To examine these different aspects, the selection process was broken down into three consecutive steps, each more closely focused on the ultimate genetic contributors to the population, and each with its associated hypothesis. However, the reverse was observed for males, for which inferences are made more difficult due to the large standard errors of the bivariate coefficients.
It is possible that short-term commercial needs that do not follow the outcome of the OCS algorithm are more likely to occur among males, compared to females, as male selection opportunities are greater and offer a more rapid response to the need. The evidence from males was equivocal, in part because of higher selection intensity among males, leading to smaller numbers of males with which to conduct the regression analyses. Expected genetic contributions and their impact on gene flow and genetic gain.
Bijma P, Woolliams JA. Prediction of genetic contributions and generation intervals in populations with overlapping generations under selection. Villanueva B, Woolliams JA. Optimization of breeding programmes under index selection and constrained inbreeding.
Genet Res. Article Google Scholar. Dynamic selection for maximizing response with constrained inbreeding in schemes with overlapping generations. Anim Sci. Optimisation of contribution of candidate parents to maximise genetic gain and restricting inbreeding using semidefinite programming. Genet Sel Evol. Meuwissen THE. Maximizing the response of selection with a predefined rate of inbreeding. J Anim Sci. Dynamic selection procedures for constrained inbreeding and their consequences for pedigree development.
A fast Newton—Raphson based iterative algorithm for large scale optimal contribution selection. An algorithm to compute optimal genetic contributions in selection programs with large numbers of candidates.
Expected increases in genetic merit from using optimized contributions in two livestock populations of beef cattle and sheep.
Article PubMed Google Scholar. Prediction of genetic gain from quadratic optimisation with constrained rates of inbreeding. Mendelian sampling terms as a selective advantage in optimum breeding schemes with restrictions on the rate of inbreeding. The advantage of factorial mating under selection is uncovered by deterministically predicted rates of inbreeding. Mate selection strategies. Balancing genetic gain and diversity in livestock improvement programs.
Kinghorn BP. An algorithm for efficient constrained mate selection. Wright S. Coefficients of inbreeding and relationship. Am Nat. A potential limitation of this approach is that the genetic and environmental treatments applied undoubtedly modify various phenotypes besides just growth rate, such that each perturbation might display unique interactions with the icuAB T1 allele.
On the contrary, fitness and growth rates with or without icuAB T1 were indistinguishable across all genetic backgrounds and incubation temperatures in MR media where cobalt is not limiting data not shown. The above results suggest that: 1 the physiological demand on cobalt uptake is higher under faster growth and 2 the selective advantage of the Icu phenotype in MP media may increase as populations adapt toward faster growth.
Despite having been discovered fortuitously, our work represents the first study to investigate the genetic basis of adaptation to metal limitation in an experimental evolution system. As a component of Cbl or vitamin B 12 , cobalt is critical to biosynthesis of this important coenzyme [54] — [56]. Low concentrations of cobalt in the agricultural and marine ecosystems has been shown to impact human and animal health and reduce vitamin B 12 production in the ocean, respectively [57] , [58].
In this study, evolution under cobalt limitation resulted in emergence of mutants with enhanced cobalt uptake from independent microbial populations. On the contrary, such mutation events were never detected in the 8 populations grown solely on succinate. The highly parallel but distinct evolutionary consequences prompted us to investigate the physiological basis of adaptation and molecular features that might promote parallel genetic evolution.
We showed that ISMex4 transposition resulted in overexpression of icuAB genes, which enhanced cobalt uptake and conferred a substantial fitness increase during growth on methanol in MP media but to a minimal extent on succinate. Our physiological assays further pinpointed the major selective advantage to the need for Cbl in the EMC pathway specifically required for methanol metabolism of Methylobacterium , likely resulting from its two AdoCbl-dependent reactions catalyzed by ECM and MCM, respectively.
Though the genome sequence suggests two additional Cbl-dependent enzymatic reactions methione synthase and two ribonucleotide reductases in Methylobaterium [39] , the specific growth defect of the WT strain on methanol in MP media and its complementation by glyoxylate support this notion. Cobalt deficiency may thus reduce biosynthesis of Cbl, further lowering its concentration in the cytosol, consequently preventing adenosylation of Cbl and its assembly into ECM and MCM.
