Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.     

Protein-DNA Complexes in Mycobacteriophage L5 Integrative Recombination

The temperate mycobacteriophage L5 integrates site specifically into the genomes of Mycobacterium smegmatis, Mycobacterium tuberculosis, and Mycobacterium bovis bacillus Calmette-Guérin. This integrative recombination event occurs between the phage L5 attP site and the mycobacterial attB site and requires the phage-encoded integrase and mycobacterial-encoded integration host factor mIHF. Here we show that attP, Int-L5, and mIHF assemble into a recombinationally active complex, the intasome, which is capable of attB capture and formation of products. The arm-type integrase binding sites within attP play specialized roles in the formation of specific protein-DNA architectures; the intasome is constructed by the formation of intramolecular integrase bridges between one pair of sites, P4-P5, and the attP core, while an additional pair of sites, P1-P2, is required for interaction with attB.     

Integration Host Factor of Mycobacterium tuberculosis,mIHF, Compacts DNA by a Bending Mechanism

The bacterial chromosomal DNA is folded into a compact structure called as ‘nucleoid’ so that the bacterial genome can be accommodated inside the cell. The shape and size of the nucleoid are determined by several factors including DNA supercoiling, macromolecular crowding and nucleoid associated proteins (NAPs). NAPs bind to different sites of the genome in sequence specific or non-sequence specific manner and play an important role in DNA compaction as well as regulation. Until recently, few NAPs have been discovered in mycobacteria owing to poor sequence similarities with other histone-like proteins of eubacteria. Several putative NAPs have now been identified in Mycobacteria on the basis of enriched basic residues or histone-like “PAKK” motifs. Here, we investigate mycobacterial Integration Host Factor (mIHF) for its architectural roles as a NAP using atomic force microscopy and DNA compaction experiments. We demonstrate that mIHF binds DNA in a non-sequence specific manner and compacts it by a DNA bending mechanism. AFM experiments also indicate a dual architectural role for mIHF in DNA compaction as well as relaxation. These results suggest a convergent evolution in the mechanism of E. coli and mycobacterial IHF in DNA compaction.     

Control of directionality in L5 integrase-mediated site-specific recombination

Mycobacteriophage L5 is a temperate phage that forms lysogens in Mycobacterium smegmatis. These lysogens carry an integrated L5 prophage inserted at a specific chromosomal location and undergo subsequent excision during induction of lytic growth. Both the integrative and excisive site-specific recombination events are catalyzed by the phage-encoded tyrosine integrase (Int-L5) and require the host-encoded protein, mIHF. The directionality of these recombination events is determined by a second phage-encoded protein, Excise, the product of gene 36 (Xis-L5); integration occurs efficiently in the absence of Xis-L5 while excision is dependent upon it. We show here that Xis-L5 binds to attR DNA, introduces a DNA bend, and facilitates the formation of an intasome-R complex. This complex, which requires mIHF, Xis-L5 and Int-L5, readily recombines with a second intasome formed by Int-L5, mIHF and attL DNA (intasome-L) to generate the attP and attB products of excision. Xis-L5 also strongly inhibits Int-L5-mediated integrative recombination but does not prevent either the protein-DNA interactions that form the attP intasome (intasome-P) or the capture of attB, but acts later in the reaction presumably by preventing the formation of a recombinagenic synaptic intermediate. The mechanism of action of Xis-L5 appears to be purely architectural, influencing the assembly of protein-DNA structures solely through its DNA-binding and DNA-bending properties.     

Revision of the subgenus Orthoscymnus Canepari of Scymnus Kugelann (Coleoptera,Coccinellidae), with descriptions of four new species

The subgenus Orthoscymnus Canepari, 1997 of Scymnus Kugelann, 1794 is herein revised. Seven species of the Orthoscymnus fauna are recognized, of which four species, Scymnus (Orthoscymnus) jilongicus sp. n., Scymnus (Orthoscymnus) paradoxus sp. n., Scymnus (Orthoscymnus) crispatus sp. n. and Scymnus (Orthoscymnus) duomaculatus sp. n., are described as new to science. Scymnus (Orthoscymnus) rhododendri Canepari is recorded from China for the first time. Scymnus (Pullus) robustibasalis Yu is transferred to the subgenus Orthoscymnus (comb. n.). All species are diagnosed, described and illustrated, and distributions are provided for each species. A key to the species is included.     

