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Results for “regulatory evolution”

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PubMed2004

The evolution of the Drosophila sex-determination pathway.

The molecular complexity of the Drosophila somatic sex-determination pathway poses formidable intellectual challenges for attempts to explain its evolutionary origins. Here we present a reconstruction of how this regulatory cascade might have evolved in a step-by-step fashion. We illustrate how mutations in genes, which were already part of the pathway or were recruited as new regulators of the pathway, were favored by sexual selection acting on the discriminatory sex-determining signal. This allows us to explain the major features of the pathway, including multiple promoter sites, alternative splicing patterns, autoregulation, and stop codons. Our hypothesis is built on the available data from Drosophila and other insect species, and we point out where it is amenable to further experimental and comparative tests.

Alternative Splicing↗

PubMed2005

Bacteriophage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium.

Salmonella spp. are Gram-negative bacteria which cause infections ranging from mild, self-limiting enterocolitis to systemic (typhoid) disease. Recent work has established that the genetic makeup varies considerably between different Salmonella strains. Phages play an important role in this diversity. In fact, Salmonella has emerged as a prime example for the involvement of virulence factor encoding phages in the emergence of new epidemic strains. Among other virulence factors, Salmonella enterica utilizes two specialized protein secretion systems termed type III secretion systems (TTSS) to deliver effector proteins into host cells which manipulate host cell signaling cascades. These two TTSS and several effectors are encoded within Salmonella pathogenicity islands 1 and 2. Some effectors including SopE, SspH1, SseI and SopE2 are encoded by phages or phage remnants. These phage-encoded effectors seem to be transferred between different Salmonella strains. They have attracted much interest because they might contribute to the evolution of Salmonella spp. Here we will focus on SopEPhi which encodes the SPI-1 effector SopE. It provides an excellent example to illustrate how horizontally transferred effector proteins are integrated into the complex regulatory network of a TTSS in a recipient bacterium. Additional data supporting the hypothesis are presented. This is a prerequisite to allow optimization of the bacterium host cell interaction by reassortment of the phage-encoded effector protein repertoire.

Bacterial Proteins↗

PubMed1995

Abnormalities in the PRAD1 (CYCLIN D1/BCL-1) oncogene are frequent in cervical and vulvar squamous cell carcinoma cell lines.

BACKGROUND: CYCLIN D1, a cell-cycle control gene, recently has been shown to be identical to an oncogene alternatively known as BCL-1 and PRAD1 and implicated in centrocytic lymphomas and parathyroid adenomas, respectively. PRAD1 complexes to the product of the retinoblastoma (Rb) tumor suppressor gene, an event followed by Rb inactivation. Squamous cell carcinomas of the cervix and vulva are gynecologic tumors in which human papillomaviruses have been implicated as an initiating event, and proteins derived from these viruses also complex with an inactivate Rb. Because of the overlap in some of the molecular processes mediated by human papillomaviruses and by the PRAD1 oncogene, the authors analyzed the PRAD1 (CYCLIN D1/BCL-1) genomic structure and expression in vulvar and cervical squamous cell carcinoma cell lines. METHODS: PRAD1 DNA and PRAD1 mRNA expression were assessed by Southern and Northern blotting, respectively, in 13 squamous cell carcinoma cell lines of gynecologic origin (10, cervical cancer; 3, vulvar cancer). RESULTS: We found low baseline levels of a 4.5-kb PRAD1 transcript in a series of control cell lines, which were derived from normal fibroblasts, various hematologic malignancies, and a choriocarcinoma. PRAD1 mRNA overexpression (> or = 10-fold greater than that in control lines) was seen in all three vulvar carcinoma cell lines, two of which also showed amplification (5-fold and > 10-fold) of PRAD1 genomic sequences. Abnormalities of PRAD1 also were seen in 4 of the 10 cervical cancer cell lines and included overexpression of PRAD1 transcripts (3-9-fold) in 3 lines and rearrangement of PRAD1 DNA in an additional line that, however, did not shown any aberration in PRAD1 mRNA as discernible by Northern blotting. PRAD1 abnormalities were observed in three of the four cervical cell lines derived from metastatic sites and in one of the six cervical lines derived from primary tissue. CONCLUSIONS: Seven of 13 squamous cell lines of gynecologic origin showed abnormalities of PRAD1. These abnormalities included amplification and rearrangement of DNA and overexpression of mRNA. The role of PRAD1 as a cell-cycle regulatory gene and its interactions with the Rb tumor suppressor gene suggests that PRAD1 deregulation may be a significant molecular event in the evolution of these tumors.

