Paralogous Gene | ScienceGate

Members of the Abdominal-B-related Hox gene subfamily (belonging to homology groups 9 to 13) are coordinately expressed during limb bud development. Only two genes from homology group 13 (Hoxa-13 and Hoxd-13) are specifically expressed in the developing distal region (the autopod), which displays the most complex and evolutionarily flexible pattern among limb ‘segments’. We report here that targeted disruption of the Hoxa-13 gene leads to a specific forelimb and hindlimb autopodal phenotype, distinct from that of the Hoxd-13 paralogous gene inactivation. In both limbs, Hoxa-13 loss of function results in the lack of formation of the most anterior digit and to altered morphogenesis of some ‘preaxial’ carpal/tarsal elements. We have generated mice with all possible combinations of disrupted Hoxa-13 and/or Hoxd-13 alleles, which allowed us to investigate the degree of functional specificity versus redundancy of the corresponding gene products in the developing limb autopod. The phenotype of any double mutant was much more severe than the sum of the phenotypes seen in the corresponding single mutants, indicating that these genes act in a partially redundant manner. Our major findings were: (1) an abnormal autopodal phenotype in Hoxa-13+/−/Hoxd-13+/− double heterozygous mutants, which mostly consists of subsets of the alterations seen in each individual homozygous mutant, and therefore appears to result from quantitative, rather than qualitative, homeoprotein deficiency; (2) partly distinct alterations in mutants harboring a single non-disrupted allele of Hoxa-13 or Hoxd-13, indicating that the remaining reduced protein amounts are not functionally equivalent; (3) a polydactyly in the forelimbs of Hoxa-13+/−/Hoxd-13−/−double mutants, consisting of seven symmetrically arranged, truncated and mostly non-segmented digits; (4) an almost complete lack of chondrified condensations in the autopods of double homozygous mutants, showing that the activity of group 13 Hox gene products is essential for autopodal patterning in tetrapod limbs.

Download Full-text

Temporal Expression Analysis of the Borrelia burgdorferi Paralogous Gene Family 54 Genes BBA64, BBA65, and BBA66 during Persistent Infection in Mice

Infection and Immunity ◽

10.1128/iai.00037-07 ◽

2007 ◽

Vol 75 (6) ◽

pp. 2753-2764 ◽

Cited By ~ 40

Author(s):

Robert D. Gilmore ◽

Rebekah R. Howison ◽

Virginia L. Schmit ◽

Andrew J. Nowalk ◽

Dawn R. Clifton ◽

...

Keyword(s):

Gene Expression ◽

Borrelia Burgdorferi ◽

Gene Family ◽

Expression Profile ◽

Persistent Infection ◽

Adaptive Immune Response ◽

Paralogous Gene ◽

Reverse Transcription Pcr ◽

Paralogous Gene Family

ABSTRACT Members of the Borrelia burgdorferi paralogous gene family 54 (pgf 54) are regulated by conditions simulating mammalian infection and are thought to be instrumental in borrelial host survival and pathogenesis. To explore the activities of these genes in vivo, a comprehensive analysis of pgf 54 genes BBA64, BBA65, and BBA66 was performed to assess the genetic stability, host antibody responses, and kinetics of gene expression in the murine model of persistent infection. DNA sequencing of pgf 54 genes obtained from reisolates at 1 year postinfection demonstrated that all genes of this family are stable and do not undergo recombination to generate variant antigens during persistent infection. Antibodies against BBA64 and BBA66 appeared soon after infection and were detectable throughout the infection, suggesting that there was gene expression during infection. However, quantitative reverse transcription-PCR revealed that BBA64 gene expression was considerably decreased in Borrelia residing in the mouse ear tissue compared to the expression in cultured spirochetes by 20 days postinfection and that the levels of expression remained low throughout the infection. Conversely, transcription of the BBA65 and BBA66 genes was increased, and both of these genes were continuously expressed until 100 days postinfection; this was followed by periods of differential expression late in infection. The expression profile of the BBA64 gene suggests that this gene has an important role during tick-to-host transmission and early infection, whereas the expression profile of the BBA65 and BBA66 genes suggests that these genes have a role in persistent infection. The differential regulation of pgf 54 genes observed during infection may help confer a survival advantage during persistent infection, influencing mechanisms for B. burgdorferi dissemination, tissue tropism, or evasion of the adaptive immune response.

Download Full-text

SIZE DISTRIBUTION OF GENE FAMILIES IN A GENOME

Mathematical Models and Methods in Applied Sciences ◽

10.1142/s0218202513500644 ◽

2014 ◽

Vol 24 (04) ◽

pp. 697-717 ◽

Cited By ~ 11

Author(s):

RYSZARD RUDNICKI ◽

JERZY TIURYN

Keyword(s):

Size Distribution ◽

Genome Evolution ◽

Gene Mutation ◽

Probabilistic Model ◽

Gene Loss ◽

Genomic Data ◽

Gene Families ◽

Paralogous Gene ◽

A Genome ◽

Theoretical Results

We consider a probabilistic model of genome evolution. We are interested in size distribution of gene families. The model is based on three fundamental evolutionary events: gene loss, duplication and accumulated change. We assume that the probability of gene loss and duplication is constant and the probability of gene mutation mi depends on the size i of a family. We prove that size distribution of paralogous gene families in a genome converges to the equilibrium as time goes to infinity. Moreover, we show how this equilibrium depends on the sequence (mi). Theoretical results are compared with the available genomic data.

