Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes.

Variable number tandem repeats (VNTRs) in mitochondrial DNA (mtDNA) of Lentinula edodes are of interest for their role in mtDNA variation and their application as genetic marker. Sequence analysis of three L. edodes mtDNAs revealed the presence of VNTRs of two categories. Type I VNTRs consist of two types of repeat units in a symmetric distribution, whereas Type II VNTRs contain tandemly arrayed repeats of 7- or 17-bp DNA sequences. The number of repeat units was variable depending on the mtDNA of different strains. Using the variations in VNTRs as a mitochondrial marker and the A mating type as a nuclear type marker, we demonstrated that one of the two nuclei in the donor dikaryon preferentially enters into the monokaryotic cytoplasm to establish a new dikaryon which still retains the mitochondria of the monokaryon in the individual mating. Interestingly, we found 6 VNTRs with newly added repeat units from the 22 mates, indicating that elongation of VNTRs occurs during replication of mtDNA. This, together with comparative analysis of the repeating pattern, enables us to propose a mechanistic model that explains the elongation of Type I VNTRs through reciprocal incorporation of basic repeat units, 5'-TCCCTTTAGGG-3' and its complementary sequence (5'-CCCTAAAGGGA-3').

Diversity of A mating type in Lentinula edodes and mating type preference in the cultivated strains.

Diversity of A mating type in Lentinula edodes has been assessed by analysis of A mating loci in 127 strains collected from East Asia. It was discovered that hypervariable sequence region with an approximate length of 1 kb in the A mating locus, spanning 5' region of HD2-intergenic region-5' region of HD1, could represent individual A mating type as evidenced by comprehensive mating analysis. The sequence analysis revealed 27 A mating type alleles from 96 cultivated strains and 48 alleles from 31 wild strains. Twelve of them commonly appeared, leaving 63 unique A mating type alleles. It was also revealed that only A few A mating type alleles such as A1, A4, A5, and A7 were prevalent in the cultivated strains, accounting for 62.5% of all A mating types. This implies preferred selection of certain A mating types in the process of strain development and suggests potential role of A mating genes in the expression of genes governing mushroom quality. Dominant expression of an A mating gene HD1 was observed from A1 mating locus, the most prevalent A allele, in A1-containing dikaryons. However, connections between HD1 expression and A1 preference in the cultivated strains remain to be verified. The A mating type was highly diverse in the wild strains. Thirty-six unique A alleles were discovered from relatively small and confined area of mountainous region in Korean peninsula. The number will further increase because no A allele has been recurrently observed in the wild strains and thus newly discovered strain will have good chances to contain new A allele. The high diversity in small area also suggests that the A mating locus has evolved rapidly and thus its diversity will further increase.

Nucleus-Selective Expression of Laccase Genes in the Dikaryotic Strain of Lentinula edodes.

In mating of Lentinula edodes, dikaryotic strains generated from certain monokaryotic strains such as the B2 used in this study tend to show better quality of fruiting bodies regardless of the mated monokaryotic strains. Unlike B2, dikaryotic strains generated from B16 generally show low yields, with deformed or underdeveloped fruiting bodies. This indicates that the two nuclei in the cytoplasm do not contribute equally to the physiology of dikaryotic L. edodes, suggesting an expression bias in the allelic genes of the two nuclei. To understand the role of each nucleus in dikaryotic strains, we investigated single nucleotide polymorphisms (SNPs) in laccase genes of monokaryotic strains to reveal nuclear origin of the expressed mRNAs in dikaryotic strain. We performed reverse transcription PCR (RT-PCR) analysis using total RNAs extracted from dikaryotic strains (A5B2, A18B2, and A2B16) as well as from compatible monokaryotic strains (A5, A18, and B2 for A5B2 and A18B2; A2 and B16 for A2B16). RT-PCR results revealed that Lcc1, Lcc2, Lcc4, Lcc7, and Lcc10 were the mainly expressed laccase genes in the L. edodes genome. To determine the nuclear origin of these laccase genes, the genomic DNA sequences in monokaryotic strains were analyzed, thereby revealing five SNPs in Lcc4 and two in Lcc7. Subsequent sequence analysis of laccase mRNAs expressed in dikaryotic strains revealed that these were almost exclusively expressed from B2-originated nuclei in A5B2 and A18B2 whereas B16 nucleus did not contribute to laccase expression in A2B16 strain. This suggests that B2 nucleus dominates the expression of allelic genes, thereby governing the physiology of dikaryons.

Proteomic Insights into Sulfur Metabolism in the Hydrogen-Producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1.

