Unique Regulatory Elements Research Articles

Advances and Challenges in Targeting TGF-β Isoforms for Therapeutic Intervention of Cancer: A Mechanism-Based Perspective.

The TGF-β family is a group of 25 kDa secretory cytokines, in mammals consisting of three dimeric isoforms (TGF-βs 1, 2, and 3), each encoded on a separate gene with unique regulatory elements. Each isoform plays unique, diverse, and pivotal roles in cell growth, survival, immune response, and differentiation. However, many researchers in the TGF-β field often mistakenly assume a uniform functionality among all three isoforms. Although TGF-βs are essential for normal development and many cellular and physiological processes, their dysregulated expression contributes significantly to various diseases. Notably, they drive conditions like fibrosis and tumor metastasis/progression. To counter these pathologies, extensive efforts have been directed towards targeting TGF-βs, resulting in the development of a range of TGF-β inhibitors. Despite some clinical success, these agents have yet to reach their full potential in the treatment of cancers. A significant challenge rests in effectively targeting TGF-βs' pathological functions while preserving their physiological roles. Many existing approaches collectively target all three isoforms, failing to target just the specific deregulated ones. Additionally, most strategies tackle the entire TGF-β signaling pathway instead of focusing on disease-specific components or preferentially targeting tumors. This review gives a unique historical overview of the TGF-β field often missed in other reviews and provides a current landscape of TGF-β research, emphasizing isoform-specific functions and disease implications. The review then delves into ongoing therapeutic strategies in cancer, stressing the need for more tools that target specific isoforms and disease-related pathway components, advocating mechanism-based and refined approaches to enhance the effectiveness of TGF-β-targeted cancer therapies.

Molecular regulatory mechanism of human myosin-7a

Myosin-7a is an actin-based motor protein essential for vision and hearing. Mutations of myosin-7a cause type 1 Usher syndrome, the most common and severe form of deafblindness in humans. The molecular mechanisms that govern its mechanochemistry remain poorly understood, primarily because of the difficulty of purifying stable intact protein. Here, we recombinantly produce the complete human myosin-7a holoenzyme in insect cells and characterize its biochemical and motile properties. Unlike the Drosophila ortholog that primarily associates with calmodulin (CaM), we found that human myosin-7a utilizes a unique combination of light chains including regulatory light chain, CaM, and CaM-like protein 4. Our results further reveal that CaM-like protein 4 does not function as a Ca2+ sensor but plays a crucial role in maintaining the lever arm's structural-functional integrity. Using our recombinant protein system, we purified two myosin-7a splicing isoforms that have been shown to be differentially expressed along the cochlear tonotopic axis. We show that they possess distinct mechanoenzymatic properties despite differing by only 11 amino acids at their N termini. Using single-molecule invitro motility assays, we demonstrate that human myosin-7a exists as an autoinhibited monomer and can move processively along actin when artificially dimerized or bound to cargo adaptor proteins. These results suggest that myosin-7a can serve multiple roles in sensory systems such as acting as a transporter or an anchor/force sensor. Furthermore, our research highlights that human myosin-7a has evolved unique regulatory elements that enable precise tuning of its mechanical properties suitable for mammalian auditory functions.

Lactose differentially modulates functionalities of antigen-presenting cells and T cells

Abstract Lactose is a milk sugar that appears to have immunomodulatory properties, but conflicting reports are available regarding its effects on inflammatory response and Treg cell functions. To delineate these aspects, we sought to test the hypothesis that lactose alters T-cell responses by modulating the functionalities of antigen-presenting cells (APCs). First, using the mouse macrophage cell line (RAW 264.7), we noted that lactose could reduce LPS-induced oxidative stress (P>0.05) without altering viability. Second, while the expression of MHC class II molecule was unchanged, an inverse relationship was noted with the costimulatory molecules [downregulated CD40 (P>0.005) and CD80 (P>0.005), and upregulated CD86 (P>0.005)], suggesting that lactose-mediated effects on APCs are heterogeneous and may involve unique regulatory elements for individual gene expression. Third, by testing the effects of lactose in the sorted mouse primary T cells, lactose moderately modulates T cell activation stimulated by anti-CD3 and anti-CD28, including IL-2 and IFN-γ production, but the cell viability was unaffected. However, upon the addition of IL-2, the reduced T cell activation was no longer apparent as evaluated by CFSE staining of CD4 and CD8 T cells, indicating that lactose’s effects on T cells may involve an IL-2-dependent mechanism. Taken together, our data support the notion that lactose could exert its effects on T cells directly or indirectly by modulating the APC functions that may have implications on health and disease.

