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How do bacteria tune transcription termination efficiency?

Bacterial operons often contain intergenic transcription terminators that terminate some, but not all, RNA polymerase molecules. In these operons, the level of terminator readthrough determines downstream gene expression and helps establish protein ratios among co-regulated genes. Despite its critical role in maintaining stoichiometric gene expression, terminator strength remains difficult to predict from DNA sequence. The necessary features of a major class of bacterial terminators - intrinsic terminators - have been known for half a century, but a strong sequence-function model has yet to be developed. Here, we summarize high-throughput approaches for probing the sequence determinants of intrinsic termination efficiency and discuss the impact of trans-acting factors on this sequence-function relationship. Building on the main lessons from these studies, we map out the experimental challenges that must be circumvented to establish a quantitative model for termination efficiency.

Transcription Termination, Genetic

A computational model for bacteriophage ϕX174 gene expression.

Bacteriophage ϕX174 has been widely used as a model organism to study fundamental processes in molecular biology. However, several aspects of ϕX174 gene regulation are not fully resolved. Here we construct a computational model for ϕX174 and use the model to study gene regulation during the phage infection cycle. We estimate the relative strengths of transcription regulatory elements (promoters and terminators) by fitting the model to transcriptomics data. We show that the specific arrangement of a promoter followed immediately by a terminator, which occurs naturally in the ϕX174 genome, poses a parameter identifiability problem for the model, since the activity of one element can be partially compensated for by the other. We also simulate ϕX174 gene expression with two additional, putative transcription regulatory elements that have been proposed in prior studies. We find that the activities of these putative elements are estimated to be weak, and that variation in ϕX174 transcript abundances can be adequately explained without them. Overall, our work demonstrates that ϕX174 gene regulation is well described by the canonical set of promoters and terminators widely used in the literature.

Gene Expression Regulation, Viral

Mapping of class II promoter sites utilized in vitro by T7-specific RNA polymerase on bacteriophage T7 DNA.

Restriction endonuclease Bgl II cleaves T7 DNA at a unique site (28.76% on the standard T7 map), yielding two fragments of molecular weights 18.9 x 10(6) (A) and 7.6 x 10(6) (B). Fragment B, representing the leftmost portion of the genome, has been purified by zone sedimentation. Transcription of fragment B by T7-specific RNA polymerase gives only r-strand-specific RNA. Analysis of the products by polyacrylamide gel electrophoresis reveals four major RNA species which have apparent molecular weights of 2.1 x 10(6), 1.36 x 10(6), 0.85 x 10(6) and 0.125 x 10(6), respectively. Each of these RNAs is reduced in size when transcription is carried out with fragment B, which has been shortened by treatment with Escherichia coli exonuclease III. Therefore, each of the transcripts must be terminated at the right end of fragment B. Analysis of the molecular weights of the four transcripts produced from whole and from exonucleolytically shortened fragment B suggests that these transcripts are read from promoters located at 13.5, 18.9, 22.6, and 27.9%, respectively, on the standard T7 map. Hence, there are at least four promoters governing the transcription of the class II region. Transcripts initiated at these promoters on intact T7 DNA appear to read through the class II and part of the class III genetic region and terminate at the strong terminator for T7-specific RNA polymerase near 61%. Transcription of fragment B which has been cleaved with the restriction endonuclease Hpa I seems to activate a fifth promoter for T7-specific RNA polymerase. This promoter appears to be identical to the promoter previously described by Oakley and Coleman (Proc. Natl. Acad. Sci. U.S.A. 74:4266-4270, 1977) that maps near 15% on the standard T7 map. Little or no RNA is read from T7 Bgl II fragment B, which has a mobility expected for a transcript read from this promoter. However, upon cleavage with Hpa I, this promoter is utilized approximately 10-fold more efficiently than the other class II promoters. The mechanism of this activation is not yet known.

Coliphages

Genetic mechanism accounting for precise immunoglobulin domain deletion in a variant of MPC 11 myeloma cells.

A variant of the MPC 11 cell line, M 311, produces a short immunoglobulin heavy chain. When compared with the parental gamma 2b heavy chain, M 311 was found to have a carboxyl terminal deletion comprising the CH3 domain. The COOH-terminal cyanogen bromide (CNBr) cleavage fragment of M 311 is identical to a corresponding segment ofa parental heavy chain CNBr fragment, with the exception of a substitution of asparagine for lysine at the COOH-terminal residue. This observation enabled prediction of both the parental DNA sequence in this region and the genetic mechanism which generated the variant, a frameshift followed by premature termination. This hypothesis is supported by studies of the DNA sequence of the MPC 11 gamma 2b constant region gene.

Animals

5'-terminal nucleotide sequences of the Rauscher leukemia virus and gibbon ape leukemia virus genomes exhibit a high degree of correspondence.