Our findings from a laboratory system might have profound implications on how cobalt limitation impacts microbial ecology and evolution in nature. Methylobacterium spp. The ability to utilize methanol, a by-product of plant cell wall synthesis, provides a substantial selective advantage to Methylobacterium during epi- and endophytic growth [61].
The importance of cobalt to C 1 metabolism of Methylobacterium makes it compelling to investigate the functional significance of icuAB during plant colonization.
In fact, cobalt limitation in plants has been demonstrated to inhibit growth and root nodulation of nitrogen-fixing rhizobia [63] , [64].
Cobalt may also play a role in the crown gall disease caused by Agrobacterium tumefaciens. This pathogen requires indoleacetic acid synthesized by a cobalt-containing enzyme to induce abnormal proliferation of plant cells [65]. It would be interesting to apply experimental evolution to study adaptation of plant-associated bacteria in plants grown in cobalt depleted soils.
On the other hand, as cobalt is nonessential to plants but essential to many plant microflora [62] , it is tempting to ask if the cobalt requirement from plant microflora causes indirect selection on regulation of plant cobalt concentration to welcome mutualistic symbionts or repel harmful pathogens. On a broader scale, low cobalt concentrations in the environment can greatly impact the supply of vitamin B 12 to ecosystems as vitamin B 12 is essential to many organisms but only synthesized by prokaryotes [66].
Across the North Atlantic Ocean, the abundance of phytoplankton and dissolved vitamin B 12 were found to correlate with cobalt concentrations 0. The same study also demonstrated the ability of cobalt to stimulate growth of phytoplankton and vitamin B 12 production in seawater. Prochlorococcus and Synechococcus , two dominant photosynthetic bacteria in the open ocean, have an absolute cobalt requirement and appear to secret high-affinity ligands to facilitate cobalt uptake [67] , [68].
Combined with genetic and genomic tools, experimental evolution with marine microorganisms represents a promising approach to unravel the genetic and physiological bases of adaptation to metal limitation in the ocean. While environmental and physiological constraints set the stage for the emergence of the Icu phenotype, parallel evolution at the genetic level appeared to be promoted by transposition preference of ISMex4, the chromosomal location of the icuAB locus, and clonal interference.
In the present study, transposition of ISMex4 conferred a selective advantage by increasing icuAB expression, whereas in another study we found an ISMex4 transposition that increased fitness by reducing the transcript level of an overexpressed gene Chou and Marx, unpublished , stressing the versatile role of IS elements in the evolution of gene expression. Transposition of most IS elements exhibit some degree of target site selectivity [69].
Analysis of ISMex4 insertion sites revealed a 4-bp conserved target sequence that tends to locate in regions prone to form a stem-loop structure. The presence of two ISMex4 copies 15 kb and 38 kb downstream of the icuAB genes, respectively, may have increased its chance of transposition into this nearby locus as several IS elements exhibit a high frequency of local-hopping.
In addition to aforementioned features that may promote recurrent ISMex4 transpositions, the predominance of the high-fitness icuAB T1 allele over the icuAB T2 allele across populations suggests a potential role for clonal competition among asexual lineages Table 1.
Identification of two methanol-evolved populations F5, F6 free of icuAB T1 and icuAB T2 alleles pointed to the possibility of alternative mutational targets. Collectively, these results suggest a model shaping genetic parallelism in our system: local-hopping and target selectivity of ISMex4 may lead to high frequency but limited types of transposition while the large fitness advantages gained by icuAB T1 and icuAB T2 alleles allow them to outcompete other weaker beneficial mutations conferring similar phenotypes in these asexual populations.
As the proposed genetic features favoring ISMex4 transposition and its resulting selective advantage can be manipulated easily through mutagenesis and trace metal supplementation, respectively, our system offers the power to experimentally address how mutation rates and the strength of natural selection affect parallel evolution and the dynamics of adaptation.
The physiological effects of an allele depend on expression levels, genetic backgrounds, and environmental conditions. Predicting the behavior and evolution of biological systems requires a comprehensive understanding of how these parameters influence physiology and thus shape the fitness landscape.
Experimental evolution offers a valuable alternative besides conventional genetic approaches to uncover biochemical functions and physiological links of genes as well as their contribution to fitness in the evolutionary context.