Blotting, Northern↗

PubMed1995

Sequence variability within the tobacco retrotransposon Tnt1 population.

Retroviruses consist of populations of different but closely related genomes referred to as quasispecies. A high mutation rate coupled with extremely rapid replication cycles allows these sequences to be highly interconnected in a rapid equilibrium. It is not known if other retroelements can show a similar population structure. We show here that when the tobacco Tnt1 retrotransposon is expressed, its RNA is not a unique sequence but a population of different but closely related sequences. Nevertheless, this highly variable population is not in a rapid equilibrium and could not be considered as a quasispecies. We have thus named the structure presented by Tnt1 RNA quasispecies-like. We show that the expression of Tnt1 in different situations gives rise to different populations of Tnt1 RNA sequences, suggesting an adaptive capacity for this element. The analysis of the variability within the total genomic population of Tnt1 elements shows that mutations frequently occur in important regulatory elements and that defective elements are often produced. We discuss the implications that this population structure could have for Tnt1 regulation and evolution.

Base Sequence↗

PubMed1983

Behavioural strategies in the regulation of food choice.

The maintenance of nutrient and energy balance in the body depends on both metabolic and behavioural mechanisms, and is integrated by the brain. The regulatory system was developed by natural selection and not by mechanical engineers. Thus, rather than having unitary mechanisms regulating intake of each nutrient, evolution has incorporated and used a multitude of behavioural traits and metabolic adaptations. The criterion for inclusion was that each one conferred a persisting advantage in the prevailing environment. Behavioural strategies in food choice include: innate preference for sweetness and an aversion towards bitter tastes, a hesitancy towards unknown foods, preference for variety among familiar foods, and a special ability (long delay learning) to acquire information about both positive and negative metabolic consequences of eating different foods. In man, these more basic mechanisms interact with and are complemented by cognitive, social and cultural influences on food choice. In a very few cases, such as regulation of energy, sodium and (perhaps) protein intakes, feeding behaviour is also guided by signals from specific internal receptors. However, for most nutrients, appetites seem to be non-specific and learned. Using studies on the regulation of protein intake from our own and other laboratories as examples, this review illustrates how innate preferences, learning, social interactions, metabolic adaptation and diet-induced changes in brain neurotransmitter metabolism can all play a role in subjective decisions about what to eat.

Animals↗

PubMed1990

Comparison of the expression of two highly homologous members of the soybean ribulose-1,5-bisphosphate carboxylase small subunit gene family.

Two soybean ribulose-1,5-bisphosphate carboxylase small subunit (SSU) genes, SRS1 and SRS4, are highly homologous over a region that includes 4 kb of 5' and 1 kb of 3' flanking sequences. The expression of these genes was compared using synthetic oligonucleotide probes. Analysis of a soybean leaf cDNA library indicates that SRS1 and SRS4 are the most highly expressed members of the soybean SSU gene family. Similar changes were observed in the RNA levels for these genes in response to white light, far-red light and darkness, although SRS1 was expressed at a four-fold higher level in total RNA than SRS4 under all conditions. However, nuclear run-on assays indicate that SRS1 is transcribed at a lower rate than SRS4, which suggests that SRS1 RNA is more stable. S1 nuclease analysis and oligonucleotide directed RNase H cleavage indicate that transcripts from both genes are polyadenylated within two principle regions separated by 35 nt. Sequence analysis of 16 independent cDNA clones identified seven different polyadenylation sites, and six of these sites lie within these two regions. Although SRS1 RNA was poorly recovered during poly(A)+ fractionation, RNase H cleavage experiments showed that transcripts from SRS1 and SRS4 had similar poly (A) tail lengths ranging from 0 to 220 nt. In addition, and despite differences in the untranslated leader sequences, SRS1 and SRS4 RNAs are assembled into polysomes with equal efficiencies. The overall similarity in expression patterns for these two genes further illustrates the coordinate evolution of individual members of a SSU gene family and is consistent with the proposal that gene conversion homogenizes both the coding and regulatory regions of these genes.