Download Full-text

Bowman?Birk inhibitors in Lens: identification and characterization of two paralogous gene classes in cultivated lentil and wild relatives

Theoretical and Applied Genetics ◽

10.1007/s00122-004-1888-1 ◽

2005 ◽

Vol 110 (3) ◽

pp. 596-604 ◽

Cited By ~ 8

Author(s):

Gabriella Sonnante ◽

Angelo De Paolis ◽

Domenico Pignone

Keyword(s):

Wild Relatives ◽

Paralogous Gene ◽

Identification And Characterization

Download Full-text

Determining the interaction status and evolutionary fate of duplicated homomeric proteins

10.1101/2020.04.08.031351 ◽

2020 ◽

Author(s):

Saurav Mallik ◽

Dan S Tawfik

Keyword(s):

Protein Interaction Data ◽

Interaction Data ◽

Common Ancestry ◽

Paralogous Gene ◽

Oligomeric Proteins ◽

E Coli ◽

Protein Protein Interaction ◽

Consistent Picture ◽

Paralogous Proteins ◽

Evolutionary Fate

AbstractOligomeric proteins are central to life. Duplication and divergence of their genes is a key evolutionary driver, also because duplications can yield very different outcomes. Given a homomeric ancestor, duplication can yield two paralogs that form two distinct homomeric complexes, or a heteromeric complex comprising both paralogs. Alternatively, one paralog remains a homomer while the other acquires a new partner. However, so far, conflicting trends have been noted with respect to which fate dominates, primarily because different methods and criteria are being used to assign the interaction status of paralogs. Here, we systematically analyzed all Saccharomyces cerevisiae and Escherichia coli oligomeric complexes that include paralogous proteins. We found that the proportions of homo-hetero duplication fates strongly depend on a variety of factors, yet that nonetheless, rigorous filtering gives a consistent picture. In E. coli about 50%, of the paralogous pairs appear to have retained the ancestral homomeric interaction, whereas in S. cerevisiae only ∼10% retained a homomeric state. This difference was also observed when unique complexes were counted instead of paralogous gene pairs. We further show that this difference is accounted for by multiple cases of heteromeric yeast complexes that share common ancestry with homomeric bacterial complexes. Our analysis settles contradicting trends and conflicting previous analyses, and provides a systematic and rigorous pipeline for delineating the fate of duplicated oligomers in any organism for which protein-protein interaction data are available.

Download Full-text

Evolutionary thrift: mycobacteria repurpose plasmid diversity during adaptation of type VII secretion systems

10.1101/067207 ◽

2016 ◽

Author(s):

Tatum D. Mortimer ◽

Alexandra M. Weber ◽

Caitlin S. Pepperell

Keyword(s):

Model Organism ◽

Gene Families ◽

Type Iv Secretion ◽

Paralogous Gene ◽

Secretion Systems ◽

Type Vii Secretion ◽

Type Iv ◽

Selection For ◽

Plasmid Diversity ◽

Chromosomal Loci

AbstractMycobacteria have a distinct secretion system, termed type VII (T7SS), which is encoded by paralogous chromosomal loci (ESX) and associated with pathogenesis, conjugation, and metal homeostasis. Evolution of paralogous gene families is of interest because duplication is an important mechanism by which novel genes evolve, but there are potential conflicts between adaptive forces that stabilize duplications and those that enable evolution of new functions. Our objective was to delineate the adaptive forces underlying diversification of T7SS. Plasmid-borne ESX were described recently, and we found evidence that the initial duplication and divergence of ESX systems occurred on plasmids and was driven by selection for advantageous mutations. Plasmid conjugation has been linked to T7SS and type IV secretion systems (T4SS) in mycobacteria, and we discovered that T7SS and T4SS genes evolved in concert on the plasmids. We hypothesize that differentiation of plasmid ESX helps to prevent conjugation among cells harboring incompatible plasmids. Plasmid ESX appear to have been repurposed following migration to the chromosome, and there is evidence of positive selection driving further differentiation of chromosomal ESX. We hypothesize that ESX loci were initially stabilized on the chromosome by mediating their own transfer. These results emphasize the diverse adaptive paths underlying evolution of novelty, which in this case involved plasmid duplications, selection for advantageous mutations in the mobile and core genomes, migration of the loci between plasmids and chromosomes, and lateral transfer among chromosomes. We discuss further implications for the choice of model organism to study ESX functions in Mycobacterium tuberculosis.

Download Full-text