Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation

Background Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. Results In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. Conclusions These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the “fossil” structure variations during genome evolution and speciation.

The effect of polyhydroxyalkanoates in Pseudomonas chlororaphis PA23 biofilm formation, stress endurance, and interaction with the protozoan predator Acanthamoeba castellanii

Pseudomonas chlororaphis PA23 is a biocontrol agent capable of protecting canola against the fungal pathogen Sclerotinia sclerotiorum. In addition to producing antifungal compounds, this bacterium synthesizes and accumulates polyhydroxyalkanoate (PHA) polymers as carbon and energy storage compounds. Because the role of PHA in PA23 physiology is currently unknown, we investigated the impact of this polymer on stress resistance, adherence to surfaces, and interaction with the protozoan predator Acanthamoeba castellanii. Three PHA biosynthesis mutants were created, PA23phaC1, PA23phaC1ZC2, and PA23phaC1ZC2D, which accumulated reduced PHA. Our phenotypic assays revealed that PA23phaC1ZC2D produced less phenazine (PHZ) compared with the wild type (WT) and the phaC1 and phaC1ZC2 mutants. All three mutants exhibited enhanced sensitivity to UV irradiation, starvation, heat stress, cold stress, and hydrogen peroxide. Moreover, motility, exopolysaccharide production, biofilm formation, and root attachment were increased in strains with reduced PHA levels. Interaction studies with the amoeba A. castellanii revealed that the WT and the phaC1 and phaC1ZC2 mutants were consumed less than the phaC1ZC2D mutant, likely due to decreased PHZ production by the latter. Collectively these findings indicate that PHA accumulation enhances PA23 resistance to a number of stresses in vitro, which could improve the environmental fitness of this bacterium in hostile environments.

THE FITNESS OF A RECOMBINANT STRAIN OF PSEUDOMONAS AERUGINOSA BACTERIA COMPARING WITH ITS PARENT STRAINS UNDER THE EGYPTIAN ENVIRONMENTAL CONDITIONS (MOWAS RIVER) IN 2020

The present study aimed to study the fitness between a trans-conjugant (recombinant strain) of Pseudomonas aeruginosa bacteria with its parents after transferring genetic material by conjugation mechanism. Whereas, environmental fitness expresses the interaction of an organism with its environment therefore it is considered a good indicator for the assessment of genetically engineered microorganisms (GEM) released into nature. Incubation time was carried out in vitro and incubating time in situ in Mowas River Zagazig city during winter and summer. Accordingly, the fitness of the parents and the recombinant strain was studied. The three strains of Pseudomonas aeruginosa (PAO1, MAM2 and PU21) were tested on chloramphenicol and tetracycline. Strain MAM2 was resistant to chloramphenicol 1200 µg/ml while was sensitive to tetracycline and has been used as the recipient. While strain PAO1 was resistant to tetracycline 200 µg/ml and was sensitive to chloramphenicol and has been used as the donor. Results proofed the presence of the plasmid in the donor and trans conjugant strains. The donor was treated with acridine orange to match the results obtained with the results at the molecular level. It was observed that bacterial fitness continued for up to 35 days in vitro, while in situ during the summer it did not last at the site for only 21 days. While it lasted 28 days during the summer. So, the risks that may be caused by releasing the genetically modified microorganisms into environments have been canceled. In addition to its ability to preserve the new genetic material, it may be able to transfer this new genetic material to other strains and species that may be live in the same ecosystem, as it is largely stable in the environment. In genetically modified microorganisms that are added to the environments for agricultural uses such as increasing soil fertility (bio-fertilizer) or biodegradation for a harmful substance such as pesticides, the soil must be re-inoculated in

Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum

The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in expression appeared in low-abundance (0.001–0.005 fmol%) proteins for polypeptides’ hydrolysis (metal-dependent hydrolase), oxidation of amino acids (FAD-dependent oxidoreductase), pyrimidine biosynthesis (aspartate carbamoyltransferase regulatory chain proteins), citrate cycle (2-oxoacid ferredoxin oxidoreductase) and ATP production (V type ATP synthase). Importantly, the cold shock induced a substantial increase (6% and 9%) in expression of the most-abundant proteins, thermosome beta subunit and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise acidic settings at low/moderate temperatures.