PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 15094797

Segmentally variable genes: a new perspective on adaptation.

Yu Zheng·Richard J Roberts·Simon Kasif
View original source ↗Export metadata ↓

Abstract

Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host-pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein-protein, protein-nucleic acid, or protein-small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment.

Explore related subjects

AcclimatizationBacillus subtilisBacterial Outer Membrane ProteinsBiological TransportCell LineageDNADatabases, GeneticEvolution, MolecularGene DuplicationGenetic VariationGenome, BacterialHelicobacter pyloriModels, StatisticalMultigene FamilyProtein Structure, TertiaryRNASignal TransductionTranscription, GeneticJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Yu Zheng, Richard J Roberts, Simon Kasif. 2004-04-13. Segmentally variable genes: a new perspective on adaptation.. https://doi.org/10.1371/journal.pbio.0020081

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2011

Adaptation to climate across the Arabidopsis thaliana genome.

Understanding the genetic bases and modes of adaptation to current climatic conditions is essential to accurately predict responses to future environmental change. We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino acid-changing variants were significantly enriched among the loci strongly correlated with climate, suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown together in a common environment. Our results provide a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.

Acclimatization↗
PubMed2006

The ecology of overwintering among turtles: where turtles overwinter and its consequences.

Turtles are a small taxon that has nevertheless attracted much attention from biologists for centuries. However, a major portion of their life cycle has received relatively little attention until recently - namely what turtles are doing, and how they are doing it, during the winter. In the northern parts of their ranges in North America, turtles may spend more than half of their lives in an overwintering state. In this review, I emphasise the ecological aspects of overwintering among turtles, and consider how overwintering stresses affect the physiology, behaviour, distributions, and life histories of various species. Sea turtles are the only group of turtles that migrate extensively, and can therefore avoid northern winters. Nevertheless, each year a number of turtles, largely juveniles, are killed when trapped by cold fronts before they move to safer waters. Evidently this risk is an acceptable trade-off for the benefits to a population of inhabiting northern developmental habitats during the summer. Terrestrial turtles pass the winter underground, either in burrows that they excavate or that are preformed. These refugia must provide protection against desiccation and lethal freezing levels. Some burrows are extensive (tortoise genus Gopherus), while others are shallow, or the turtles may simply dig into the ground to a safe depth (turtle genus Terrapene). In the latter genus, freeze tolerance may play an adaptive role. Most non-marine aquatic turtles overwinter underwater, although Clemmys (Actinemys) marmorata routinely overwinters on land when it occurs in riverine habitats, Kinosternon subrubrum often overwinters on land, and several others may overwinter terrestrially on occasion, especially in more southern climates. For northern species that overwinter underwater, there are two physiological groupings, those that are anoxia-tolerant and those that are relatively anoxia-intolerant. All species fare well physiologically in water with a high partial pressure of oxygen (PO2). A lack of anoxia tolerance limits the types of habitats that a freshwater turtle may live in, since unlike sea turtles, they cannot travel long distances to hibernate. Hatchlings of some species of turtles spend their first winter in or below the nest cavity, while hatchlings of other species in the same area, including northern areas, emerge in the autumn and presumably hibernate underwater. All hatchlings are relatively anoxia-intolerant, and there are no studies to date of where hatchling turtles that do not overwinter in or below the nest cavity spend their first winter. Equally little is known of the ontogeny of anoxia tolerance, other than that adults of all species are more anoxia-tolerant than their hatchlings, probably because of their better ossified shells, which provide adults with more buffer reserves and a larger site in which to sequester lactate. The northern limits of turtles are most likely determined by reproductive limitations (time for egg-laying, incubation, and hatching) than by the rigors of hibernation. Mortality is typically lower in turtle populations during hibernation than it is during their active periods. However, episodic mortality events do occur during hibernation, due to freezing, prolonged anoxia, or predation.

Acclimatization↗
PubMed2006

Physiological and biochemical responses of fruit exocarp of tomato (Lycopersicon esculentum Mill.) mutants to natural photo-oxidative conditions.

Photo-oxidative stress was imposed under natural solar radiation on exposed and shaded sections of detached fruit of immature green tomato (Lycopersicon esculentum Miller = Solanum lycopersicum L.) mutants (anthocyanin absent, beta-carotene, Delta, and high pigment-1) and their nearly isogenic parents ('Ailsa Craig' and 'Rutgers'). After 5 h exposure to high solar irradiance, either with or without ultraviolet (UV) radiation, surface colour changes, pigment composition, photosynthetic efficiency, antioxidant metabolites and enzyme activities, and selected flavonoids and antioxidant proteins in exocarp tissue were evaluated. The imposed photo-oxidative stress reproduced the symptoms observed on attached fruit. Both high temperature and solar irradiance caused fruit surface discoloration with faster degradation of chlorophyll (Chl) than carotenoids (Car), leading to an increase in the Car/Chl ratio. Surface bleaching was mostly caused by visible light, whereas elevated temperatures were mostly responsible for the inactivation of photosynthesis, measured as decreased F(v)/F(m). Ascorbate, glutathione, and total soluble protein concentrations decreased in the exocarp as the duration of exposure increased. Specific activities of superoxide dismutase, ascorbate peroxidase, dehydroascorbate reductase, monodehydroascorbate reductase (MDHAR), glutathione reductase (GR), and catalase increased with exposure, suggesting that these proteins were conserved during the imposed stress. GR protein expression remained stable during the imposed stress, whereas, MDHAR protein expression increased. Quercetin and kaempferol concentrations increased rapidly upon exposure, but not to UV radiation, suggesting rapid photo-protection in response to visible light; however, naringenin synthesis was not induced. The apparent increased tolerance of hp-1 fruit is discussed.

Acclimatization↗