Base Sequence↗

PubMed2006

Evolutionary divergence of LFY function in the mustards Arabidopsis thaliana and Leavenworthia crassa.

LEAFY (LFY), a transcription factor involved in the regulation of flower development in Arabidopsis thaliana, has been identified as a candidate gene in the diversification of plant architecture in Brassicaceae. Previous research with Leavenworthia crassa, which produces solitary flowers in the axils of rosette leaves, has shown that the L. crassa LFY ortholog, LcrLFY, rescues most aspects of flower development in A. thaliana but showed two novel traits: flowers produced additional petals and inflorescences produced terminal flowers. In this paper, we explore the molecular mechanisms responsible for these novel phenotypes. We used microarray hybridizations to identify 32 genes differentially expressed between a transgenic LcrLFY line and a control transgenic LFY line. Of particular interest, TERMINAL FLOWER 1 (TFL1) transcripts were found at elevated levels in LcrLFY lines. To distinguish regulatory versus functional changes within the LcrLFY locus, reciprocal chimeric transgenes between LcrLFY and LFY were constructed. These lines implicate divergence of LcrLFY cis-regulation as the primary cause of both novel transgenic phenotypes but implicate divergence of LcrLFY protein function as the primary cause of elevated TFL1 levels. Taken together these results show that LcrLFY has diverged from A. thaliana in both the cis-regulatory and protein-coding regions and imply that molecular coevolution of LcrLFY and the L. crassa TFL1 ortholog, LcrTFL1, contributed to the evolution of rosette flowering.

Arabidopsis↗

PubMed2026

Engineering Bacillus Subtilis for Efficient Biosynthesis of Riboflavin: Current Knowledge and Future Perspectives.

Riboflavin is an essential water-soluble vitamin that serves as a precursor for the biosynthesis of the flavin cofactors FMN and FAD, which play pivotal roles in numerous redox and energy metabolism reactions. With the growing global demand for sustainable vitamin production, microbial fermentation has become an attractive alternative to chemical synthesis due to its environmental and economic advantages. Among microbial hosts, Bacillus subtilis has emerged as a leading cell factory for riboflavin production owing to its GRAS status, well-characterized genetics, and efficient protein secretion system. This review provides a comprehensive overview of recent advances in metabolic engineering strategies to enhance riboflavin biosynthesis in B. subtilis. Key topics include strengthening biosynthetic and precursor pathways, relieving feedback inhibition, balancing metabolic flux and cell growth, employing adaptive laboratory evolution, and utilizing omics-guided optimization and 13C metabolic flux analysis. Moreover, the integration of synthetic biology tools such as riboswitch engineering, regulatory element design, and high-throughput screening has significantly accelerated strain improvement. Despite remarkable progress, challenges remain in achieving precise regulatory control, optimizing multi-gene expression, and enhancing genome integration efficiency. Future research combining multi-omics data, synthetic regulatory design, and machine learning-driven predictive modeling is expected to further advance the development of intelligent B. subtilis cell factories. However, the practical implementation of these systems remains constrained by the metabolic burden of overproduction and the lack of universal regulatory models that can predict strain performance across varying industrial scales.

Bacillus subtilis↗

PubMed2005

Conservation of the drought-inducible DS2 genes and divergences from their ASR paralogues in solanaceous species.