In this study, growth phenotypes of icuAB knockout mutants are minute and unspecific to either carbon substrate or growth media, providing no clue to the functional significance of this gene cassette. Nevertheless, by characterizing the phenotypes of beneficial mutations and reconstructing their fitness effect through overexpression experiments, our results revealed the biochemical function of this gene cassette and demonstrated an intermediate optimal expression level that constrains the breadth of phenotypic evolution.
Moreover, identification of the physiological processes icuAB T1 and icuAB T2 contribute to sets the stage to address whether they interact with other mutations or environments in a manner similar to those tested for deleterious mutations. Previous work has shown that growth defects of deleterious mutations tend to be reduced by either environmental stress or the presence of other deleterious mutations [7] , [70] , [71].
These results have supported a simple model where growth rate is mainly limited by the slowest physiological process [7]. It has remained unclear whether the same principle would apply to certain beneficial mutations, such that they become more advantageous when limitations imposed by other physiological processes are relieved. By modulating growth rate through either incubation temperatures or genetic backgrounds, we found a consistent increase in the selective advantage of a beneficial mutation with increasing growth rate.
This growth-rate dependence is in accord with the model described above: By alleviating genetic or environmental constraints, increases in growth rate raised the fitness effect of increased cobalt uptake. The synthesis of previous work with deleterious mutations and current findings from a beneficial mutation suggest a physiology-mediated mechanism through which mutations and environments interact.
This mechanism has two profound implications for the evolution and function of biological systems: 1 Some mutations will only be beneficial or deleterious when favorable mutations or environmental changes alleviate other physiological limitations, suggesting a general mechanism for historical contingency and environment-dependent evolutionary potential.
Unmarked allelic exchange plasmids for introducing adaptive mutations or deleting genes were constructed based on pCM, a sacB -based suicide plasmid [72].
A constitutive expression plasmid and a fluorescent promoter-probe plasmid were constructed based on pCM, a broad-host-range plasmid conferring kanamycin resistance [51]. A bp synthetic fragment containg the constitutive promoter P tac was inserted upstream of this reporter to make pHC Expression plasmids, pHC60 and pHC91, were generated by cloning the aforementioned bp fragment containing P tac and a bp synthetic fragment containing the P lac promoter into pHC41, respectively.
Instead, two genes belonging to the foreign glutathione-dependent formaldehyde oxidation pathway of Paracoccus denitrificans flhA , encoding hydroxymethyl-glutathione dehydrogenase and fghA , encoding formyl-glutathione hydrolase were expressed from the strong P mxaF promoter in plasmid pCM [51]. This replacement resulted in restoration of growth on methanol at a one-third the rate of WT [36].
EM-derived strains carrying one of the three other adaptive mutations from strain CM were generated as above. These beneficial mutations affected the expression of aforementioned fghA , pntAB , and gshA genes. Further analysis of the physiological effects of these beneficial mutations will be described subsequently Chou and Marx, unpublished.
Gene knockouts of icuA , icuB , and icuAB were generated by deleting the whole open reading frames from the WT strain. The genotypes of resultant mutants were confirmed by PCR. Strains carrying promoter-probe plasmids or expression plasmids were made by introducing these plasmids from E. The general formula for one liter of all growth media consists of 1 ml of TMS, ml of phosphate buffer The growth media used for evolution experiments were prepared with this photoactive TMS stored under variable light exposure [35].
MP media were prepared with the same TMS but stored in dark to prevent photochemical reactions. This modified TMS consisted of 10 ml of Instead, each of the 7 trace metal species was supplemented as 0. Glassware used with EDTA-free media was pre-washed with 0.
All populations were grown in 9. Growth media for evolution experiments consisted of identical minimal growth media supplemented with different carbon sources: A and F populations with 15 mM methanol, B populations with 3. Due to the slow growth of the EM strain, the F populations were transferred at the same dilution rate every four days in the first generations of evolution.
Transfers of the F populations after generation were switched to two-day cycles. For each strain, three independent mid-exponential phase cultures defined as half-maximal OD were harvested and processed by a method described previously [31].
The preliminary microarray experiment used three independent RNA isolations from each strain that were pooled together with equal quantity.
The rpsB gene encoding 30S ribosomal protein S2 was chosen as the reference gene for data normalization. Data analysis was performed with the Opticon Monitor v. The average threshold cycle Ct value for each gene was calculated from triplicate reactions for RNA samples by following a previously described method [78]. Reference entries selective advantage n.
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