Complete Genome Sequences and Characteristics of Seven Novel Mycobacteriophages Isolated in East Texas

Full-genome sequences of seven mycobacteriophages isolated from environmental soil samples are presented. These bacteriophages, with their respective clusters or subclusters are Duplo (A2), Dynamo (P1), Gilberta (A11), MaCh (A11), Nikao (K1), Phloss (N), and Skinny (M1). All had siphovirus-like morphologies, with genome sizes ranging from 43,107 to 82,071 bp.

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Genomic diversity of bacteriophages infecting Microbacterium spp

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Structural and mutational analysis of the xeroderma pigmentosum group D (XPD) gene

Individuals affected by the autosomal recessive disease xeroderma pigmentosum (XP) are acutely sensitive to sunlight and predisposed to skin cancer on exposed areas. Cells cultured from XP patients are both UV sensitive and defective in the nucleotide excision repair of damaged DNA. These cellular phenotypes are amenable to experimental strategies employing complementation, an approach previously used to demonstrate the correction of XP-D phenotypes following the introduction of the XPD (ERCC2) gene. In the present study, we have characterized the genomic organization of the XPD (ERCC2) gene and found it to be comprised of 23 exons. These data were helpful in evaluating the functional integrity of alleles in two XP-D cell lines. In cell line GM436 a C-->G transversion was found at nucleotide position 1411 in the XPD (ERCC2) cDNA, a change expected to result in a Leu461Val substitution. Cell line XP67MA carries a C-->T transition in genomic DNA at nucleotide position 2176 in exon 22, introducing the termination codon TAG at amino acid 726. The latter would be expected to produce a protein truncated by 34 amino acids. Although expression of the normal XPD cDNA could be shown to correct the UV sensitivity phenotype in XP-D cells, cDNA constructs bearing either of the two mutations failed to yield complementation. These results confirm the role of ERCC2 in XP-D and illustrate the power of utilizing cellular phenotypes to evaluate the significance of single nucleotide substitutions.

Chromosome rearrangements recovered following transformation of Neurospora crassa

New chromosome rearrangements were found in 10% or more of mitotically stable transformants. This was shown for transformations involving a variety of different markers, vectors and recipient strains. Breakpoints were randomly distributed among the seven linkage groups. Controls using untransformed protoplasts of the same strains contained almost no rearrangements. A study of molecularly characterized Am+ transformants showed that rearrangements are frequent when multiple ectopic integration events have occurred. In contrast, rearrangements are absent or infrequent when only the resident locus is restored to am+ by a homologous event. Sequences of the transforming vector were genetically linked to breakpoints in 6 of 10 translocations that were examined using Southern hybridization or colony blots.

Cloning and characterisation of pepC, a gene encoding a serine protease from Aspergillus niger

We have cloned a gene, pepC, encoding a serine proteinase, PEPC, from Aspergillus niger by screening a phage lambda genomic DNA library with a gene (PRB1) from Saccharomyces cerevisiae which codes for proteinase YscB. The nucleotide (nt) sequence of pepC revealed that the gene is composed of two exons of 369 nt and 1230 nt separated by a single 70-nt intron. The deduced protein of 533 amino acids (aa) has a putative signal sequence for transport into the endoplasmic reticulum. Based on the extensive homology shown with serine proteinases (SerP) of the subtilisin family, which includes the active site triad, we hypothesise that the protein is made as a larger precursor which is matured by the cleavage of 130-140 aa from its N terminus and possibly by the removal of approx. 70 aa from its C terminus.

Distant upstream regulatory sequences control the level of expression of the am (GDH) locus of Neurospora crassa

We have constructed deletions in the 5' noncoding sequences of the cloned Neurospora crassa am gene. Vectors with a truncated fragment of the am gene were used in transformation experiments to introduce the deletions into the chromosome by homologous recombination. Analysis of glutamate dehydrogenase (GDH) expression by enzyme assay and immunoblots, as well as Northern and dot blots of poly (A)+ RNA, in the deletion strains indicates that there are two upstream regulatory sequences that control the level of gene expression. The closer of these two elements (URSam alpha) is at approximately 1.4 kb upstream of the transcriptional start site. The second elements (URSam beta) is located between 2.1 and 3.2 kb upstream of the transcription start site. Deletion of either of these two elements reduces am expression to about 50% of the wild-type level. Deletion of both elements reduce am expression to from 5-16% of the wild-type level. Deletion of 1.1 kb of sequence just downstream of URSam alpha, which brings this element to within 300 bp of the transcription start site, had no effect on am expression. Likewise, deletion of 3.5 kb of sequence upstream of URSam beta had no effect on expression. None of these deletions had any effect on the expression of usg-1, a gene of unknown function that is transcribed in the same direction as the am gene, and which terminates about 3.5 kb upstream of the URSam beta element.

Nucleotide sequence and nuclear protein binding of the two regulatory sequences upstream of the am (GDH) gene in Neurospora

We have constructed a series of deletions in the 5' non-coding sequences of the cloned Neurospora crassa am gene which specifies NADP specific glutamate dehydrogenase. All of the deletions begin at -4.4 kb with respect to the am transcription start site and extend for various distances toward the am gene. Using vectors with a truncated fragment of the am gene, we introduced these deletions into the chromosome upstream of am by transformation. Analysis of glutamate dehydrogenase expression in strains with the deletion mutations confirmed that there are two upstream regulatory sequences (URS) that control the expression of the am gene. The more distal of these elements (URSam beta) has been limited to the 157 bp between -1924 and -2081 with respect to the start of am transcription. The proximal element (URSam alpha) was limited to the 97 bp between -1296 and -1393. The DNA sequence of the entire region was determined. Within the sequences that contain the URS elements several regions of homology with yeast UAS sequences were found. Gel mobility assays with DNA fragments containing the URS elements indicated that sequences in both elements are bound by nuclear proteins from Neurospora. The interaction of these proteins and the DNA fragments was found to be specific.

Use of transformation to make targeted sequence alterations at the am (GDH) locus of Neurospora

Specific in vitro-generated insertion, replacement, and deletion mutations have been integrated near the chromosomal locus of am (NADP-specific glutamate dehydrogenase) of Neurospora crassa. Two approaches have been successful. One approach used am+-containing vectors capable of integrating at any site in the genome. This technique was used to introduce a specific 700 bp insertion near the am locus and to replace chromosomal sequences near am with plasmid DNA. Efficiency was low, however, and many transformants had to be screened to find the desired alterations among the ectopic insertions unless the incoming DNA had a large region of homology with the am region. A second approach increased the efficiency by using vectors containing a truncated am gene, so that prototrophs could arise only by homologous recombination. Overall transformation frequency was reduced relative to the first method, but a large fraction of the transformations involved specific alterations of the am region.