The 5'-terminal regions of gibbon ape leukemia virus-Hall's Island and Rauscher murine leukemia virus have been completely sequenced. The chain length for the 5'-terminal region of Rauscher murine leukemia virus is 140 nucleotides, and that for gibbon ape leukemia virus-Hall's Island is 144 nucleotides. An alignment of the sequences maximizing the number of ocrrespondences with the minimum introduction of gaps shows 81% nucleotide matches. From the complementary RNA, secondary structures of this region have been proposed. These data demonstrate the conservation of the 5'-terminal genetic sequences of these viruses and strongly reinforce the concept that viruses of murine origin and viruses of the gibbon ape leukemia virus-Simian sarcoma-associated virus group are closely related.

Animals

[Spontaneous transformation characteristics of Bacillus subtilis bacteria. I. The relatively low transforming activity of spontaneously released DNA for markers located close to the origin and termination points of chromosome replication].

Relative efficiencies of spontaneous Bacillus subtilis transformation for markers placed in different areas of the cell chromosome were studied. As donor of genetic material, an untransformable strain BD224 trpC2 thr5 rec4 was used during its early log-phase. It was found that for markers placed near points of origin and termination of the chromosome replication the relative transformation efficiencies are significantly lower than those in the case of transformation with DNA extracted from the same donor cells. If a contact of spontaneously released DNA with the recipient cells was delayed for about 60 minutes ("separate" experiment) this difference proved to be less pronounced for ade16 placed near the origin, but remained practically unchanged for metB placed near the termination point. The results obtained can be explained by permanent attachment of chromosome regions, carrying "origin" and "termination" points, to a cytoplasmic membrane. During spontaneously release of cellular genetic material, "origin" and "terminal" DNA fragments carrying ade16 and metB respectively, can retain the contact with components of cell membrane. Hence, their penetration in the recipient cell and (or) participation in recombination can be violated. The first of two fragments becomes free from structurating substances more easy.

Bacillus subtilis

Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.

Essentiality studies have traditionally focused on coding regions, often overlooking other small genetic regulatory elements. To address this, we combined transposon libraries containing promoter or terminator sequences to obtain a high-resolution essentiality map of a genome-reduced bacterium, at near-single-nucleotide precision when considering non-essential genes. By integrating temporal transposon-sequencing data by k-means unsupervised clustering, we present a novel essentiality assessment approach, providing dynamic and quantitative information on the fitness contribution of different genomic regions. We compared the insertion tolerance and persistence of the two engineered libraries, assessing the local impact of transcription and termination on cell fitness. Essentiality assessment at the local base-level revealed essential protein domains and small genomic regions that are either essential or inaccessible to transposon insertion. We also identified structural regions within essential genes that tolerate transposon disruptions, resulting in functionally split proteins. Overall, this study presents a nuanced view of gene essentiality, shifting from static and binary models to a more accurate perspective. Additionally, it provides valuable insights for genome engineering and enhances our understanding of the biology of genome-reduced cells.

DNA Transposable Elements

Three species of polyoma virus tumor antigens share common peptides probably near the amino termini of the proteins.

Detergent extracts of polyoma virus-infected mouse cells contain three major proteins of approximately 100,000--108,000 (100K), 55,000 (55K) and 21,500 (22K) daltons, which react with sera obtained from rats carrying tumors induced by the virus. A comparison of the 35S-methionine-, 3H-leucine- and 3H-proline-labeled tryptic peptides of each of these proteins by cation-exchange chromatography followed by descending paper chromatography has shown that: at least five peptides are shared by all three T-reactive proteins; at least three peptides are shared by the 55K and 22K proteins, but not by the 100K protein; at least three peptides are found only in the 22K protein; at least six peptides are found only in the 55K protein; and at least sixteen peptides are found only in the 100K protein. The results are consistent with the hypothesis that the polypeptide chains of the 100K, 55K and 22K dalton tumor antigens of polyoma virus share a common virus-coded amino terminal region. The data also suggest that there is a portion of the polypeptide chains (probably immediately adjacent to the common amino terminal region of the molecules) that is shared by the 55K and 22K proteins, but not by the 100K protein (perhaps because this portion of the genetic information is spliced out of the messenger RNA coding for the 100K protein). The facts that all the peptides common to the 100K and 55K proteins are also found in the 22K protein and are thus assigned to the common amino terminal region of the molecules, and that there are several peptides unique to the 100K protein, as well as several peptides unique to the 55K protein, suggest that the presumed carboxy terminal portion of the polypeptide chain of the 100K protein is considerably, if not entirely, different from that of the 55K protein.

