Dataset Information

Unique genes in giant viruses: regular substitution pattern and anomalously short size.

ABSTRACT: Large DNA viruses, including giant mimivirus with a 1.2-Mb genome, exhibit numerous orphan genes possessing no database homologs or genes with homologs solely in close members of the same viral family. Due to their solitary nature, the functions and evolutionary origins of those genes remain obscure. We examined sequence features and evolutionary rates of viral family-specific genes in three nucleo-cytoplasmic large DNA virus (NCLDV) lineages. First, we showed that the proportion of family-specific genes does not correlate with sequence divergence rate. Second, position-dependent nucleotide statistics were similar between family-specific genes and the remaining genes in the genome. Third, we showed that the synonymous-to-nonsynonymous substitution ratios in those viruses are at levels comparable to those estimated for vertebrate proteomes. Thus, the vast majority of family-specific genes do not exhibit an accelerated evolutionary rate, and are thus likely to specify functional polypeptides. On the other hand, these family-specific proteins exhibit several distinct properties: (1) they are shorter, (2) they include a larger fraction of predicted transmembrane proteins, and (3) they are enriched in low-complexity sequences. These results suggest that family-specific genes do not correspond to recent horizontal gene transfer. We propose that their characteristic features are the consequences of the specific evolutionary forces shaping the viral gene repertoires in the context of their parasitic lifestyles.

SUBMITTER: Ogata H

PROVIDER: S-EPMC1950904 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Unique genes in giant viruses: regular substitution pattern and anomalously short size.

Ogata Hiroyuki H Claverie Jean-Michel JM

Genome research 20070725 9

Large DNA viruses, including giant mimivirus with a 1.2-Mb genome, exhibit numerous orphan genes possessing no database homologs or genes with homologs solely in close members of the same viral family. Due to their solitary nature, the functions and evolutionary origins of those genes remain obscure. We examined sequence features and evolutionary rates of viral family-specific genes in three nucleo-cytoplasmic large DNA virus (NCLDV) lineages. First, we showed that the proportion of family-speci ...[more]

PMID: 17652424

Similar Datasets

Project description:The folding rates of two-state single-domain proteins are generally resistant to small-scale changes in amino acid sequence. For example, having surveyed here over 700 single-residue substitutions in 24 well-characterized two-state proteins, we find that the majority (55%) of these substitutions affect folding rates by less than a factor of 2, and that only 9% affect folding rates by more than a factor of 8. Among those substitutions that significantly affect folding rates, we find that accelerating substitutions are an order of magnitude less common than those that decelerate the process. One of the most extreme outliers in this data set, an arginine-to-phenylalanine substitution at position 48 (R48F) of chymotrypsin inhibitor 2 (CI2), accelerates the protein's folding rate by a factor of 36 relative to that of the wild-type protein and is the most accelerating substitution reported to date in a two-state protein. In order to better understand the origins of this anomalous behavior, we have characterized the kinetics of multiple additional substitutions at this position. We find that substitutions at position 48 in CI2 fall into two distinct classes. The first, comprising residues that ablate the charge of the wild-type arginine but retain the hydrophobicity of its alkane chain, accelerate folding by at least 10-fold. The second class, comprising all other residues, produces folding rates within a factor of two of the wild-type rate. A significant positive correlation between hydrophobicity and folding rate across all of the residues we have characterized at this position suggests that the hydrophobic methylene units of the wild-type arginine play a significant role in stabilizing the folding transition state. Likewise, studies of the pH dependence of the histidine substitution indicate a strong correlation between folding rate and charge state. Thus, mutations that ablate the arginine's positive charge while retaining the hydrophobic contacts of its methylene units tend to dramatically accelerate folding. Previous studies have suggested that arginine 48 plays an important functional role in CI2, which may explain why it is highly conserved despite the anomalously large deceleration it produces in the folding of this protein.

Dataset Information

Unique genes in giant viruses: regular substitution pattern and anomalously short size.

Publications

Unique genes in giant viruses: regular substitution pattern and anomalously short size.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets