Birth and Death of Orphan Genes in Rickettsia

Abstract

The origin and evolution of the thousands of species-specific genes with unknown functions, the so-called orphan genes, has been a mystery. Here, we have studied the rates and patterns of orphan sequence evolution, using the Rickettsia as our reference system. Of the Rickettsia conorii orphans examined in this study, 80% were found to be short gene fragments or fusions of short segments from neighboring genes. We reconstructed the putative sequences of the full-length genes from which the short orphan fragments are thought to have originated. One of the genes thus reconstructed displays weak similarity to the ankyrin-repeat protein family, an identification that is strongly supported by comparative molecular modeling. Studies of the patterns of gene fragmentation underscore the importance of short repeated sequences as targets for recombination events that result in sequence loss and the formation of short, transient open reading frames. Our analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species. Such reconstructions support the identification of lost protein functions and hint at important lifestyle changes.

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

“…Whereas the degenerative or accelerated evolution of ancestral genes can serve as a mechanism for generating ORFans both in bacteria species undergoing genome reduction (Amiri et al 2003) and in eukaryotes (Domazet-Loso and Tautz 2003), the extreme differences in base composition of ORFans and native genes indicate that this is not the case for ORFans in E. coli. Because all bacterial genomes with G+C contents >30% have intergenic regions that are relatively A+T rich, it has also been suggested that ORFans arise from errors in annotating noncoding regions (Charlebois et al 2003).…”

“…ORFans, particularly those that are short, have been attributed to errors in gene annotation or possibly pseudogenes (Fischer and Eisenberg 1999;Amiri et al 2003;Charlebois et al 2003). One method for determining the functional status of a sequence is by a comparative approach.…”

“…In the first, ORFans are the remnants of ancestral sequences that result from the erosion and degradation of previously functional genes, and their presence is viewed as an indicator of genome dynamics (Amiri et al 2003). In the second, ORFans elaborate new functions that are potentially beneficial to the organism and represent a means of bacterial adaptation.…”

Mimivirus Giant Particles Incorporate a Large Fraction of Anonymous and Unique Gene Products

“…Such coding regions without sequence similarity to other genes in databases are considered orphan open reading frames (ORFs) and termed "ORFans" (12). The origin and function of ORFan genes are still a matter of controversy, with opinions ranging from considering them pieces of junk DNA (1,8,40,44) to seeing them as quickly evolving sequences encoding normally expressed functional proteins (38, 39). Recent clinical evidence raised the possibility that mimivirus might be a human pathogen causing pneumonia (4, 24, 34), as suspected when it was first isolated from a cooling tower following an outbreak of pneumonia (23).…”

Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

“…However, study of these genes is helpful to aid in the comprehensive understanding of a species. With the increasing development of sequencing technologies, we have gained access to a number of genomes and transcriptomes from a wide range of species, which has aided the extensive study of the LSGs within mammals [8][9][10], insects [2,11,12], fish [13], plants [5,[14][15][16], and microbial species [17][18][19][20]. However, the LSGs in C. elegans have not yet been researched through genomewide methods.…”