Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes

Determination of codon pattern and evolutionary forces acting on genes linked to inflammatory bowel disease

Inflammatory bowel disease (IBD) is an inflammatory disorder of the gastrointestinal tract. The present study attempted to understand the codon usage preferences in genes associated with IBD progression. Compositional analysis, codon usage bias (CUB), Relative synonymous codon usage (RSCU), RNA structure, and expression analysis were performed to obtain a comprehensive picture of codon usage in IBD genes. Compositional analysis of 62 IBD-associated genes revealed that G and T are the most and least abundant nucleotides, respectively. ApG, CpA, and TpG dinucleotides were overrepresented or randomly used, while ApC, CpG, GpT, and TpA dinucleotides were either underrepresented or randomly used in genes related to IBD. The codons influencing the codon usage the most in IBD genes were CGC and AGG. A comparison of codon usage between IBD, and pancreatitis (non-IBD inflammatory disease) indicated that only codon CTG codon usage was significantly different between IBD and pancreatitis. At the same time, there were codons ATA, ACA, CGT, CAA, GTA, CCT, ATT, GCT, CGG, TTG, and CAG for whom codon usage was significantly different for IBD and housekeeping gene sets. The results suggest similar codon usage in at least two inflammatory disorders, IBD and pancreatitis. The analysis helps understand the codon biology, factors affecting gene expression of IBD-associated genes, and the evolution of these genes. The study helps reveal the molecular patterns associated with IBD.

Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures

Dinucleotide biases have been widely investigated in the genomes of eukaryotes and viruses, but not in bacteria. We assembled a dataset of bacterial genomes (>15 000), which are representative of the genetic diversity in the kingdom Eubacteria, and we analyzed dinucleotide biases in relation to different traits. We found that TpA dinucleotides are the most depleted and that CpG dinucleotides show the widest dispersion. The abundances of both dinucleotides vary with genomic G + C content and show a very strong phylogenetic signal. After accounting for G + C content and phylogenetic inertia, we analyzed different bacterial lifestyle traits. We found that temperature preferences associate with the abundance of CpG dinucleotides, with thermophiles/hyperthemophiles being particularly depleted. Conversely, the TpA dinucleotide displays a bias that only depends on genomic G + C composition. Using predictions of intrinsic cyclizability we also show that CpG depletion may associate with higher DNA bendability in both thermophiles/hyperthermophiles and mesophiles, and that the former are predicted to have significantly more flexible genomes than the latter. We suggest that higher bendability is advantageous at high temperatures because it facilitates DNA positive supercoiling and that, through modulation of DNA mechanical properties, local or global CpG depletion controls genome organization, most likely not only in bacteria.

CpG usage in RNA viruses: data and hypotheses

CpG repression in RNA viruses has been known for decades, but a reasonable explanation has not yet been proposed to explain this phenomenon. In this study, we calculated the CpG odds ratio of all RNA viruses that have available genome sequences and analyzed the correlation with their genome polarity, base composition, synonymous codon usage, phylogenetic relationship, and host. The results indicated that the viral base composition, synonymous codon usage and host selection were the dominant factors that determined the CpG bias in RNA viruses. CpG usage variation between the different viral groups was caused by different combinations of these pressures, which also differed from each other in strength. The consistent under-representation of CpG usage in −ssRNA viruses is determined predominantly by base composition, which may be a consequence of the U/A preferred mutation bias of −ssRNA viruses, whereas the CpG usage of +ssRNA viruses is affected greatly by their hosts. As a result, most +ssRNA viruses mimic their hosts' CpG usage. Unbiased CpG usage in dsRNA viruses is most likely a result of their dsRNA genome, which allows the viruses to escape from the host-driven CpG elimination pressure. CpG was under-represented in all reverse-transcribing viruses (RT viruses), suggesting that DNA methylation is an important factor affecting the CpG usage of retroviruses. However, vertebrate-infecting RT viruses may also suffer host' CpG elimination pressure that also acts on +ssRNA viruses, which results in further under-representation of CpG in the vertebrate-infecting RT viruses.

