Improvement of the Fatty Acid Composition of an Oil-Producing Filamentous Fungus, Mortierella alpina 1S-4, through RNA Interference with Δ12-Desaturase Gene Expression

An oleaginous fungus, Mortierella alpina 1S-4, is used commercially for arachidonic acid production. Δ12-Desaturase, which desaturates oleic acid (18:1n-9) to linoleic acid (18:2n-6), is a key enzyme in the arachidonic acid biosynthetic pathway. To determine if RNA interference (RNAi) by double-stranded RNA occurs in M. alpina 1S-4, we silenced the Δ12-desaturase gene. The silenced strains accumulate 18:2n-9, 20:2n-9, and Mead acid (20:3n-9), which are not detected in either the control strain or wild type strain 1S-4. The fatty acid composition of stable transformants was similar to that of Δ12-desaturation-defective mutants previously identified. Thus, RNAi occurs in M. alpina and could be used to alter the types and relative amounts of fatty acids produced by commercial strains of this fungus without mutagenesis or other permanent changes in the genetic background of the producing strains.     

Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions

The wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group confers conformational rigidity of mcm⁵s²U by largely fixing the C3′-endo ribose puckering, ensuring stable and accurate codon–anticodon pairing. We have identified five genes in Saccharomyces cerevisiae, YIL008w (URM1), YHR111w (UBA4), YOR251c (TUM1), YNL119w (NCS2) and YGL211w (NCS6), that are required for 2-thiolation of mcm⁵s²U. An in vitro sulfur transfer experiment revealed that Tum1p stimulated the cysteine desulfurase of Nfs1p, and accepted persulfide sulfurs from Nfs1p. URM1 is a ubiquitin-related modifier, and UBA4 is an E1-like enzyme involved in protein urmylation. The carboxy-terminus of Urm1p was activated as an acyl-adenylate (-COAMP), then thiocarboxylated (-COSH) by Uba4p. The activated thiocarboxylate can be utilized in the subsequent reactions for 2-thiouridine formation, mediated by Ncs2p/Ncs6p. We could successfully reconstitute the 2-thiouridine formation in vitro using recombinant proteins. This study revealed that 2-thiouridine formation shares a pathway and chemical reactions with protein urmylation. The sulfur-flow of eukaryotic 2-thiouridine formation is distinct mechanism from the bacterial sulfur-relay system which is based on the persulfide chemistry.     

Specific conformation and Ca(2+)-binding mode of yeast calmodulin: insight into evolutionary development

The vertebrate calmodulin is configured with two structurally independent globular lobes in N- and C-terminus, and a flexible central linker. Distinctly, two lobes of calmodulin from Saccharomyces cerevisiae (yCaM) interact and influence the Ca(2+)-binding profile of each other. We explored this further using the mutant proteins with eliminated Ca(2+)-binding ability in one of the lobes and found that the Ca(2+)-bound N-lobe associates with the Ca(2+)-free C-lobe to gain the Ca(2+) affinity of a wild-type level. Next, analysing series of C-terminal residue truncation mutant, we found that the truncation of C-terminal three residues induce the hyper Ca(2+) affinity. These residues are also important for the general structural behaviour of calmodulin, such as Ca(2+)-induced slow mobility shift in polyacrylamide gel electrophoresis and for the ability to activate Cmk1p (yeast calmodulin kinase). These suggest: (i) when Ca(2+) occupies only N-lobe, two lobes interact and form the stable intermediate leading to a proper level of Ca(2+) affinity; (ii) the C-terminal three residues are required to prohibit abnormal stabilization of the intermediate promoting abnormally high Ca(2+) affinity and for recognition of target enzymes. A model for Ca(2+) and target bindings of yCaM is proposed. Evolutional aspect concerning the biological significance of this model was discussed.     

Frequent occurrence of familial aggregations of high lipoprotein(a) levels associated with small apolipoprotein(a) isoforms

School-age children with high lipoprotein(a) [Lp(a)] levels were screened and family studies were conducted to examine the relationship between high Lp(a) levels and apolipoprotein(a) [apo(a)] isoforms in families. All the probands from 17 families had one of the A2 to A12 apo(a) isoforms, which are the smaller apo(a) isoforms of the 25 different isoforms thus far detected. The ratio of subjects with high plasma Lp(a) levels was 0.47 among the first-degree relatives. All 15 relatives with high plasma Lp(a) levels shared one of the small apo(a) isoforms with the proband in each family, while 16 of 17 relatives with normal Lp(a) levels did not. These data indicate the frequent occurrence of familial aggregations of high Lp(a) levels associated with one of the small apo(a) isoforms.     

Synchronized expression of FLOWERING LOCUS T between branches underlies mass flowering in Fagus crenata

Masting is the intermittent and synchronized production of a large amount of flower and seed in plant populations. This population-level phenomenon is caused by individual-level variability in reproduction and its synchrony between individuals. The variability at the individual level is induced by synchronized reproduction between branches within an individual because a tree is an assemblage of branches that are considered as semiautonomous units. However, there have been no empirical studies that quantify the degree of reproductive synchrony at the branch level within the same tree in masting species. Here, we evaluated the reproductive synchrony within individuals by monitoring flowering dynamics and expression level of a flowering-time gene at the branch-level in a typical masting species, Fagus crenata Blume. The 4-year census showed that the branch-level gene expression was highly variable between years and was strongly synchronized between branches. The branch-level synchrony in flowering-time gene expression was followed by coherent flowering cycle at the whole individual. To examine the causal relationship between gene expression and climatic factors, we performed a nonlinear statistical analysis called convergent cross-mapping using the time course data of gene expression and environmental variables. Our results indicated that the observed gene expression pattern was well cross-mapped by temperature or precipitation. However, this cross-mapping skill was lower than that of randomly generated seasonal dynamics, implying a combination of internal and external environmental signals is more likely to regulate gene expression dynamics in F. crenata. Our results provide the first empirical evidence that synchronized expression of a flowering-time gene between branches underlies integrated flowering behavior at the individual level.