The drought-inducible DS2 genes of potatoes are members of the ASR (abscisic acid, stress and ripening) gene family. Previously it was shown that expression of DS2 genes is highly dehydration-specific in potato leaves, is not inducible by cold, heat, salt, hypoxia or oxidative stresses, and is independent of abscisic acid (ABA). Now it is shown that StDS2 does not respond either to sucrose or any plant hormones. Conservation of DS2 genes with this unique mode of regulation was studied in the solanaceous species with different relationships to potatoes. DS2 orthologues were identified by DNA sequence alignment in the closely related Lycopersicon and Capsicum species but not in the more distantly related Nicotiana sp. DNA and RNA gel blot analysis revealed the presence of a gene highly homologous to the potato gene StDS2 in tomato (LeDS2) with the same desiccation-specific expression in leaves and organ-specific expression in flowers and green fruits. The LeDS2 promoter was isolated and found to be almost identical in sequence with the promoter of StDS2, except for a 45-bp insertion in tomato. In contrast, no gene highly similar to StDS2 was detected in Nicotiana species on DNA gel blots. Neither StDS2 nor LeDS2 promoter regions were able to confer expression for the beta-glucuronidase (GUS) reporter gene in transgenic tobacco plants indicating that the trans regulatory factors necessary for DS2 expression are not conserved either in Nicotiana tabacum. These data suggest a narrow species-specificity and late evolution of the DS2-type genes within the family Solanaceae.

Base Sequence↗

PubMed2001

The expression profiles of neurotrophins and their receptors in rat and chicken tissues during development.

Neurotrophic factors are target-derived proteins that promote the survival and differentiation of the innervating neurons. Increasing evidence indicate the involvement of these factors and receptors during the formation and maturation of the neuromuscular junction. To gain further insight on the expression pattern of these factors and receptors in developing spinal cord and skeletal muscle during the critical stages of synapse formation, a systematic study was performed with chicken and rat tissues using Northern blot analysis. The expression of all the neurotrophins was detected in skeletal muscle early in development, coincidental with the appearance of their corresponding receptors in the spinal cord. Taken together, the similar regulatory patterns observed in both rat and chicken tissues suggest that the potential roles of neurotrophins at the neuromuscular synapse are conserved throughout evolution.

Animals↗

PubMed2005

Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster.

In natural populations of Drosophila melanogaster, there are many amylase (AMY) isozymes encoded by the duplicated genes, but their adaptive significance remains unclear. One approach to elucidate this issue is to understand the molecular basis of functional differences between the allelic classes. In this study, the effects of nucleotide polymorphism in 5'-flanking (cis-regulatory) and coding regions on AMY activity were examined, both on glucose and starch food media and in larvae and adults, using three chimeric Amylase (Amy) genes, Amy(c111), Amy(c161) and Amy(fc661). In this notation, the first number in the superscript indicates the sequence of the 5'-flnaking region (similar to Amy1 or Amy6), the second number refers to the coding region and the third number to the 3'-flanking region. We found that effect of nucleotide polymorphism in the coding region differed between larvae and adults. In larvae, the coding sequence of the Amy6 allele resulted in higher AMY activity than that of Amy1 allele, indicating the post-transcriptional differences between them. The cis-regulatory region derived from the Amy6 allele resulted in higher AMY activity in both larvae and adults. Thus, two fitness components, developmental time and productivity, were measured to examine whether polymorphism in the cis-regulatory region between the two alleles has an effect on them, but no significant difference was detected. We raise the implications for the evolution of subfunctionalization in multigene families.

Alleles↗

PubMedDate not supplied

Developmental system drift and flexibility in evolutionary trajectories.

The comparative analysis of homologous characters is a staple of evolutionary developmental biology and often involves extrapolating from experimental data in model organisms to infer developmental events in non-model organisms. In order to determine the general importance of data obtained in model organisms, it is critical to know how often and to what degree similar phenotypes expressed in different taxa are formed by divergent developmental processes. Both comparative studies of distantly related species and genetic analysis of closely related species indicate that many characters known to be homologous between taxa have diverged in their morphogenetic or gene regulatory underpinnings. This process, which we call "developmental system drift" (DSD), is apparently ubiquitous and has significant implications for the flexibility of developmental evolution of both conserved and evolving characters. Current data on the population genetics and molecular mechanisms of DSD illustrate how the details of developmental processes are constantly changing within evolutionary lineages, indicating that developmental systems may possess a great deal of plasticity in their responses to natural selection.