Post-transcriptional elements within NLRP3 mRNA set the activation threshold of the inflammasome.

Abstract NOD-like receptor protein 3 (NLRP3) is an intracellular sensor and a major component of the canonical inflammasome pathway, which causes inflammation and cell death when activated by two temporally discrete signals. While novel putative activators of the NLRP3 inflammasome have been identified, the mechanisms that regulate expression of NLRP3 itself are less understood. Alternative polyadenylation (AP) is a mechanism by which cells modulate expression through varying the length of the 3′ untranslated region (3′UTR). Through AP, the longer forms may provide unique regulatory elements, that allow for differential regulation of mRNA stability and translation. Here we sought to thoroughly characterize the features of the NLRP3 3′UTR and hypothesized that AP may significantly control the threshold of inflammasome activation. We examined AP in THP-1 monocytes and found that they express both long and short forms, with the long form demonstrating decreased stability relative to the short. We have attributed these differences to the presence of AU-rich elements (ARE), as ablation of AREs results in increased stability of the long NLRP3 mRNA. Additionally, we have demonstrated that a known post-transcriptional regulator of NLRP3, miR-223, preferentially regulates the long transcript as well as augments the kinetics of pyroptotic cell death. These studies demonstrate that alternative polyadenylation of the 3′UTR of NLRP3 has a marked impact on the threshold of inflammasome activation.

Pro54DB: a database for experimentally verified sigma-54 promoters.

In prokaryotes, the σ54 promoters are unique regulatory elements and have attracted much attention because they are in charge of the transcription of carbon and nitrogen-related genes and participate in numerous ancillary processes and environmental responses. All findings on σ54 promoters are favorable for a better understanding of their regulatory mechanisms in gene transcription and an accurate discovery of genes missed by the wet experimental evidences. In order to provide an up-to-date, interactive and extensible database for σ54 promoter, a free and easy accessed database called Pro54DB (σ54 promoter database) was built to collect information of σ54 promoter. In the current version, it has stored 210 experimental-confirmed σ54 promoters with 297 regulated genes in 43 species manually extracted from 133 publications, which is helpful for researchers in fields of bioinformatics and molecular biology. Pro54DB is freely available on the web at http://lin.uestc.edu.cn/database/pro54db with all major browsers supported. greatchen@ncst.edu.cn or hlin@uestc.edu.cn

An Ikaros Promoter Element with Dual Epigenetic and Transcriptional Activities.

Ikaros DNA binding factor plays critical roles in lymphocyte development. Changes in Ikaros expression levels during lymphopoiesis are controlled by redundant but also unique regulatory elements of its locus that are critical for this developmental process. We have recently shown that Ikaros binds its own locus in thymocytes in vivo. Here, we evaluated the role of an Ikaros binding site within its major lympho-myeloid promoter. We identified an Ikaros/Ets binding site within a promoter sub-region that was highly conserved in mouse and human. Deletion of this binding site increased the percentage of the reporter-expressing mouse lines, indicating that its loss provided a more permissive chromatin environment. However, once transcription was established, the lack of this site decreased transcriptional activity. These findings implicate a dual role for Ikaros/Ets1 binding on Ikzf1 expression that is exerted at least through its promoter.

Unique molecular features of the HIV-1 subtype C enhancer and core promoter and their influence on the viral gene expression