Amino Acid Sequence

Restriction-enzyme-cleavage maps of bacteriophage M13. Existence of an intergenic region on the M13 genome.

Replicative form DNA of bacteriophage M13 was cleaved into specific fragments by an endonuclease isolated from Hemophilus aegyptius (endoR.HaeII) and an endonuclease from Arthrobacter luteus (endoR.AluI). The fragments were ordered as to construct a circular map of the phage M13 genome by: (a) using each fragment as a primer for the synthesis in vitro of its respective neighbour and (b) digesting the isolated fragments with the Hemophilus aegyptius enzyme endoR.HaeII or the Hemophilus aphirophilus enzyme endoR.HapII and subsequent analysis of the overlapping sets of fragments. The resulting physical map was correlated with the M13 genetic map by marker rescue experiments with amber mutant phage DNAs and purified wild-type fragments. From the results of these analyses it has been concluded that gene II and gene V are contiguous on the genetic map. Evidence is provided that there is an internal start of RNA synthesis within the C-terminal region of gene II which then ultimately leads to the synthesis of X protein. Furthermore, we conclude that there is an intergenic space of considerable length (450-500 base pairs) which is located between gene II and gene IV on the M13 genome. The function of this intergenic region as the origin site for phage DNA replication is discussed.

Arthrobacter

Characterization of the 3'-terminal region of the large molecular weight RNA subunits from normal and transformation-defective Rous sarcoma virus.

In avian sarcoma viruses a function required to transform cells is frequently lost giving rise to non-transforming virus. The genetic information for this function is localized near the 3' end of the genome. Short 3'-terminal poly(A)-linked RNA fragments from the genomes of a transforming Rous sarcoma virus and its non-transforming derivative were isolated and gave rise to identical fingerprint patterns, suggesting that internal deletion rather than terminal elimination leads to non-transforming virus.

Avian Sarcoma Viruses

Retinoblastoma. A model of hereditary fragile chromosomal regions.

Direct karyotyping of tumour cells from three familial and two sporadic cases of retinoblastoma revealed the existence of a Dq- marker chromosome. The hypothesis is launched that a specific region on the long arm of one of the D chromosomes is the site of a locus which is essential for the sustained differentiation of specialized retinal tissue and may be the site of other loci essential for the maturation of other embryonic tissues. Fragility of this region and its potentiality for breakage under the influence of various environmental insults could be the basic cytological event leading to the development of sporadic retinoblastoma. Mutants at these loci, including those of sustained differentiation, could be a less common operational event whereby some variants could enhance the fragility of their respective chromosomal region and thereby explain the genetic transmission of retinoblastoma in certain families. It is common for the critical functional disruption of the locus to precede the deletion which may then be considered the terminal event in the fragile region.

Child, Preschool

The branched respiratory system of photosynthetically grown Rhodopseudomonas capsulata.

Various respiratory electron transport activities of Rhodopseudomonas capsulata were studied in membrane fragments prepared from photosynthetically grown cells of a parental strain and two terminal oxidase-defective mutant strains. The NADH and succinate oxidase activities of the mutant having a functional N,N,N1,N1-tetramethyl-p-phenylenediamine oxidase, M6, were consideraly more sensitive to inhibition by either antimycin A or cyanide than the corresponding activities of the mutant lacking a functional N,N,N1,N1-tetramethyl-p-phenylenediamine oxidase, M7. The parental strain, Z-1, but not the mutants, showed biphasic inhibitory responses of NADH and succinate oxidase activities with either antimycin A or cyanide. In certain reactions no differences in inhibitor susceptibility were found among the strains tested, implying that the pathways involved were unaffected in the mutants. In this category were the actions of rotenone on NADH oxidase, antimycin A on cytochrome c reductase and, in M6 and Z-1, cyanide on N,N,N'N'-tetramethyl-p-phenylenediamine oxidase. These results suggest that the respiratory chain of the parental strain branches at the ubiquinone-cytochrome b region into two pathways, each branch goes to a distinct terminal oxidase, and either may be blocked independently by genetic mutation.

Antimycin A

Comprehensive analysis of a novel LYST mutation in a Tunisian patient with Chediak-Higashi syndrome.