The hyperthermophilic archaeon Thermococcus onnurineus NA1 has been shown to produce H2 when using CO, formate, or starch as a growth substrate. This strain can also utilize elemental sulfur as a terminal electron acceptor for heterotrophic growth. To gain insight into sulfur metabolism, the proteome of T. onnurineus NA1 cells grown under sulfur culture conditions was quantified and compared with those grown under H2-evolving substrate culture conditions. Using label-free nano-UPLC-MSE-based comparative proteomic analysis, approximately 38.4% of the total identified proteome (589 proteins) was found to be significantly up-regulated (≥1.5-fold) under sulfur culture conditions. Many of these proteins were functionally associated with carbon fixation, Fe-S cluster biogenesis, ATP synthesis, sulfur reduction, protein glycosylation, protein translocation, and formate oxidation. Based on the abundances of the identified proteins in this and other genomic studies, the pathways associated with reductive sulfur metabolism, H2-metabolism, and oxidative stress defense were proposed. The results also revealed markedly lower expression levels of enzymes involved in the sulfur assimilation pathway, as well as cysteine desulfurase, under sulfur culture condition. The present results provide the first global atlas of proteome changes triggered by sulfur, and may facilitate an understanding of how hyperthermophilic archaea adapt to sulfur-rich, extreme environments.

Genome Sequence of Arthrobacter sp. MWB30, Isolated from a Crude Oil-Contaminated Seashore.

We report here the draft genome sequence of Arthrobacter sp. MWB30 strain, isolated from a crude oil-contaminated seashore in Tae-an, South Korea, which is able to degrade the crude oil and its derivatives. The draft genome sequence of 4,647,008 bp provides a resource for the identification of crude oil-degrading mechanisms in strain MWB30.

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium.

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil-contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%.

Sensing and responding to UV-A in cyanobacteria.

Ultraviolet (UV) radiation can cause stresses or act as a photoregulatory signal depending on its wavelengths and fluence rates. Although the most harmful effects of UV on living cells are generally attributed to UV-B radiation, UV-A radiation can also affect many aspects of cellular processes. In cyanobacteria, most studies have concentrated on the damaging effect of UV and defense mechanisms to withstand UV stress. However, little is known about the activation mechanism of signaling components or their pathways which are implicated in the process following UV irradiation. Motile cyanobacteria use a very precise negative phototaxis signaling system to move away from high levels of solar radiation, which is an effective escape mechanism to avoid the detrimental effects of UV radiation. Recently, two different UV-A-induced signaling systems for regulating cyanobacterial phototaxis were characterized at the photophysiological and molecular levels. Here, we review the current understanding of the UV-A mediated signaling pathways in the context of the UV-A perception mechanism, early signaling components, and negative phototactic responses. In addition, increasing evidences supporting a role of pterins in response to UV radiation are discussed. We outline the effect of UV-induced cell damage, associated signaling molecules, and programmed cell death under UV-mediated oxidative stress.

Proteome analyses of hydrogen-producing hyperthermophilic archaeon Thermococcus onnurineus NA1 in different one-carbon substrate culture conditions.

Thermococcus onnurineus NA1, a sulfur-reducing hyperthermophilic archaeon, is capable of H(2)-producing growth, considered to be hydrogenogenic carboxydotrophy. Utilization of formate as a sole energy source has been well studied in T. onnurineus NA1. However, whether formate can be used as its carbon source remains unknown. To obtain a global view of the metabolic characteristics of H(2)-producing growth, a quantitative proteome analysis of T. onnurineus NA1 grown on formate, CO, and starch was performed by combining one-dimensional SDS-PAGE with nano UPLC-MS(E). A total of 587 proteins corresponding to 29.7% of the encoding genes were identified, and the major metabolic pathways (especially energy metabolism) were characterized at the protein level. Expression of glycolytic enzymes was common but more highly induced in starch-grown cells. In contrast, enzymes involved in key steps of the gluconeogenesis and pentose phosphate pathways were strongly up-regulated in formate-grown cells, suggesting that formate could be utilized as a carbon source by T. onnurineus NA1. In accordance with the genomic analysis, comprehensive proteomic analysis also revealed a number of hydrogenase clusters apparently associated with formate metabolism. On the other hand, CODH and CO-induced hydrogenases belonging to the Hyg4-II cluster, as well as sulfhydrogenase-I and Mbx, were prominently expressed during CO culture. Our data suggest that CO can be utilized as a sole energy source for H(2) production via an electron transport mechanism and that CO(2) produced from catabolism or CO oxidation by CODH and CO-induced hydrogenases may subsequently be assimilated into the organic carbon. Overall, proteomic comparison of formate- and CO-grown cells with starch-grown cells revealed that a single carbon compound, such as formate and CO, can be utilized as an efficient substrate to provide cellular carbon and/or energy by T. onnurineus NA1.

Cyanobacterial phytochrome Cph2 is a negative regulator in phototaxis toward UV-A.

