A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes

Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5′ UTR, gene body, and 3′-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the K_a/K_s value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB ( https://www.depts.ttu.edu/igcast/sorbmutdb.php ) and SorghumBase ( https://sorghumbase.org/ ). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.     

Expression of Myelin Proteolipid Protein and Basic Protein in Normal and Dysmyelinating Mutant Mice

Expression of myelin proteins was studied in the brains of 21-day-old normal mice and three dysmyelinating mutants-jimpy, quaking, and shiverer. Total brain polyribosomes and poly(A)+ mRNA were translated in two cell-free systems and the levels of synthesis of the myelin basic proteins (MBPs) and proteolipid protein (PLP) were determined. Synthesis of the MBPs in quaking homozygotes was at or above normal levels but PLP synthesis was significantly reduced to approximately 15% of control values, indicating independent effects on the expression of these proteins in this mutant. Immunoblot analysis of 21-day-old quaking brain homogenates showed a reduction in the steady-state levels of MBPs and PLP, suggesting a failure of newly synthesized MBPs to be incorporated into a stable membrane structure such as myelin. In the shiverer mutant very little synthesis of MBPs was observed, whereas greater synthesis of PLP occurred (approximately 50% of control). Almost no MBP, and low levels of PLP, were detected in the immunoblots, suggesting the possibility of a partial failure of PLP to be assembled into myelin in shiverer. In the jimpy mutant, low levels of MBP synthesis were observed in vitro (approximately 26% of controls) and very little synthesis of PLP was evident. The immunoblots of 21-day jimpy brain homogenates revealed no appreciable steady-state levels of PLP or MBP, again indicating that most newly synthesized MBPs were not incorporated into a stable membrane structure in this mutant. In sum, the data show that in the three cases examined, the mutation appears to affect the expression of the MBPs and PLP independently. Furthermore, regardless of their absolute levels of synthesis these proteins may or may not be assembled into myelin.     

Site-directed mutagenesis on the heme axial-ligands of cytochrome b559 in photosystem II by using cyanobacteria Synechocystis PCC 6803

Cytochrome (cyt) b559 has been proposed to play an important role in the cyclic electron flow processes that protect photosystem II (PSII) from light-induced damage during photoinhibitory conditions. However, the exact role(s) of cyt b559 in the cyclic electron transfer pathway(s) in PSII remains unclear. To study the exact role(s) of cyt b559, we have constructed a series of site-directed mutants, each carrying a single amino acid substitution of one of the heme axial-ligands, in the cyanobacterium Synechocystis sp. PCC6803. In these mutants, His-22 of the α or the β subunit of cyt b559 was replaced with either Met, Glu, Tyr, Lys, Arg, Cys or Gln. On the basis of oxygen-evolution and chlorophyll a fluorescence measurements, we found that, among all mutants that were constructed, only the H22Kα mutant grew photoautotrophically, and accumulated stable PSII reaction centers (∼ 81% compared to wild-type cells). In addition, we isolated one pseudorevertant of the H22Yβ mutant that regained the ability to grow photoautotrophically and to assemble stable PSII reaction centers (∼ 79% compared to wild-type cells). On the basis of 77 K fluorescence emission measurements, we found that energy transfer from the phycobilisomes to PSII reaction centers was uncoupled in those cyt b559 mutants that assembled little or no stable PSII. Furthermore, on the basis of immunoblot analyses, we found that in thylakoid membranes of cyt b559 mutants that assembled little or no PSII, the amounts of the D1, D2, cyt b559α and β polypeptides were very low or undetectable but their CP47 and PsaC polypeptides were accumulated to the wild-type level. We also found that the amounts of cyt b559β polypeptide were significantly increased (larger than two folds) in thylakoid membranes of cyt b559 H22YβPS+ mutant cells. We suspected that the increase in the amounts of cyt b559 H22YβPS+ mutant polypeptides in thylakoid membranes might facilitate the assembly of functional PSII in cyt b559 H22YβPS+ mutant cells. Moreover, we found that isolated His-tagged PSII particles from H22Kα mutant cells gave rise to redox-induced optical absorption difference spectra of cyt b559. Therefore, our results concluded that significant fractions of H22Kα mutant PSII particles retained the heme of cyt b559. Finally, this work is the first report of cyt b559 mutants having substitutions of an axial heme-ligands that retain the ability to grow photoautotrophically and to assemble stable PSII reaction centers. These two cyt b559 mutants (H22Kα and H22YβPS+) and their PSII reaction centers will be very suitable for further biophysical and biochemical studies of the functional role(s) of cyt b559 in PSII.     