On the validity of Epeorella Ulmer, 1939 (Ephemeroptera,Heptageniidae) with general considerations on the Heptageniidae of the Sunda Islands

The type material of Epeorella borneonia Ulmer, 1939, the sole species of the genus Epeorella Ulmer, 1939 is reinvestigated and a lectotype (male imago) is designated. Based on several morphological structures, the synonymy with Epeorus Eaton, 1881 (Rhithrogeninae) is rejected. Epeorella stat. prop., known only at the winged stages, belongs to the subfamily Ecdyonurinae, and is a probable endemic of the island of Borneo. The newly erected genus Darthus Webb & McCafferty, 2007, also endemic to Borneo and only known by one species at the nymphal stage, is shown to be a junior subjective synonym of Epeorella. The new combination Epeorella vadora (Webb & McCafferty, 2007) is proposed for the species. The distribution of known heptageniid species from the Sunda Islands is discussed.     

Change in State following Transposition of a Regulatory Element of the Enhancer System in Maize

From an original A2 allele (colored aleurone), a mutable allele, a2-m-4 1629, that changes from a2 to A2 is described. Mutability is expressed as a very distinct pattern limited to the last cell division.—The mutability of a2-m-4 1629 is autonomously controlled by an En at the a2 locus. This En, inactive on standard a testers for En, is partially active on a2-m-1, an a2 tester for En, and expresses varied levels of activity from limited to nearly full suppression of the a2-m-1 color phenotype.—When the En of the a2-m-4 1629 allele transposes from the a2 locus, it behaves, at the new position, like a standard En in triggering a2-m-1, a-m-1 and a-m(r), which express colored spots on a colorless background. The activity of En is therefore different following the change in chromosome location. This finding supports the "position" hypothesis that has been proposed to explain diverse patterns observed among controlling elements. In this case mutation is related to the terminal cell state and not to tissue differences as shown with some phase-variation regulatory elements.     

The genus Erechthias Meyrick of Ascension Island,including discovery of a new brachypterous species (Lepidoptera,Tineidae)

One previously named and two new species of the tineid genus Erechthias Meyrick are described and illustrated from the small, remote, mid-Atlantic Ascension Island. With these additions the Lepidoptera fauna of Ascension now totals 38 known species. Little is known regarding the biology of the two new species of Erechthias, and none of the species has been reared from larvae from Ascension. Erechthias minuscula (Walsingham) is a widespread, largely pantropical species first described from the West Indies. Larvae of Erechthias minuscula are known to be scavengers on a wide variety of dead plant material. Erechthias ascensionae,new species, is one of two species of Erechthias now known to be endemic to the island. The other endemic species, Erechthias grayi, new species, is further remarkable in having wing reduction occurring in both sexes. It is one of the few species of Lepidoptera known where this extreme of brachyptery involving both sexes has evolved. The larvae of Erechthias grayi are believed to be lichenivorous, and larval cases suspected to represent this species are illustrated.     