We investigated the wavelength dependence and photon-fluence rate response relationship for phototaxis of wild-type and a cyanobacterial phytochrome 2 (cph2) mutant in cyanobacterium Synechocystis sp. PCC 6803. Compared to wild-type, the cph2 mutant exhibited maximal activity for positive phototaxis at the near-UV spectral range. Two cysteine to serine substitutions in two chromophore-binding domains showed a similar cph2 mutant phenotype under UV-A. Epistasis of a pixJ mutation over a cph2 mutation implied that pixJ gene acts downstream of the cph2 gene with respect to UV-A-induced positive phototaxis. Therefore, we suggest that Cph2 is essential for the inhibition of positive phototaxis toward UV-A.

Sensing UV/blue: pterin as a UV-A absorbing chromophore of cryptochrome.

Cyanobacteria sense and respond to changes in an ambient light environment using highly specialized photoreceptors coupled to signal transduction pathways. Synechocystis sp. PCC 6803 is currently used as a model system to study light signal transduction in cyanobacteria. Recently, several important players, including photoreceptors and other signaling partners, have been identified in Synechocystis sp. PCC 6803. However, the nature of the molecules that act as UV/blue light sensors (and their downstream signaling mechanism) has not been elucidated. It has been postulated that pterins might serve as possible photoreceptor pigments for some behavioral responses induced by UV/blue light. By investigating the photomovement of wild-type and a pgtA mutant to UV/blue light, we demonstrated that cyanopterin is indeed involved in inhibiting negative phototaxis under UV/blue light. In this addendum, we provide additional evidence showing that the UV/blue action spectrum of the phototactic response coincides with the fluorescence spectrum of the in vivo cyanobacterial cryptochrome, DASH. Based on these results, we discuss the potential role of pterin as a UV-A absorbing chromophore of the cryptochrome in Synechocystis sp. PCC 6803.

The role of cyanopterin in UV/blue light signal transduction of cyanobacterium Synechocystis sp. PCC 6803 phototaxis.

We analyzed the effects of inactivating the pteridine glycosyltransferase gene (pgtA) on the photomovement of the cyanobacterium Synechocystis sp. PCC 6803 under different light conditions. The pgtA mutant displayed abnormal photomovement under UV-A/blue light. In particular, the pgtA mutant showed a negative phototactic response under UV-A (315-400 nm), whereas the wild-type did not show any photomovement. Inhibition of pterin biosynthesis by N-acetylserotonin (NAS), an inhibitor of sepiapterin reductase, also inhibited a positive phototactic response of the wild-type under white and blue light. In addition, negative phototaxis of the pgtA mutant was observed under UV-A/blue light in the presence of NAS. These results indicated that the product of the PgtA enzyme, cyanopterin, is involved in the inhibition of the negative phototaxis of the wild-type by sensing the UV-A. However, 2,4-diamino-6-hydroxypyrimidine-mediated inhibition of GTP cyclohydrolase I, the rate-limiting enzyme for pterin biosynthesis, significantly increased the positive phototaxis toward UV-A in the wild-type and the pgtA mutant. Furthermore, we measured the action spectrum of phototaxis in vivo for the wild-type and pgtA mutant. Maximal activity of the wild-type was at 300, 380 and 440 nm, indicating absorption by pterins and flavin. In particular, the UV-A/ blue peak at 380 and 440 nm obtained from the action spectrum of phototaxis was found to be closely correlated with the in vitro absorption spectrum previously reported for the cyanobacterial cryptochrome DASH. By investigating the photomovement of the wild-type and pgtA mutant to UV and blue light, we suggest that pterin can function as the chromophore of putative UV/blue photoreceptor(s) in cyanobacterial phototaxis.

Calcium is involved in photomovement of cyanobacterium Synechocystis sp. PCC 6803.

The unicellular cyanobacterium Synechocystis sp. PCC 6803 (Syn6803) exhibits photomovement through gliding motility. For a better understanding of photomovement in Syn6803, we examined the effects of Ca2+ on photoorientation and motility using a computer-assisted videomicroscope motion analysis system. When calcium ion was chelated from the basic motility medium by adding 0.5 mM ethylene glycol-bis-(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA), the photoorientation was completely inhibited, whereas the gliding motility remained approximately 70% of the control. Photoorientation impaired by EGTA was nearly recovered within 30 min upon addition of 1 mM Ca2+. The recovery of photoorientation by Ca2+ was mimicked by either Mn2+ or Mg2+ but not by Ba2+ or Sr2+. Lanthanum ion at 10 microM completely inhibited both phototactic orientation and gliding motility of Syn6803. Furthermore, pimozide (voltage-gated L-type calcium channel inhibitor), orthovanadate (calcium efflux blocker) and A23187 (calcium ionophore) partially inhibited phototactic orientation and gliding motility. Interestingly, photoorientation was prevented with increasing concentrations of calmodulin antagonist such as trifluoperazine (TFP) and chlorpromazine, but gliding motility was inhibited in proportion to the concentration of TFP. The results we present strongly indicate that Ca2+ plays a significant role in regulating the photomovement of Syn6803.