Background The HIV-1 Subtype C, among other viral subtypes, is responsible for nearly 50% of the global infections including approximately 99% of the infections in India (UNAIDS 2012). HIV-1 subtype C is characterized by the presence of three NF-B binding sites in the enhancer as opposed to one or two such elements in other viral subtypes. Additionally, NF- Bs ite proximal to the Sp1 motifs, referred to here as the C-B site, is genetically distinct from the other two canonical NF- Bs ites (H-B sites). Furthermore, the Sp1III site proximal to the C-B motif also demonstrates subtype-specific genetic variations. Here, we examined the functional significance of the two unique regulatory elements, the C-B and the Sp1III motifs, for gene expression regulation from the viral promoter (Perkins et al. 1997). Methods and results Using several panels of reporter vectors expressing luciferase under the control of variant viral promoters, we examined gene expression in different mammalian cells under diverse activation conditions. The data confirm that the proximity and orientation of two sites, the C- Ba nd Sp1III motifs, are critical for optimal gene expression from the viral promoter. We found that a functional cooperation among the three NF-B sites is necessary for maximal promoter activity. Collectively, the data appeared to suggest that in addition to conferring a quantitative gain-offunction on the viral promoter, the presence of C-B site may have catalyzed associated genetic variation in the proximal Sp1III site through a positive selection pressure. To understand the functional association between these two sites under more relevant conditions, we constructed viral promoters consisting of only the C-B and the Sp1III sites, in the absence of other NF- Ba nd Sp1 sites. The subtype C specific Sp1III site showed higher magnitude of gene expression with the H- but not with the C- Bs ite. Experiments, using infectious viruses and the chromatin immunoprecipitation analysis, have also suggested the functional association between the two sites. In gel-shift assays the C-B site recruited the p50 and p65 heteroduplexes at a level comparable to that of the H- Bs ite. Importantly, given that the C- Bs ite is a G/C-centric motif, we asked and found that the C-B site is responsive to the p52:Bcl3 complex in contrast to the A/T-centric H-B site known to be more responsive to the p50:p65 complex promoter. Conclusions Collectively our data are suggestive of co-evolution of the two unique regulatory elements, the C- Ba nd the C-Sp1III motifs, that confer qualitative gain-of-function on the subtype C promoter thus probably playing a critical role towards the global predominance of the viral subtype. We further hypothesize that the C- Bs ite being aG /Ccentric motif, in combination with the two upstream H-B sites, confers a sustained and prolonged gene expression on HIV-1 subtype C viral promoter.

Unique translation initiation of mRNAs-containing TISU element

Translation Initiator of Short 5′ UTR (TISU) is a unique regulatory element of both transcription and translation initiation. It is present in a sizable number of genes with basic cellular functions and a very short untranslated region (5′ UTR). Here, we investigated translation initiation from short 5′ UTR mRNAs with AUG in various contexts. Reducing 5′ UTR length to the minimal functional size increases leaky scanning from weak and strong initiators but hardly affects translation initiation and ribosomal binding directed by TISU. Ribosome interaction with TISU mRNA is cap dependent and involves AUG downstream nucleotides that compensate for the absent 5′ UTR contacts. Interestingly, eIF1 inhibits cap-proximal AUG selection within weak or strong contexts but not within TISU. Furthermore, TISU-directed translation is unaffected by inhibition of the RNA helicase eIF4A. Thus, TISU directs efficient cap-dependent translation initiation without scanning, a mechanism that would be advantageous when intracellular levels of eIF1 and eIF4A fluctuate.

Distal Regions of the Human IFNG Locus Direct Cell Type-Specific Expression

Genes, such as IFNG, which are expressed in multiple cell lineages of the immune system, may employ a common set of regulatory elements to direct transcription in multiple cell types or individual regulatory elements to direct expression in individual cell lineages. By employing a bacterial artificial chromosome transgenic system, we demonstrate that IFNG employs unique regulatory elements to achieve lineage-specific transcriptional control. Specifically, a one 1-kb element 30 kb upstream of IFNG activates transcription in T cells and NKT cells but not in NK cells. This distal regulatory element is a Runx3 binding site in Th1 cells and is needed for RNA polymerase II recruitment to IFNG, but it is not absolutely required for histone acetylation of the IFNG locus. These results support a model whereby IFNG uses cis-regulatory elements with cell type-restricted function.

Recent advances in the photochemical control of protein function

Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented.

Distal regions of the human IFNG locus direct cell-type specific expression (88.12)

Abstract Genes, such as IFNG, which are expressed in multiple cell lineages of the immune system, may employ a common set of regulatory elements to direct transcription in multiple cell types or individual regulatory elements to direct expression in individual cell lineages. By employing a BAC transgenic system, we demonstrate that IFNG employs unique regulatory elements to achieve lineage specific transcriptional control. Specifically, a one 1-kb element 30 kb upstream of IFNG activates transcription in T cells and NKT cells but not NK cells, macrophages and dendritic cells. This distal regulatory element is a Runx3 binding site in Th1 cells, and is needed for RNA polymerase II recruitment to IFNG, but not for histone acetylation of the IFNG locus. These results support a model whereby IFNG utilizes distinct regulatory elements to achieve cell-type expression.

C-terminal Tail Residue Arg1400 Enables NADPH to Regulate Electron Transfer in Neuronal Nitric-oxide Synthase

The neuronal nitric-oxide synthase (nNOS) flavoprotein domain (nNOSr) contains regulatory elements that repress its electron flux in the absence of bound calmodulin (CaM). The repression also requires bound NADP(H), but the mechanism is unclear. The crystal structure of a CaM-free nNOSr revealed an ionic interaction between Arg(1400) in the C-terminal tail regulatory element and the 2'-phosphate group of bound NADP(H). We tested the role of this interaction by substituting Ser and Glu for Arg(1400) in nNOSr and in the full-length nNOS enzyme. The CaM-free nNOSr mutants had cytochrome c reductase activities that were less repressed than in wild-type, and this effect could be mimicked in wild-type by using NADH instead of NADPH. The nNOSr mutants also had faster flavin reduction rates, greater apparent K(m) for NADPH, and greater rates of flavin auto-oxidation. Single-turnover cytochrome c reduction data linked these properties to an inability of NADP(H) to cause shielding of the FMN module in the CaM-free nNOSr mutants. The full-length nNOS mutants had no NO synthesis in the CaM-free state and had lower steady-state NO synthesis activities in the CaM-bound state compared with wild-type. However, the mutants had faster rates of ferric heme reduction and ferrous heme-NO complex formation. Slowing down heme reduction in R1400E nNOS with CaM analogues brought its NO synthesis activity back up to normal level. Our studies indicate that the Arg(1400)-2'-phosphate interaction is a means by which bound NADP(H) represses electron transfer into and out of CaM-free nNOSr. This interaction enables the C-terminal tail to regulate a conformational equilibrium of the FMN module that controls its electron transfer reactions in both the CaM-free and CaM-bound forms of nNOS.

The v-SNARE Vti1a Regulates Insulin-stimulated Glucose Transport and Acrp30 Secretion in 3T3-L1 Adipocytes

Regulated exocytosis in adipocytes mediates key functions, exemplified by insulin-stimulated secretion of peptides such as adiponectin and recycling of intracellular membranes containing GLUT4 glucose transporters to the cell surface. Using a proteomics approach, the v-SNARE Vti1a (vps10p tail interacting 1a) was identified by mass spectrometry in purified GLUT4-containing membranes. Insulin treatment of 3T3-L1 adipocytes decreased the amounts of both Vti1a and GLUT4 in these membranes, confirming that Vti1a is a component of insulin-sensitive GLUT4-containing vesicles. In the basal state, endogenous Vti1a colocalizes exclusively with perinuclear GLUT4. Although Vti1a has previously been reported to be a v-SNARE localized in the trans-Golgi network, treatment with brefeldin A failed to significantly modify Vti1a or GLUT4 localization while completely dispersing Golgi and trans-Golgi network marker proteins. Furthermore, depletion of Vti1a protein in cultured adipocytes through small interfering RNA-based gene silencing significantly inhibited both adiponectin secretion and insulin-stimulated deoxyglucose uptake. Taken together, these results suggest that the v-SNARE Vti1a may regulate a step common to both GLUT4 and Acrp30 trafficking in 3T3-L1 adipocytes.

Perspectives for artificial insemination and genomics to improve global swine populations

Civilizations throughout the world continue to depend on pig meat as an important food source. Approximately 40% of the red meat consumed annually worldwide (94 million metric tons) is pig meat. Pig numbers (940 million) and consumption have increased consistent with the increasing world population (FAO 2002). In the past 50 years, research guided genetic selection and nutrition programs have had a major impact on improving carcass composition and efficiency of production in swine. The use of artificial insemination (AI) in Europe has also had a major impact on pig improvement in the past 35 years and more recently in the USA. Several scientific advances in gamete physiology and/or manipulation have been successfully utilized while others are just beginning to be applied at the production level. Semen extenders that permit the use of fresh semen for more than 5 days post-collection are largely responsible for the success of AI in pigs worldwide. Transfer of the best genetics has been enabled by use of AI with fresh semen, and to some extent, by use of AI with frozen semen over the past 25 years. Sexed semen, now a reality, has the potential for increasing the rate of genetic progress in AI programs when used in conjunction with newly developed low sperm number insemination technology. Embryo cryopreservation provides opportunities for international transport of maternal germplasm worldwide; non-surgical transfer of viable embryos in practice is nearing reality. While production of transgenic animals has been successful, the low level of efficiency in producing these animals and lack of information on multigene interactions limit the use of the technology in applied production systems. Technologies based on research in functional genomics, proteomics and cloning have significant potential, but considerable research effort will be required before they can be utilized for AI in pig production. In the past 15 years, there has been a coordinated worldwide scientific effort to develop the genetic linkage map of the pig with the goal of identifying pigs with genetic alleles that result in improved growth rate, carcass quality, and reproductive performance. Molecular genetic tests have been developed to select pigs with improved traits such as removal of the porcine stress (RYR1) syndrome, and selection for specific estrogen receptor (ESR) alleles. Less progress has been made in developing routine tests related to diseases. Major research in genomics is being pursued to improve the efficiency of selection for healthier pigs with disease resistance properties. The sequencing of the genome of the pig to identify new genes and unique regulatory elements holds great promise to provide new information that can be used in pig production. AI, in vitro embryo production and embryo transfer will be the preferred means of implementing these new technologies to enhance efficiency of pig production in the future.

Identification of regulatory elements in the Plasmodium falciparum genome

There is little information regarding regulatory sequences in the newly sequenced genome of the malaria parasite, Plasmodium falciparum. Thus, for the first time, a bioinformatic strategy was utilized to identify regulatory elements in this genome using the P. falciparum heat shock protein (hsp) gene family as a model system. Our analysis indicates that the P. falciparum hsp genes do not contain standard eukaryotic regulatory elements. However, a novel G-rich regulatory element named the G-box was identified upstream of several P. falciparum hsp genes and the P. yoelii yoelii, P. berghei, and P. vivax hsp86 genes. Remarkably, the Plasmodium sp. G-boxes were required for maximal reporter gene expression in transient transfection assays. The G-box is not homologous to known eukaryotic elements, and is the best-defined functional element elucidated from Plasmodium sp. Our analysis also revealed several other elements necessary for reporter gene expression including an upstream sequence element, the region surrounding the transcription start site, and the 5' and 3' untranslated regions. These data demonstrate that unique regulatory elements are conserved in the genomes of Plasmodium sp., and demonstrate the feasibility of bioinformatic approaches for their identification.

Identification of a Novel Set of Genes Regulated by a Unique Liver X Receptor-α-mediated Transcription Mechanism

We have reported previously that liver X receptor-alpha (LXRalpha) can mediate a novel cAMP-dependent increase in renin and c-myc gene transcription by binding as a monomer to a unique regulatory element termed the cAMP-negative response element (CNRE). To determine whether this novel action of LXRalpha has global implications on gene regulation, we employed expression profiling to identify other genes regulated by this unique mechanism. Here we report the existence of a set of known and unknown transcripts regulated in parallel with renin. Querying the Celera Mouse Genome Assembly revealed that a majority of these genes contained the consensus CNRE. We have confirmed the functionality of these CNREs by competition for LXRalpha binding via electrophoretic mobility shift assays (EMSA) and by the use of CNRE decoy molecules documenting the abolishment of the cAMP-mediated gene induction. Taken together, these results demonstrate that the interaction between cAMP-activated LXRalpha and the CNRE enhancer element is responsible for widespread changes in gene expression and identify a set of LXRalpha/cAMP-regulated genes that may have important biological implications.

SPACRCAN in the interphotoreceptor matrix of the mouse retina: molecular, developmental and promoter analysis

SPACRCAN 1 1 Human SPACRCAN gene is designated by uppercase italicized letters. Mouse SPACRCAN gene is designated by italicized letters with uppercase for the initial letter and lowercase for the rest. SPACRCAN protein is designated by uppercase letters in standard fonts. is a novel proteoglycan present in the interphotoreceptor matrix (IPM) of the rat and human retina that resists aqueous extraction through its binding to hyaluronan. The purpose of this study was: to clone mouse Spacrcan; to characterize the promoter elements; to define the deduced amino acid sequence; to establish the time of Spacrcan expression during retinal development; and to determine the time of appearance and distribution of SPACRCAN protein. Spacrcan cDNA clone was obtained through PCR amplification of a mouse retina cDNA library, and RT-PCR amplification and 5′RACE of mouse retina RNA. The deduced polypeptide sequence of mouse SPACRCAN contains a signal peptide at the N-terminal, seven N-link glycosylation sites, numerous potential O-linked glycosylation sites in a central mucin-like domain, two glycosaminoglycan attachment sites, five potential hyaluronan-binding motifs, two epidermal growth factor-like domains, and a hydrophobic stretch of 23 amino acids near the C-terminal. Comparison of the genomic structure of mouse and human SPACRCAN showed significant structure conservation. Analysis of the promoter region revealed several important putative regulatory elements including a Ret-1/PCE-1 element, an 11 base motif for Crx binding, six copies of PIRE, a Ret-4 element, three copies of AP-1, a CRE element, and five copies of GATA3. Northern blot analysis and immunohistochemistry were used to determine the tissue specificity of Spacrcan mRNA and to localize SPACRCAN in developing retina. Spacrcan mRNA is expressed in both retina and pineal gland and was detectable as early as embryonic day 15. The protein is first detectable in the IPM at postnatal day 8 where it increases in concert with the extension of photoreceptor inner and outer segments from the outer retinal surface. The presence of several unique regulatory elements in the promoter region and characteristic molecular features shared with the orthologue in human and rat suggest an important functional role of SPACRCAN in the IPM. The time of appearance of the SPACRCAN protein during retinal development suggests that this matrix protein may establish the extracellular microenvironment into which photoreceptor outer segments are elaborated.

