-
Jeong-Sun Seo,
Hyonyong Chong,
Hyun Seok Park,
Kyoung-Oh Yoon,
Cholhee Jung,
Jae Joon Kim,
Jin Han Hong,
Hyungtae Kim,
Jeong-Hyun Kim,
Joon-Il Kil, [......],
Jung-Soon Lee,
Su-Jung Jin,
Hye-Won Um,
Hee-Jong Lee,
Soo-Jin Oh,
Jae Young Kim,
Hyung Lyun Kang,
Se Yong Lee,
Kye Joon Lee, Hyen Sam Kang
[show abstract]
[hide abstract]
ABSTRACT: We report the complete genome sequence of Zymomonas mobilis ZM4 (ATCC31821), an ethanologenic microorganism of interest for the production of fuel ethanol. The genome consists of 2,056,416 base pairs forming a circular chromosome with 1,998 open reading frames (ORFs) and three ribosomal RNA transcription units. The genome lacks recognizable genes for 6-phosphofructokinase, an essential enzyme in the Embden-Meyerhof-Parnas pathway, and for two enzymes in the tricarboxylic acid cycle, the 2-oxoglutarate dehydrogenase complex and malate dehydrogenase, so glucose can be metabolized only by the Entner-Doudoroff pathway. Whole genome microarrays were used for genomic comparisons with the Z. mobilis type strain ZM1 (ATCC10988) revealing that 54 ORFs predicted to encode for transport and secretory proteins, transcriptional regulators and oxidoreductase in the ZM4 strain were absent from ZM1. Most of these ORFs were also found to be actively transcribed in association with ethanol production by ZM4.
Nature Biotechnology 02/2005; 23(1):63-8. · 23.27 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In the yeast Saccharomyces diastaticus, expression of the STA1 gene, which encodes an extracellular glucoamylase, is activated by the specific DNA-binding activators Flo8, Mss11, Ste12, and Tec1 and the Swi/Snf chromatin-remodeling complex. Here we show that Flo8 interacts physically and functionally with Mss11. Flo8 and Mss11 bind cooperatively to the inverted repeat sequence TTTGC-n-GCAAA (n = 97) in UAS1-2 of the STA1 promoter. In addition, Flo8 and Mss11 bind indirectly to UAS2-1 of the STA1 promoter by interacting with Ste12 and Tec1, which bind to the filamentation and invasion response element (FRE) in UAS2-1. Furthermore, our findings indicate that the Ste12, Tec1, Flo8, and Mss11 activators and the Swi/Snf complex bind sequentially to the STA1 promoter, as follows: Ste12 and Tec1 bind first to the FRE, whereby they recruit the Swi/Snf complex to the STA1 promoter. Next, the Swi/Snf complex enhances Flo8 and Mss11 binding to UAS1-2. In the final step, Flo8 and Mss11 directly promote association of RNA polymerase II with the STA1 promoter to activate STA1 expression. In the absence of glucose, the levels of Flo8 and Tec1 are greatly increased, whereas the abundances of two repressors, Nrg1 and Sfl1, are reduced, suggesting that the balance of transcriptional regulators may be important for determining activation or repression of STA1 expression.
Molecular and Cellular Biology 12/2004; 24(21):9542-56. · 5.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In the yeast Saccharomyces diastaticus, expression of the STA1 gene, which encodes an extracellular glucoamylase, is negatively regulated by glucose. Here we demonstrate that glucose-dependent repression of STA1 expression is imposed by both Sfl1 and Nrg1, which serve as direct transcriptional repressors. We show that Nrg1 acts only on UAS1, and Sfl1 acts only on UAS2, in the STA1 promoter. When bound to its specific site, Sfl1 (but not Nrg1) prevents the binding to UAS2 of two transcriptional activators, Ste12 and Tec1, required for STA1 expression. We also found that Sfl1 contributes to STA1 repression by binding to the promoter and inhibiting the expression of FLO8, a gene that encodes a third transcriptional activator involved in STA1 expression. In addition, we show that the levels of Nrg1 and Sfl1 increase in glucose-grown cells, suggesting that the effects of glucose are mediated, at least in part, through an increase in the abundance of these repressors. NRG1 and SFL1 expression requires the Srb8-11 complex, and correspondingly, the Srb8-11 complex is also necessary for STA1 repression. However, our evidence indicates that the Srb8-11 complex does not associate with either the SFL1 or the NRG1 promoter and thus plays an indirect role in activating NRG1 and SFL1 expression.
Molecular and Cellular Biology 10/2004; 24(17):7695-706. · 5.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The pga gene of Escherichia coli W ATCC11105 encodes a penicillin G acylase whose expression is regulated at both the transcriptional and post-transcriptional level. In this work we have shown that PaaX is the repressor of pga expression, and we have identified its binding consensus as TGATTC(N27)GAATCA. We conclude that the process of "PAA induction" actually involves relief of pga from repression by PaaX. Other features of the pga promoter have also been characterized. (i) It has a native class III cAMP-receptor protein (CRP)-dependent promoter with two CRP-binding sites. (ii) The downstream CRP-binding site II has higher affinity. (iii) Binding of cAMP-CRP to both sites (I + II) is required for maximal expression. We have also shown that the PaaX-binding site overlaps with the CRP-binding site I. This implies that PaaX and the cAMP-CRP compete for binding to the region around the CRP-binding site I and therefore have antagonistic effects on pga expression.