BACKGROUND: Chediak-Higashi Syndrome (CHS) is a rare autosomal recessive disorder characterized by oculocutaneous albinism, recurrent infections, bleeding tendencies, and progressive neurological impairment. The syndrome is caused by mutations in the LYST gene, which plays a crucial role in lysosomal trafficking. OBJECTIVE: This study aims to characterize the molecular basis of CHS in a Tunisian patient by identifying mutations in the LYST gene and analyzing their impact on the protein function, correlating these findings with the patient's clinical presentation. METHODS: A comprehensive clinical assessment was conducted on the patient, followed by biochemical, hematological, and microbiological analyses. Additionally, LYST protein levels were quantified in the patient and their parents using an ELISA assay. Genomic DNA was extracted from the patient's blood, and Whole Exome Sequencing (WES) was performed to identify mutations in the LYST gene. The findings were confirmed through Sanger sequencing, and bioinformatic tools were employed to predict the functional consequences of the detected mutations. RESULTS: The patient presented with classical symptoms of CHS, including silver hair, hypopigmented skin, recurrent infections, and neurological decline, with an unusually late onset at 18 years. ELISA results demonstrated significantly reduced LYST levels in the patient (1.8 ng/ml) compared to heterozygous parents (7.8 ng/ml and 8.1 ng/ml) and controls (9.2 ng/ml). Genetic analysis revealed a novel homozygous deletion, c.10269_10275del (p.Gly3424SerfsTer15), in the LYST gene, leading to a frameshift mutation and premature termination of the protein. Bioinformatic analysis demonstrated that this mutation leads to the deletion of five out of sven WD40 repeats in the protein's C-terminal region, which are critical for protein-protein interactions and lysosomal trafficking. CONCLUSION: The study identifies a novel LYST mutation in a Tunisian patient with CHS, expanding the spectrum of known genetic variants associated with the disease. The findings highlight the importance of genetic screening in populations with high consanguinity and underscore the need for targeted therapies to address the molecular defects in CHS.

Adolescent

Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids.

Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between G. hirsutum and G. barbadense. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC5F1 plants, while the average frequency of donor alleles in BC5F2 segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.

Humans

Fine specificity of regulatory T cells. II. Suppressor and helper T cells are induced by different regions of hen egg-white lysozyme in a genetically nonresponder mouse strain.

We have examined the ability of two purified peptide fragments derived from hen (chicken) egg-white lysozyme (HEL); N-terminal, Co-terminal peptide (a.a. 1--17:cys 6--cys 127:120--129) and mixed disulfide LII peptide (LII) (a.a. 13--105) to induce antigen-specific suppression or help in B10 (H-2b) nonresponder and B10.A (H-2a) responder mice. An anti-HEL primary in vitro antibody response can be obtained in either strain by stimulation with HEL coupled to erythrocytes (RBC). Preimmunization with HEL-complete Freund's adjuvant-(CFA) or N-C-CFA-induced suppression of the anti-HEL PFC response to HEL-RBC in spleen cell cultures from B10 mice, whereas helper activity was demonstrated in cultures from B10.A mice similarly immunized. LII-CFA priming elicited helper cells in both C57BL/10 Sn (B10) and B10.A/SgSn (B10.A) mice. The genetic nonresponsiveness of B10 mice to HEL can therefore be attributed to the activation of suppressor T cells by a limited portion of the molecule (e.g., N-C) which prevent the potential response directed against other epitopes on the same molecule (e.g., LII). One manifestation of major histocompatibility complex gene activity appears to be the intramolecular selection of different antigenic determinants leading to activation of functionally different T-cell subpopulations.

Amino Acid Sequence

Viral Enhancers Orchestrate Kaposi's Sarcoma-Associated Herpesvirus Transcription.

Kaposi's sarcoma-associated herpesvirus (KSHV), the etiological agent of Kaposi's sarcoma and other lymphoproliferative disorders, presents a delicate balance between host cell manipulation, and orchestrating its transcriptional repertoire. Like all herpes viruses, the virus can reside in latency, expressing only a handful of proteins or launch a lytic program that expresses over 80 proteins responsible for the generation and release of new virions. Enhancers, as their name suggests, can enhance the transcription rate from a promoter depending on the cellular environment and tissue. While the promoters in KSHV have been extensively studied, the enhancers were only recently identified. Here we will describe our current view on KSHV enhancers.

Herpesvirus 8, Human

Comparative structural studies on the light chains of human immunoglobulins. I. Protein Ka with the Inv(3) allotypic marker.

The primary structure of the variable region of the human type K Bence-Jones Protein Ka with Inv(3) genetic marker was determined by sequence analysis of 25 major tryptic peptides covering 214 residues isolated from completely reduced and aminoethylated protein. The complete sequences of 18 of these peptides were determined. These comprised the entire variable NH2-terminal half and 7 peptides from the COOH-terminal half of the protein. For the remaining peptides covering the COOH-terminus, only partial sequences or the amino acid compositions were determined. On the basis of these results all the tryptic peptides could be arranged in order. The sequence of the variable region differed from other previosly reported in 21 to 51 residues, but no variation was found in the sequence of the last 107 residues. On the basis of sequence homology the protein was classified in the kI subgroup. A brief discussion of the possible genetic mechanism of sequence variability in relation to subgroup specificity is presented.

Amino Acid Sequence