Animals↗

PubMed2000

Histone acetylation and gene expression analysis of sex lethal mutants in Drosophila.

The evolution of sex determination mechanisms is often accompanied by reduction in dosage of genes on a whole chromosome. Under these circumstances, negatively acting regulatory genes would tend to double the expression of the genome, which produces compensation of the single-sex chromosome and increases autosomal gene expression. Previous work has suggested that to reduce the autosomal expression to the female level, these dosage effects are modified by a chromatin complex specific to males, which sequesters a histone acetylase to the X. The reduced autosomal histone 4 lysine 16 (H4Lys16) acetylation results in lowered autosomal expression, while the higher acetylation on the X is mitigated by the male-specific lethal complex, preventing overexpression. In this report, we examine how mutations in the principal sex determination gene, Sex lethal (Sxl), impact the H4 acetylation and gene expression on both the X and autosomes. When Sxl expression is missing in females, we find that the sequestration occurs concordantly with reductions in autosomal H4Lys16 acetylation and gene expression on the whole. When Sxl is ectopically expressed in Sxl(M) mutant males, the sequestration is disrupted, leading to an increase in autosomal H4Lys16 acetylation and overall gene expression. In both cases we find relatively little effect upon X chromosomal gene expression.

Acetylation↗

PubMed2026

Di-, tri-, and tetranucleotide frequencies covary with lifespan and genome size across protostome invertebrates.

Animal lifespans span orders of magnitude, yet how genome sequence covaries with lifespan remains poorly characterized outside vertebrates. Although promoter CpG density has been linked to vertebrate longevity due to its gene-regulatory function through DNA methylation, it is unclear whether such patterns are promoter- and CpG-specific, or if they reflect broader sequence evolution. We curated maximum lifespan estimates for 466 protostome species spanning eight phyla with available genome assemblies and quantified mono-, di-, tri-, and tetranucleotide composition across whole genomes, intergenic regions, and six gene-associated regions (two upstream regions, exons, introns, and two downstream regions) defined using Benchmarking Universal Single-Copy Orthologs. Dinucleotide observed/expected ratios showed significant associations with lifespan and genome size in different ways. Lifespan-associated motifs were most pronounced in gene-associated non-coding regions, especially in introns and downstream regions, whereas genome-size effects were strongest in whole-genome and intergenic sequence. Tri- and tetranucleotide observed/expected ratios broadly recapitulated this regional organization. In contrast, GC content was not associated with lifespan across regions, indicating that the observed signals are not explained by mononucleotide composition but instead by how those nucleotides are arranged into short sequence motifs. These results suggest that lifespan and genome size show distinct but overlapping associations with regional sequence composition across invertebrate species and that lifespan-associated motif evolution extends beyond vertebrate promoter methylation architectures.

CpG density↗

PubMed1983

The determinants of social policy. A case study: regulating health and safety at the workplace in Sweden.

This article presents an analysis and critique of the "technocratic" view of occupational health and safety policies, which sees the values of the personnel of the "postindustrial" regulatory agencies as the most important determinant of those policies. An alternate position is put forth which explains those occupational health and safety policies as primarily the result of different degrees of political power of the two major classes (capital and labor) and the set of influences exerted on the regulatory agencies by the instruments (e.g., political parties, unions, trade organizations) of those classes. It is shown how an analysis of the historical evolution of those classes in Sweden and their conflict in both civil and political societies better explains the Swedish occupational health and safety policies than the mere analysis of the regulators' views. It is concluded that the occupational health and safety policies in Sweden are not identical to the U.S. policies--as the "technocratic" theorists assume--but rather they offer more protection to the workers than the U.S. ones. This situation is a result of labor's greater power in Sweden than in the United States. The different class formations and class behavior in both societies are compared, and the implications of this comparison for occupational health and safety policies are discussed.

