Genome Sequence of Avery's Virulent Serotype 2 Strain D39 ofStreptococcus pneumoniaeand Comparison with That of Unencapsulated Laboratory Strain R6

Abstract

Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenesis. To date, the complete genome sequences have been reported for only two S. pneumoniae strains: TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report here the genome sequences and new annotation of two different isolates of strain D39 and the corrected sequence of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only five relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single-basepair changes, six deletions, and four insertions and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, the relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed.Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen that causes several serious diseases, including pneumonia, otitis media (ear infection), sinusitis, meningitis, and septicemia (reviewed in references 81, 112, and 114). Invasive pneumococcal diseases result in high rates of mortality and morbidity, especially among young, elderly, debilitated, and immunosuppressed individuals (54, 55). It is estimated that more than 1 million people die each year from pneumococcal infections worldwide, especially in developing countries (59, 80). In the United States and elsewhere, resistance to a range of antibiotics is increasing at an alarming rate among clinical isolates of S. pneumoniae (6, 60). As part of its life cycle, pneumococcus exists as a commensal bacterium that inhabits and colonizes the nasopharynx of up to 20 and 50% of healthy adults and children, respectively, at any time (81, 113). The transition from commensal bacterium to opportunistic pathogen often occurs after another respiratory tract infection.For example, pneumococcal pneumonia has been a leading secondary infection and cause of death during influenza pandemics (9).Strains of S. pneumoniae are categorized into seroty...

The Capsular Serotype ofStreptococcus pneumoniaeIs More Important than the Genetic Background for Resistance to Complement

“…Since the mutants of these two studies were constructed independently, the source of the TIGR4 parent strain (serotype 4) could affect the results. Laboratory strains purchased from different sources could have accumulated different mutations as has been observed for D39 and its derivatives (23). It is also possible that the methodologies applied and sera used as a source of complement could result in differences between the studies.…”

Streptococcus pneumoniae

“…SPD_0065 is annotated as a ␤-galactosidase 3 gene. It is present in all sequenced pneumococcal genomes (16,27,47) and was identified as part of the core genomes of strains associated with colonization and invasive disease (37).…”

“…Given that carbohydrate is the principal pneumococcal energy source and at least one-third of the genome is devoted to sugar metabolism (16,27,47), we hypothesized that in addition to previously described pneumococcal glycosidases, there are likely to be others whose action is required to degrade host glycoconjugates, such as mucins. The search for novel and previously uncharacterized sugar hydrolases resulted in the identification of a ␤-galactosidase (SPD_0065) which is involved in the degradation of glycoproteins, including mucins.…”

“…The roles of other glycosidases remain unknown, yet at least one-third of the pneumococcal genome encodes proteins involved in sugar transport, degradation, and processing, suggesting that carbohydrate metabolism has a central impact on pneumococcal biology (16,27,47). In the sequenced pneumococcal genome, several genes are annotated as sugar hydrolases (otherwise known as glycosidases); however, the importance of these in glycoprotein degradation is not known.…”

“…In the sequenced pneumococcal genome, several genes are annotated as sugar hydrolases (otherwise known as glycosidases); however, the importance of these in glycoprotein degradation is not known. In this study we explored the role in glycoprotein degradation and virulence of SPD_0065, annotated as ␤-galactosidase 3 in the D39 genome (27). During preparation of this paper, Jeong et al (20) reported some properties of SPD_0065.…”