single sspE gene; this is the most abundant protein found in spores of a number of species and comprises 5 to 8% of total spore protein (18-20, 29-32, 39). In contrast to the highly conserved sequences of ␣/␤-type SASP, sequences of ␥-type SASP are not well conserved across species, and this has allowed the use of sspE and SASP-␥ sequences to distinguish closely related Bacillus strains and species (17).In Bacillus subtilis, genes encoding both ␣/␤-type and ␥-type SASP are transcribed in parallel late in spore development when the various SASP are synthesized, and the transcription of ssp genes is mediated by the RNA polymerase sigma factor, G (22). The SASP are degraded soon after spores complete the germination process and begin outgrowth, and one function of these proteins is to serve as a reservoir of amino acids (aa) for protein synthesis early in outgrowth (12,30,32). The latter is an important function, since spores become deficient in a number of amino acid biosynthetic enzymes during spore formation and synthesize these enzymes only during spore outgrowth. In addition to serving as a reservoir of amino acids, the ␣/␤-type SASP have an additional function, as these proteins saturate spore DNA and protect it from many types of damage and are thus very important for long-term spore survival (30-32). However, other than serving as an amino acid reservoir, no additional function has been demonstrated for ␥-type SASP (12, 30, 32).In the current work, we have examined genome sequence information for spore-forming Firmicutes and have confirmed that (i) spore-forming Clostridiales species appear to lack sspE genes; (ii) most bu...

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Section: Discussionmentioning

confidence: 99%

Extremely Variable Conservation of -Type Small, Acid-Soluble Proteins from Spores of Some Species in the Bacterial Order Bacillales

Vyas¹,

Cox²,

Setlow³

et al. 2011

Journal of Bacteriology

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“…Data were compiled from (Zheng et al, 2015) and (Kochiwa et al, 2007). The y-axis represents the percent of genes on the chromosome that are co-oriented with respect to replication.…”

Section: Supplementary Materialsmentioning

confidence: 99%

Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis

Lang

Hall

Merrikh

et al. 2017

Cell

198

287

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SUMMARY Replication-transcription collisions shape genomes, influence evolution, and promote genetic diseases. Although unclear why, head-on transcription (lagging strand genes) is especially disruptive to replication and promotes genomic instability. Here, we find that head-on collisions promote R-loop formation in Bacillus subtilis. We show that pervasive R-loop formation at head-on collision regions completely blocks replication, elevates mutagenesis, and inhibits gene expression. Accordingly, the activity of the R-loop processing enzyme RNase HIII at collision regions is crucial for stress survival in B. subtilis, as many stress response genes are head-on to replication. Remarkably, without RNase HIII, the ability of the intracellular pathogen Listeria monocytogenes to infect and replicate in hosts is weakened significantly, most likely because many virulence genes are head-on to replication. We conclude that the detrimental effects of head-on collisions stem primarily from excessive R-loop formation and that the resolution of these structures is critical for bacterial stress survival and pathogenesis.

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“…DNA-damaging agents are known to have a profound effect on RNase HII activity (3,36). Although RNase H genes have evolved to avoid functional redundancy (25), it has been observed that the location and/or the activity of RNase H proteins may be influenced by other domains present on the same protein chain (10), indicating a possible interrelation between the RHII and RSD activities of MS_RHII-RSD. A basal level of (p)ppGpp is essential to destabilize RNA polymerases and maintain genomic integrity during DNA replication (54).…”

mentioning

confidence: 99%

MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Synthetase from Mycobacterium smegmatis

Murdeshwar

Chatterji

2012

J Bacteriol

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Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes

Cited by 43 publications

References 60 publications

Extremely Variable Conservation of -Type Small, Acid-Soluble Proteins from Spores of Some Species in the Bacterial Order Bacillales

Extremely Variable Conservation of -Type Small, Acid-Soluble Proteins from Spores of Some Species in the Bacterial Order Bacillales

Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis

MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Synthetase from Mycobacterium smegmatis

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