The level of cytosine is usually much higher than the level of guanine in two-fold degenerated sites from third codon positions of genes from Simplex- and Varicelloviruses with G+C higher than 50%

We studied usage of cytosine and guanine in 914 genes from completely sequenced genomes of five Simplex- and seven Varicelloviruses. In genes with total GC-content higher than 50% usage of cytosine is usually higher than usage of guanine (an average difference for genes with G+C higher than 70% reaches 4.0%). This difference is caused mostly by the elevated usage of cytosine in two-fold degenerated sites situated in third codon positions relatively to the usage of guanine in two-fold degenerated sites situated in third codon positions (an average difference for genes with G+C higher than 70% is equal to 28.2%). The usage of amino acids that are encoded by codons containing cytosine in two-fold degenerated sites situated in third codon positions (AA2TC) is much higher than the usage of amino acids encoded by codons containing guanine in two-fold degenerated sites situated in third codon positions (AA2AG). The usage of AA2AG declines much more steeply with the growth of GC-content than the usage of AA2TC. This effect is the consequence of the nature of genetic code and of the negative selection. In GC-rich genes the usage of cytosine in four-fold degenerated sites is only a little (but significantly) higher than the usage of guanine (in genes with G+C higher than 70% an average difference is equal to 4.3%). This difference may be caused by transcription-associated mutational pressure.

GC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylation

Background

Fractional DNA methylation in sea squirts evolved to global DNA methylation in fish. The impact of global DNA methylation is reflected by more CpG depletions and/or more A/T to G/C changes at CpG flanking positions due to context-dependent mutations of methylated CpG sites.

Methods and Findings

In this report, we demonstrate that the sea squirt genes have undergone more CpG to TpG/CpA substitutions than the fish orthologs using homologous fragments from orthologous genes among Ciona intestinalis, Ciona savignyi, fugufish and zebrafish. To avoid premature transcription, the TGA sites derived from CGA were largely converted to TGG in sea squirt genes. By contrast, a significant increment of GC content at CpG flanking positions was shown in fish genes. The positively selected A/T to G/C substitutions, in combination with the CpG to TpG/CpA substitutions, are the sources of the extremely low CpG observed/expected ratios in vertebrates. The nonsynonymous substitutions caused by the GC content increase have resulted in frequent amino acid replacements in the directions that were not noticed previously.

Conclusion

The increased GC content at CpG flanking positions can reduce CpG loss in fish genes and attenuate the impact of DNA methylation on CpG-containing codons, probably accounting for evolution towards vertebrates.

The universal trend of amino acid gain-loss is caused by CpG hypermutability

Understanding the cause of the changes in the amino acid composition of proteins is essential for understanding the evolution of protein functions. Since the early 1970s, it has been known that the frequency of some amino acids in protein sequences is increasing and that of others is decreasing. Recently, it was found that the trends of amino acid changes were similar in 15 taxa representing Bacteria, Archaea, and Eukaryota. However, the cause of this similarity in the trend of the gains and losses of amino acids continued to be debated. Here, we show that this trend of the gain and loss of amino acids can be simply explained by CpG hypermutability. We found that the frequency of amino acids coded by codons with TpG dinucleotides and those with CpA dinucleotides is increasing, while that of amino acids coded by codons with CpG dinucleotides is decreasing. We also found that organisms that lack DNA methyltransferase show different trends of the gain and loss of amino acids. DNA methyltransferase methylates CpG dinucleotides and induces CpG hypermutability. The incorporation of CpG hypermutability into models of protein evolution will improve studies on protein evolution in different organisms.