A revision of Bremia graminicola

Bremia graminicola (Chromista, Peronosporales) is a common downy mildew pathogen of Arthraxon spp. (Poaceae) in Central to East Asia and the only species of Bremia parasitic on grasses. Despite its widespread occurrence and apparent differences in host range and morphology compared with other species of the genus, its placement in Bremia has not been challenged for the past 90 y. Its current taxonomic position is revised based on sporangiophore morphology and ultrastructure, haustorium morphology, and nu-rDNA sequence analysis. Haustorium morphology and sporangiophore ultrastructure indicate that B. graminicola is not a member of the genus Bremia, which shows affinities to Plasmopara and Paraperonospora. Based on haustorium morphology, B. graminicola appears to be more closely related to Viennotia oplismeni, although the sporangiophore morphology is strikingly different between these two taxa. This is supported by molecular analyses based on a near-representative sample of nuLSU rDNA sequences of downy mildew genera, whereby B. graminicola is revealed as the sister taxon of V. oplismeni with 100 % BS support under all phylogenetic optimality criteria applied. Relationships of this clade to other groups are less clear. However, network and reduced-consensus analyses show that this lack of resolution is mainly due to the ambiguous molecular affinities of Sclerospora graminicola. Omitting this highly divergent taxon results in considerable support for a clade comprised of taxa with globose to pyriform haustoria, including B. lactucae, and for the sister-group relationship of B. graminicola and V. oplismeni with Hyaloperonospora. Consequently, a new genus, Graminivora, is described to accommodate B. graminicola.     

Introduced Pheidole of the world: taxonomy,biology and distribution

The objective of this study is to provide a detailed taxonomic resource for identifying and studying ants in the genus Pheidole that have established beyond their native ranges. There is an increasing need for systematists to study taxa of specific concern to 21^st century environmental, food security and public health challenges. Systematics has an important role to play in both the theoretical and applied disciplines of invasion biology. Few invaders impact terrestrial ecosystems more than ants. Among the world’s 100 worst invasive species is the cosmopolitan and highly destructive Pheidole megacephala (Fabricius). Accurate identification of Pheidole megacephala is imperative for the success of screening, management and eradication programs designed to protect native ecosystems from the impacts of this destructive species. However, accurate identification of Pheidole species is difficult because of their taxonomic diversity, dimorphic worker caste and lack of taxonomic resources. Illustrated keys are included, along with the taxonomic history, taxonomic diagnoses, biological notes and risk statements for the 14 most invasive members of the genus. Global distribution maps based on over 14,000 specimen and literature records are presented for each species. These results of this work will facilitate identification of pest species, determination of climatic and habitat requirements, discovery of pest origins, horizon scanning and assessment of invasion pathways. The following new synonym is proposed, with the senior synonym listed first and the junior synonyms in parentheses: Pheidole indica Mayr (= Pheidole teneriffana Forel, and its synonyms Pheidole taina Aguayo and Pheidole voeltzkowii Forel). Pheidole navigans Forel, stat. rev., stat. n. is removed from synonymy and elevated to species rank. It is proposed that records of Pheidole moerens Forel outside of the Mesoamerica and the Caribbean refer instead to Pheidole navigans or other heterospecific taxa in the Pheidole flavens species complex. We propose that the names Pheidole anastasii Emery and Pheidole floridana Emery have been widely misapplied to North American outdoor records of Pheidole bilimeki Mayr. It is suggested that the synonymy of Pheidole lauta Wheeler be transferred from Pheidole floridana Emery to Pheidole bilimeki Mayr.     

Molecular phylogeny of Hyphoderma and the reinstatement of Peniophorella

Hyphoderma is a large genus of corticioid homobasidiomycetes. In earlier homobasidiomycete-wide molecular phylogenetic studies the genus has appeared as polyphyletic. This paper describes the results from phylogenetic analyses of 22 species of Hyphoderma using nuclear 5.8 S and 28 S rDNA. Species with echinocysts and stephanocysts form a distinct clade well separated from Hyphoderma s. str. For this group the old genus name Peniophorella is available with P. pubera as the type species. Nineteen new combinations in Peniophorella are made and a key to the species is given. The clade representing Hyphoderma in its restricted sense receives only indicative support and a further subdivision of the genus may become necessary. H. capitatum, H. orphanellum, and H. sibiricum belong neither to Peniophorella nor to Hyphoderma s. str. Hypochnicium is a sister group to Hyphoderma. The phylogenetic analyses support the segregation of Hypochnicium analogum and H. vellereum as Gloeohypochnicium analogum and Granulobasidium vellereum, respectively, and the inclusion of H. detriticum in Hyphodontia. Hyphodermopsis and Bulbillomyces are best regarded as synonyms of Hypochnicium.     