Journal of Biological Chemistry 09/2004; 279(32):33253-62. · 4.77 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The expression of STA genes that encode extracellular glucoamylase isozymes is repressed in most laboratory Saccharomyces cerevisiae strains, which are believed to contain an undefined repressor, designated STA10. To identify the regulator involved in STA10 repression, we investigate the FLO8, MSN1, MSS11, STE12, and TEC1 genes. The Deltaflo8 or Deltamss11 deletion mutants in the sta10 genetic background exhibit both a loss of flocculation ability and a reduction in extracellular glucoamylase activity, as in the STA10 strain. Moreover, the STA10 repression is suppressed completely or partially by the introduction of a single copy of the FLO8 or MSS11 genes. Sequence analysis and complementation testing of the STA10 strain reveal that it has an inactive, mutated flo8-1 allele. A random spore analysis and transplacement (allele replacement) experiment confirms that the repressive phenotype of STA10 is due to the amber mutation of the transcriptional activator, FLO8.
Current Genetics 01/2004; 44(5):261-7. · 2.56 Impact Factor
-
Seung-Whan Kim,
Cheolho Cheong,
Young-Chang Sohn,
Young-Hwa Goo,
Wan Je Oh,
Jung Hwan Park,
So Young Joe, Hyen-Sam Kang,
Duk-Kyung Kim,
Changwon Kee,
Jae Woon Lee,
Han-Woong Lee
[show abstract]
[hide abstract]
ABSTRACT: ASC-2, a recently isolated transcriptional coactivator molecule, stimulates transactivation by multiple transcription factors, including nuclear receptors. We generated a potent dominant negative fragment of ASC-2, encompassing the N-terminal LXXLL motif that binds a broad range of nuclear receptors. This fragment, termed DN1, specifically inhibited endogenous ASC-2 from binding these receptors in vivo, whereas DN1/m, in which the LXXLL motif was mutated to LXXAA to abolish the receptor interactions, was inert. Interestingly, DN1 transgenic mice but not DN1/m transgenic mice exhibited severe microphthalmia and posterior lenticonus with cataract as well as a variety of pathophysiological phenotypes in many other organs. Our results provide a novel insight into the molecular and histopathological mechanism of posterior lenticonus with cataract and attest to the importance of ASC-2 as a pivotal transcriptional coactivator of nuclear receptors in vivo.
Molecular and Cellular Biology 01/2003; 22(24):8409-14. · 5.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: TheuvsH DNA repair gene ofAspergillus nidulans has been cloned by complementation of theuvsH77 mutation with a cosmid library containing genomic DNA inserts from a wild-type strain. Methylmethane sulfonate (MMS)-resistant transformants were obtained on medium containing 0.01% MMS, to whichuvsH mutants exhibit high sensitivity . Retransformation ofuvsH77 mutants with the rescued cosmids from the MMS-resistant transformants resulted in restoration of both UV and MMS resistance to wild-type levels. Nucleotide sequence analysis of the genomic DNA and cDNA of theuvsH gene shows that it has an open reading frame (ORF) of 1329 bp, interrupted by two introns of 51 and 61 bp. A 2.4 kb transcript of theuvsH gene was detected by Northern blot analysis. Primer extension analysis revealed that transcription starts at 31 by upstream from the translation initiation codon. This gene encodes a predicted polypeptide of 443 amino acids, which has two unique zinc finger motifs. The proposed polypeptide displays 39% identity to theNeurospora crassa UVS-2 protein and 24% identity to theSaccharomyces cerevisiae RAD18 protein. The sequence similarity is particularly high in three domains. One zinc finger (RING finger) motif is located in the first domain close to the N-terminus. The other zinc finger motif is in the second domain. In the third domain, the mutation sites in both theuvsH77 anduvsH304 alleles were identified. TheuvsH77 allele has three base changes, resulting in a Thr Pro alteration at amino acid 267 and Glu Len at 268. TheuvsH304 mutation is caused by one base change, resulting in an Asn Asp alteration at amino acid 274.
MGG - Molecular and General Genetics 06/1995; 248(2):174-181.
-
[show abstract]
[hide abstract]
ABSTRACT: The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure(1), but may be involved in the initiation of SV40 DNA replication in a sequence-specific manner. Two mutants, base-substituted at a primase initiation site nucleotide 5214(2), showed dramatic decreases in DNA replication in monkey cells. Despite earlier reports to the contrary (3,4), disruption of the cruciform configuration or polypyrimidine tract does not invariably lead to lack of replication function, as some mutants unable to form this structure replicate normally. Gel retention assays and DNase I footprinting with the nuclear proteins of monkey cells showed that the 5′GAGGC3′ pentanucleotide repeats on either side of early palindrome domain interact with monkey nuclear protein. The early palindrome domain may affect the interaction of SV40 DNA with nuclear protein, and participate in SV40 DNA replication.