The recombination hot spot chi is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme.

Homologous recombination in Escherichia coli is stimulated at DNA sequences known as chi sites. Stimulation requires the multifunctional RecBCD enzyme, which is both a helicase and a 3' --> 5' exonuclease. Upon recognition of a properly oriented chi site, the 3' --> 5' exonuclease activity is attenuated. Here we show that in addition to attenuation of the 3' --> 5' exonuclease activity, recognition of chi by the RecBCD enzyme also up-regulates a nuclease activity of the opposite polarity, resulting in an enzyme that now preferentially degrades 5' --> 3'. These results demonstrate that chi is a unique regulatory element that converts the antirecombinogenic form of the RecBCD enzyme into a recombinogenic form by causing two distinct enzymatic changes: attenuation of the 3' --> 5' nuclease activity, and up-regulation of the 5' --> 3' nuclease activity. The consequence of chi recognition is the production of a recombination intermediate possessing a 3'-ssDNA overhang terminating at the chi sequence. This processing of a dsDNA end to a 3'-ssDNA overhang parallels that which occurs during the initation of homologous recombination in other pathways in E. coli, and in other organisms such as the yeast Saccharomyces cerevisiae.

The recombination hotspot χ is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme

The RecBCD enzyme is a multifunctional enzyme that is essential for homologous recombination in E. coli. In vitro, the RecBCD enzyme degrades linear double-stranded DNA nonspecifically during the process of unwinding the double-stranded DNA. Here we demonstrate that this DNA degradation is asymmetric, with the strand that is 3′ terminal at the entry site of RecBCD enzyme being degraded much more vigorously than the 5′ terminal strand. Furthermore, interaction with the recombination hotspot χ causes an attenuation of the nuclease activity but not of the hellcase activity and is accompanied by a pause of RecBCD enzyme at the χ site. These results demonstrate that χ is a unique regulatory element that acts by controlling the degradative function of RecBCD enzyme and, thereby, enhancing its recombination function.

Cis-acting regulatory elements involved in oxygen and light control of puc operon transcription in Rhodobacter sphaeroides

Transcriptional expression of the puc operon in Rhodobacter sphaeroides is highly regulated by both oxygen and light. The approximately 600 bp of DNA upstream of the 5' ends of the two puc-specific transcripts encompasses two functionally separable cis-acting domains. The upstream regulatory region (URS) (-629 to -150) is responsible for enhanced transcriptional regulation of puc operon expression by oxygen and light. The more proximal upstream region (downstream regulatory region [DRS]), containing putative promoter(s), operator(s), and factor binding sites (-150 to -1), is involved in unenhanced transcriptional expression of the puc operon under aerobic and anaerobic conditions. Thus, the DRS shows normal derepression of puc operon expression when cells are shifted from aerobic to photosynthetic growth conditions in terms of percent change but does not show the potential range of expression that is only observed when elements of the URS are present. Because of these observations, we have made a distinction between anaerobic control (describing the shift) and oxygen control (describing the magnitude of derepression). Promoter(s) and/or activator function(s) of the puc operon is associated with a 35-bp DNA region between -92 and -57. Homologous sequences at -10 to -27 and -35 to -52 appear to involve additional regulatory elements: mutations at -12 (A to C) and -26 (G to A) result in partial derepression of puc operon expression under conditions of high aeration. Both point mutations require the upstream regulatory region (-629 to -150) to be present in cis for partial derepression of puc operon transcription under aerobic conditions. Immediately upstream of the promoter and/or activator region are overlapping consensus sequences for IHF (integratin host factor) and FNR (fumarate nitrate reductase) (-105 to -129). This region appears to be essential for enhanced expression of the puc operon. Thus, these two regulatory domains (URS and DRS) appear to involve approximately seven unique regulatory elements. In addition, the data reveal a direct interaction between the URS (-629 to -150) and the DRS (-150 to -1).