Patterns of evolution and host gene mimicry in influenza and other RNA viruses

It is well known that the dinucleotide CpG is under-represented in the genomic DNA of many vertebrates. This is commonly thought to be due to the methylation of cytosine residues in this dinucleotide and the corresponding high rate of deamination of 5-methycytosine, which lowers the frequency of this dinucleotide in DNA. Surprisingly, many single-stranded RNA viruses that replicate in these vertebrate hosts also have a very low presence of CpG dinucleotides in their genomes. Viruses are obligate intracellular parasites and the evolution of a virus is inexorably linked to the nature and fate of its host. One therefore expects that virus and host genomes should have common features. In this work, we compare evolutionary patterns in the genomes of ssRNA viruses and their hosts. In particular, we have analyzed dinucleotide patterns and found that the same patterns are pervasively over- or under-represented in many RNA viruses and their hosts suggesting that many RNA viruses evolve by mimicking some of the features of their host's genes (DNA) and likely also their corresponding mRNAs. When a virus crosses a species barrier into a different host, the pressure to replicate, survive and adapt, leaves a footprint in dinucleotide frequencies. For instance, since human genes seem to be under higher pressure to eliminate CpG dinucleotide motifs than avian genes, this pressure might be reflected in the genomes of human viruses (DNA and RNA viruses) when compared to those of the same viruses replicating in avian hosts. To test this idea we have analyzed the evolution of the influenza virus since 1918. We find that the influenza A virus, which originated from an avian reservoir and has been replicating in humans over many generations, evolves in a direction strongly selected to reduce the frequency of CpG dinucleotides in its genome. Consistent with this observation, we find that the influenza B virus, which has spent much more time in the human population, has adapted to its human host and exhibits an extremely low CpG dinucleotide content. We believe that these observations directly show that the evolution of RNA viral genomes can be shaped by pressures observed in the host genome. As a possible explanation, we suggest that the strong selection pressures acting on these RNA viruses are most likely related to the innate immune response and to nucleotide motifs in the host DNA and RNAs.

Viruses are obligate intracellular parasites that use different strategies to sequester host cell machinery and avoid the host immune system. In this paper we explore the genomes of viruses that encode their genetic information in single-stranded RNA, a different material than the one used by their hosts (double-stranded DNA). It is interesting to observe that these viruses share some of the host's characteristics. For instance, one of the most underrepresented motifs in the DNA of vertebrates is the dinucleotide CpG. This is commonly thought to be due to methylation and deamination of cytosine residues in this dinucleotide. Surprisingly, the same CpG suppression is observed in vertebrate RNA viruses but not in RNA phages. We show that RNA viruses present similar dinucleotide pressures as their host genes. We find that the influenza A virus, which originated from an avian reservoir and replicated in humans over many generations, evolves to reduce the frequency of CpG dinucleotides mimicking the human genes. Influenza B, which has been in humans longer, exhibits an extremely low CpG dinucleotide content. These observations suggest that the evolution of RNA viruses is shaped by pressures observed in the host genome.

Toll-like receptor 2-dependent and -independent activation of macrophages by group B streptococci

Group B streptococcus (GBS), a capsulated gram-positive bacterium, is a major cause of newborn infections. Although the innate immune receptor Toll-like receptor (TLR) 2 has been shown to primarily recognize gram-positive bacterial products, the production of TNF by macrophages treated with heat-killed GBS (HK-GBS) does not depend on TLR2. In this report, we have characterized HK-GBS-induced activation of macrophages derived from wildtype and TLR2-deficient mice. Microarray analysis demonstrated that HK-GBS activation of macrophages induces both TLR2-independent and -dependent signals. While the expression of a major fraction of genes in macrophages induced by HK-GBS does not depend on TLR2, induction of several important molecules involved in host innate immunity such as IL-6, IL-1beta, and lipocalin 2 is severely impaired in the absence of TLR2 signaling. Furthermore, we show that HK-GBS utilizes centrifugation sensitive components to induce rapid activation of TLR2(-/-) macrophages and that HK-GBS-induced activation of macrophages is not mediated through its genomic DNA. Together, our results demonstrate that HK-GBS induces TLR2-dependent antimicrobial gene activation and provide further understanding of the molecular basis of host innate response to GBS infection.