The possible functional significance of phosphatidylinositol in G1 arrest of Saccharomyces cerevisiae

Individual phospholipids were assayed in exponentially growing and G₁-arrested temperature-sensitive cell division cycle (cdc) mutants of Saccharomyces cerevisiae. It was observed that cdc28 cells which are known to arrest at ‘start’ when shifted to their non-permissive temperature, resulted in a 40% decrease in phosphatidylinositol (PI) level while the phosphatidylserine (PS) content was doubled in these cells. The reduced level of PI was restored in cdc4 and cdc7 mutants which are known to arrest past the ‘start’. The increase in PS level in cdc8 mutant which was probably to compensate the intrinsic charging of membrane environment, was also reduced in cdc4 and cdc7 mutants. Our results demonstrate that PI may play a role in yeast cell division and growth that the abnormalities of cdc28 could also be related to PI decrease.     

Nikkomycin-resistant mutants ofMucor rouxii: physiological and biochemical properties

We isolated three nikkomycin-resistant mutants of the dimorphic fungusM. rouxii which were physiologically characterized regarding their response to yeast-phase inducing conditions and their sensitivity to bacilysin. Mutant strains G21 and G23, showed a qualitatively normal, though delayed, dimorphic transition and partial cross-resistance to bacilysin. Mutant strain G27 showed an altered dimorphism, producing a high proportion (50%) of hyphal cells, and a wild-type sensitivity to bacilysin. Cell-free extracts from this mutant exhibited an activity of both basal and protease-activated chitin synthetase which was overexpressed as compared with the parental strain and mutants G21 and G23. Results are discussed in terms of the different genetic background of the mutants.Abbreviations NTG N-methyl-N-nitro-N-nitrosoguanidine - UDP-GlcNAc uridine 5-diphospho-N-acetylglucosamine - GlcNAc N-acetylglucosamine     

Giant, Krüppel, and caudal act as gap genes with extensive roles in patterning the honeybee embryo

In Drosophila, gap genes translate positional information from gradients of maternal coordinate activity and act to position the periodic patterns of pair-rule gene stripes across broad domains of the embryo. In holometabolous insects, maternal coordinate genes are fast-evolving, the domains that gap genes specify often differ from their orthologues in Drosophila while the expression of pair-rule genes is more conserved. This implies that gap genes may buffer the fast-evolving maternal coordinate genes to give a more conserved pair-rule output. To test this idea, we have examined the function and expression of three honeybee orthologues of gap genes, Krüppel, caudal, and giant. In honeybees, where many Drosophila maternal coordinate genes are missing, these three gap genes have more extensive domains of expression and activity than in other insects. Unusually, honeybee caudal mRNA is initially localized to the anterior of the oocyte and embryo, yet it has no discernible function in that domain. We have also examined the influence of these three genes on the expression of honeybee even-skipped and a honeybee orthologue of engrailed and show that the way that these genes influence segmental patterning differs from Drosophila. We conclude that while the fundamental function of these gap genes is conserved in the honeybee, shifts in their expression and function have occurred, perhaps due to the apparently different maternal patterning systems in this insect.     

Chemical and UV mutagenesis in Zymomonas mobilis

Mutagenesis of the facultative anaerobe Zymomonas mobilis was accomplished by three different mutagens. Ultra-violet (UV) irradiation, whose effectiveness relies on misrepair of damaged DNA via an error-prone pathway, was a poor mutagen for this organism. Ethyl methane sulphonate (EMS) gave results very similar to UV-irradiation. N-methyl-N-nitro-N-nitrosoguanidine (MNNG), which is believed to act by multiple mutagenic mechanisms, was the most powerful mutagen, always resulting in a large number of mutants of all types examined (i.e. auxotrophs, antibiotic resistant, heavy metal resistant and ultraviolet sensitive). Reversion frequencies of MNNG-induced mutants were very low. Evidence is provided that mutagenesis of Z. mobilis is affected by photoreactivation, adaptive response and error-prone repair mechanisms. Moreover, cells treated with alkylating agents and allowed to recover under anaerobic conditions clearly demonstrated that anaerobiosis plays a significant role in repair, but not in the induction of mutants.     

Characterization and regeneration of salt- and water-stress mutants from protoplast culture of Nicotiana plumbaginifolia (Viviani)

Summary Protoplast-derived colonies of haploid N. plumbaginifolia leaves were used to select for resistance to NaCl, KCl and polyethylene glycol 6000 (PEG). Salt-and PEG-tolerant cell lines were isolated on the basis of growth in a culture medium containing inhibitory concentrations of either NaCl or KCl (200 mM) or PEG (25%). The frequency of resistant lines ranged from 10^-5 to 10^-6. One resistant line from each treatment was regenerated into plants. All resistant lines produced 10–25 times more proline than the wild type when grown on a non-selective medium. Similar values were also observed in the leaves of resistant progeny plants. In each mutant line, salt or PEG resistance was transmitted as a single dominant nuclear gene as shown by segregation ratios in progenies of crosses between resistant and wild-type plants. The latter observation demonstrates clearly the existence of a genetic basis for increased salt tolerance.