The rate of allelism of lethal genes in a geographically structured population

The expected rate of allelism, E[I(x)], of lethal genes between two colonies with distance x in a structured population is studied by using one- and two-dimensional stepping-stone models. It is shown that E[I(x)] depends on the magnitude of selection in heterozygous condition (h), the rate of migration among adjacent colonies (m), the number of loci which produce lethal mutations (n) and the effective population size of each colony (N).——E[I(x)] always decreases with distance x. The rate of decrease is affected strongly by the magnitude of m. The rate of decrease is faster when m is small. E[I(x)] also decreases with increasing N and n. The effect of h on E[I(x)] is somewhat complicated. However, E[I(0)] is always smaller when h is small than when it is large.——For large x, the following approximate formulae may be obtained: (see PDF) where q and Var (q) are the mean and the variance of gene frequencies in each colony, t is approximated as t=h, (see PDF), -h for the partially recessive, completely recessive, and overdominant lethals, respectively, and C₀ is a function of m and t. It is clear that E[I(x)] declines exponentially with x in a one-dimensional habitat. The decrease E[I(x)] is faster in a two-dimensional habitat than in a one-dimensional habitat. The present result is applied to some of the existing data and the estimation of population parameters is also discussed.     

Three new genera of Neotropical Mimallonidae (Lepidoptera,Mimallonoidea, Mimallonidae) with descriptions of three new species

Three new genera of Mimallonidae are described. The monotypic genus Tostallo gen. n. is erected to contain “Perophora” albescens Jones, 1912, which was previously placed in the preoccupied genus Perophora Harris, 1841 and was never formally moved to a valid genus. Perophora is a junior homonym of Cicinnus Blanchard, 1852, but the name albescens is not appropriately placed in Cicinnus due to external and genitalia characteristics entirely unique to the species albescens. The female of Tostallo albescens comb. n. is described and both sexes are figured for the first time. Auroriana gen. n. is erected to contain Auroriana florianensis (Herbin, 2012), comb. n. previously described as Cicinnus florianensis, and two new species: Auroriana colombiana sp. n. from Colombia and Auroriana gemma sp. n. from southeastern and southern Brazil. The female of Auroriana florianensis is described and figured for the first time. Finally, the monotypic genus Micrallo gen. n. is erected to include a new species, Micrallo minutus sp. n. described from northeastern Brazil.     

Different UmuC requirements for generation of different kinds of UV-induced mutations in Escherichia coli

An Escherichia coli strain bearing the dnaQ49 mutation, which results in a defective s subunit of DNA polymerase III, and carrying the lexA71 mutation, which causes derepression of the SOS regulon, is totally unable to maintain high-copy-number plasmids containing the umuDC operon. The strain is also unable to maintain the pAN4 plasmid containing a partial deletion of the umuD gene but retaining the wild-type umuC gene. These results suggest that a high cellular level of UmuC is exceptionally harmful to the defective DNA polymerase III of the dnaQ49 mutant. We have used this finding as a basis for selection of new plasmid umuC mutants. The properties of two such mutants, bearing the umuC61 or umuC95 mutation, are described in detail. In the umuC122:: Tn 5 strain harbouring the mutant plasmids, UV-induced mutagenesis is severely decreased compared to that observed with the parental umuDC ⁺ plasmid. Interestingly, while the frequency of UV-induced GC → AT transitions is greatly reduced, the frequency of AT → TA transversions is not affected. Both mutant plasmids bear frameshift mutations within the same run of seven A residues present in umuC ⁺; in umuC61 the run is shortened to six A whereas in umuC95 is lengthened to eight A. We have found in both umuC61 and umuC95 that translation is partially restored to the proper reading frame. We propose that under conditions of limiting amounts of UmuC, the protein preferentially facilitates processing of only some kinds of UV-induced lesions.