Accidents, Occupational↗

PubMed2003

Bloodborne pathogens. What you need to know--Part I.

Since the emergence of the AIDS epidemic in the early 1980s, progressive regulatory strategies have been aimed at decreasing the risk of bloodborne pathogen exposures in health care workers. It is important to understand the evolution of these bloodborne pathogen strategies that have been vital to maintaining the health and safety of workers in potentially high risk environments. Occupational health clinicians need to communicate to employees how each of these strategies has helped decrease the day to day risks health care workers potentially face. Standard precautions remain one of the best ways health care workers can protect themselves against exposures. It has been more than 15 years since standard precautions were first introduced. Some health care workers have become lax in using these very simple techniques. Occupational health clinicians need to remind employees of the importance of taking care of themselves by using proper protective equipment. Recent federal and state needle safe legislation has heightened employee and employer awareness about the importance of new, safer medical devices. These devices [table: see text] must be used properly to truly decrease the potential risks to health care workers. Occupational health care clinicians can be pivotal in the forefront of needle safety initiatives in their institution. Occupational health nurses in health care settings should be active members of needle safe and bloodborne pathogen committees and participate in product evaluation. Clinicians should advocate for employees to be properly trained to use new devices and reinforce the importance of using safety devices properly to employees. The risks of transmission for HIV, HBV, and HCV are indisputable in environments where workers are potentially exposed to blood or body fluids. Knowledge about how exposure occurs, the risks of transmission in health care workers, and preventive strategies available can assist the employee to work safely without unnecessary fear or anxiety. Part II of this article (February 2003) is a more indepth discussion about each of the three bloodborne pathogens of greatest concern to health care workers. The general prevalence, risk groups, prophylaxis, and treatment of HBV, HCV, and HIV are elaborated. Common blood tests for each of these pathogens are also explained.

Blood-Borne Pathogens↗

PubMed1992

Human erythroid 5-aminolevulinate synthase. Gene structure and species-specific differences in alternative RNA splicing.

Erythroid 5-aminolevulinate synthase (ALAS) is expressed exclusively in differentiating erythroid cells as the principal isoform of the enzyme to catalyze the first step of the heme biosynthetic pathway. The human gene encoding this isozyme was isolated from a cosmid library, and its structure was characterized with restriction mapping followed by sequencing of fragments. The gene is 22 kilobases long and has 11 exons. Exon 2 encodes the N-terminal signal sequence required for mitochondrial import, exons 3 and 4 encode a variable portion of the N-terminal end, and exons 5-11 the highly conserved C-terminal portion of the mature protein, respectively. Enzymatic amplification of human reticulocyte RNA using PCR techniques revealed two erythroid ALAS mRNA transcripts predicted to encode both the prototypical 64-kDa isoform as well as a novel smaller isoform with a deletion of 37 amino acids near the N terminus. The two mRNA isoforms are generated by alternative splicing of exon 4 and are expressed in fetal erythroid cells as well as at all stages of erythroid development tested, so that there is no evidence of differentiation-specific regulation of exon 4 splicing. However, striking species-specific differences were observed in that alternative splicing of exon 4 was found in man but not dog or mouse; also, the previously described alternative splicing within exon 3 in mouse was not observed in man. This transcript heterogeneity suggests the existence of erythroid ALAS protein isoforms with potentially distinct functional or regulatory roles. The occurrence of species-specific splicing in the least conserved region of the enzyme may reflect another mechanism of gene evolution in eukaryotes.

5-Aminolevulinate Synthetase↗

PubMed2006

Compassionate caring.

Beginning with a concerned society, from individuals, to visiting nurse associations, and to publicly traded corporations, home care and hospice have been meaningful threads in the American fabric for over a hundred years. Today, advances in technology, a burgeoning regulatory environment, and universal health care cost concerns make continued change expected and certain. While external health care environmental pressures incessantly shape the evolution of home care and hospice, a central value lives on in the heart of what we do as caregivers, in what is nowtermed our "industry". It is a value we must safeguard from evolutionary extinction.

Community Health Nursing↗